diff --git a/HiPRGen/gen_euvl_testset.py b/HiPRGen/gen_euvl_testset.py new file mode 100644 index 0000000..39542de --- /dev/null +++ b/HiPRGen/gen_euvl_testset.py @@ -0,0 +1,72 @@ +print("Importing required files...") +from pymatgen.core.structure import Molecule +from pymatgen.analysis.graphs import MoleculeGraph +from pymatgen.analysis.local_env import OpenBabelNN +from monty.serialization import loadfn, dumpfn +from mol_entry import MoleculeEntry +from initial_state import find_mol_entry_by_entry_id +import copy +print("Done!") + +#list of mol_ids for species you want to find with each mol_id occupying its own line. Must have an empty line +#at the end of the file, but empty lines will not be copied. +print("Opening and reading species id file...") +with open('atom_mapping_set.txt') as mol_id_doc: #open the text file and copy each line as the element of a list, removing '\n' + mol_id_list = [] + for line in mol_id_doc: + if line.strip(): #excludes empty lines + mol_id_list.append(line[0:len(line)-1]) +print("Done!") + +print("Opening json file...") +mol_json = "032923.json" +database_entries = loadfn(mol_json) #loads the json file to a list of dictionaries +print("Done!") + +print("Reading molecule entries from json file...") #converts dictionary from loaded json file to a list +mol_entries= [MoleculeEntry.from_mp_doc(e) for e in database_entries] +print("Done!") + +final_mol_ids = [] + +print('Copying desired molecules to a new list...') +for mol_id in mol_id_list: #takes the list of ids, finds their corresponding molecules in the json file + for mol_entry in mol_entries: + m_id = mol_entry.entry_id + if m_id == mol_id: + graph = mol_entry.mol_graph + for entry in mol_entries: #(as well as differently charged variants) and adds them to the list + molecule_graph = entry.mol_graph #tests if other charges found + if molecule_graph.isomorphic_to(graph): + final_mol_ids.append(entry.entry_id) + +to_remove = ['nbo', 'alpha', 'beta'] + +test_set = [] +for entry in database_entries: + if entry['molecule_id'] in final_mol_ids: + new_entry = copy.deepcopy(entry) + for name in entry.keys(): + for remove in to_remove: + if remove in name: + val = new_entry.pop(name) + test_set.append(new_entry) + +dumpfn(test_set, 'atom_mapping_set.json') + +new_mol_json = loadfn('atom_mapping_set.json') +new_mol_entries= [MoleculeEntry.from_mp_doc(e) for e in new_mol_json] + +new_id_list = [] + +for molecule in new_mol_entries: + new_id_list.append(molecule.entry_id) + +new_id_set = set(new_id_list) +mol_id_set = set(mol_id_list) +differences = mol_id_set - new_id_set +if differences == set(): + print('All desired entries successfully copied') +else: + for elem in differences: + print('entry ', elem, ' not copied successfully') \ No newline at end of file diff --git a/HiPRGen/initial_state.py b/HiPRGen/initial_state.py index 588dcbf..2e84f2b 100644 --- a/HiPRGen/initial_state.py +++ b/HiPRGen/initial_state.py @@ -1,7 +1,6 @@ from pymatgen.core.structure import Molecule from pymatgen.analysis.graphs import MoleculeGraph -from pymatgen.analysis.local_env import OpenBabelNN -from pymatgen.analysis.fragmenter import metal_edge_extender +from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender#, oxygen_edge_extender import sqlite3 @@ -15,7 +14,8 @@ def find_mol_entry_from_xyz_and_charge(mol_entries, xyz_file_path, charge): ) # correction to the molecule graph - target_mol_graph = metal_edge_extender(target_mol_graph) + target_mol_graph = metal_edge_extender(target_mol_graph, cutoff=3.4, metals=None,coordinators=("O")) + #target_mol_graph = metal_edge_extender(target_mol_graph) match = False index = -1 @@ -71,8 +71,8 @@ def insert_initial_state( mol_entries, initial_state_db, factor_zero = 1.0, - factor_two = 1.0, - factor_duplicate = 0.5 + factor_two = 0.5, + factor_duplicate = 1.0, ): """ initial state is a dict mapping species ids to counts. diff --git a/HiPRGen/mc_analysis.py b/HiPRGen/mc_analysis.py index e6254c7..9fae5de 100644 --- a/HiPRGen/mc_analysis.py +++ b/HiPRGen/mc_analysis.py @@ -527,7 +527,7 @@ def reaction_tally_report( for (reaction_index, number) in sorted( reaction_tally.items(), key=lambda pair: -pair[1]): if number > cutoff: - report_generator.emit_text(str(number) + " occourances of:") + report_generator.emit_text(str(number) + " occurrences of:") report_generator.emit_reaction( network_loader.index_to_reaction(reaction_index), label=str(reaction_index) @@ -551,7 +551,7 @@ def species_report(network_loader, species_report_path): report_generator.emit_text(str(mol.entry_id)) report_generator.emit_text( "formula: " + mol.formula) - + report_generator.emit_text("free energy = " + str(mol.free_energy) + " eV") report_generator.emit_molecule(i) report_generator.emit_newline() @@ -750,7 +750,7 @@ def export_pathways_to_json(pathfinding, species_id, path): -def generate_pathway_report( +def pathway_report( pathfinding, species_id, report_file_path, @@ -839,7 +839,7 @@ def compute_expected_final_state(self): ) for seed in self.network_loader.trajectories: - state = np.copy(self.network_loader.initial_state_array) + state = np.copy(self.network_loader.initial_state_array[seed]) for step in self.network_loader.trajectories[seed]: reaction_index = self.network_loader.trajectories[seed][step][0] time = self.network_loader.trajectories[seed][step][1] @@ -858,6 +858,24 @@ def compute_expected_final_state(self): self.expected_final_state = ( self.expected_final_state / len(self.network_loader.trajectories)) + def compute_trajectory_final_states(self): + self.final_states = {} + for seed in self.network_loader.trajectories: + state = np.copy(self.network_loader.initial_state_array[seed]) + for step in self.network_loader.trajectories[seed]: + reaction_index = self.network_loader.trajectories[seed][step][0] + time = self.network_loader.trajectories[seed][step][1] + reaction = self.network_loader.index_to_reaction(reaction_index) + + for i in range(reaction['number_of_reactants']): + reactant_index = reaction['reactants'][i] + state[reactant_index] -= 1 + + for j in range(reaction['number_of_products']): + product_index = reaction['products'][j] + state[product_index] += 1 + self.final_states[seed] = state + def compute_production_consumption_info(self): self.consuming_reactions = {} self.producing_reactions = {} @@ -888,13 +906,13 @@ def compute_production_consumption_info(self): self.producing_reactions[product_index][reaction_index] += 1 def compute_state_time_series(self, seed): - state_dimension_size = len(self.network_loader.initial_state_array) + state_dimension_size = len(self.network_loader.initial_state_array[seed]) step_dimension_size = len(self.network_loader.trajectories[seed]) time_series = np.zeros( (step_dimension_size, state_dimension_size), dtype=int) - state = np.copy(self.network_loader.initial_state_array) + state = np.copy(self.network_loader.initial_state_array[seed]) for step in self.network_loader.trajectories[seed]: reaction_index = self.network_loader.trajectories[seed][step][0] time = self.network_loader.trajectories[seed][step][1] @@ -918,9 +936,11 @@ def time_series_graph( seeds, species_of_interest, path, + custom_y_max=None, + custom_colorstyle_list=None, colors = list(mcolors.TABLEAU_COLORS.values()), - styles = ['solid', 'dotted', 'dashed', 'dashdot'], - internal_index_labels=True + styles = ['solid', 'dotted', 'dashed', 'dashdot','solid', 'dotted', 'dashed', 'dashdot','solid', 'dotted', 'dashed', 'dashdot','solid', 'dotted', 'dashed', 'dashdot'], + internal_index_labels=True, ): @@ -952,11 +972,16 @@ def time_series_graph( line_dict = {} i = 0 - for species_index in species_of_interest: - r = i % len(colors) - q = i // len(colors) - line_dict[species_index] = (colors[r], styles[q]) - i += 1 + if custom_colorstyle_list is None: + for species_index in species_of_interest: + r = i % len(colors) + q = i // len(colors) + line_dict[species_index] = (colors[r], styles[q]) + i += 1 + else: + for species_index in species_of_interest: + line_dict[species_index] = (custom_colorstyle_list[i][0], custom_colorstyle_list[i][1]) + i += 1 fig, (ax0, ax1, ax2) = plt.subplots( @@ -965,15 +990,19 @@ def time_series_graph( gridspec_kw={'height_ratios':[2,2,1]}) y_max = 0 - for step in range(total_time_series.shape[0]): - for species_index in species_of_interest: - y_max = max(y_max, total_time_series[step,species_index]) + if custom_y_max is None: + for step in range(total_time_series.shape[0]): + for species_index in species_of_interest: + y_max = max(y_max, total_time_series[step,species_index]) + y_max += 1 + else: + y_max = custom_y_max ax0.set_xlim([0,total_time_series.shape[0]]) - ax0.set_ylim([0,y_max+1]) + ax0.set_ylim([0,y_max]) ax1.set_xlim([0,total_time_series.shape[0]]) - ax1.set_ylim([0,(y_max+1)/10]) + ax1.set_ylim([0,(y_max)/10]) ticks = np.arange(0, total_time_series.shape[0]) @@ -1097,8 +1126,8 @@ def sink_filter(self, species_index): mol = self.network_loader.mol_entries[species_index] if (number_of_consuming_reactions + number_of_producing_reactions > 0 and ratio > 1.5 and - expected_value > 0.1 and - mol.spin_multiplicity == 1): + expected_value > 0.1):# and + #mol.spin_multiplicity == 1): return True else: return False @@ -1121,11 +1150,11 @@ def export_consumption_to_json(simulation_replayer, species_index, path): } reactions[reaction_id] = json_reaction - dumpfn({ - 'reactions' : reactions, - 'producing_reactions' : producing_reactions, - 'consuming_reactions' : consuming_reactions}, - path) + dumpfn({ + 'reactions' : reactions, + 'producing_reactions' : producing_reactions, + 'consuming_reactions' : consuming_reactions}, + path) def pad_time_series(time_series, max_number_of_steps): num_steps = time_series.shape[0] @@ -1144,15 +1173,22 @@ def pad_time_series(time_series, max_number_of_steps): -def export_sinks_to_json(simulation_replayer, path): - sink_data = simulation_replayer.sink_data +def export_full_sink_data_to_json(simulation_replayer, path): sink_data_json = {} - for i in sink_data: + for i in simulation_replayer.sink_data: # All molecules formed at least once are in sink_data mol = simulation_replayer.network_loader.mol_entries[i] - sink_data_json[mol.entry_id] = sink_data[i] + sink_data_json[mol.entry_id] = simulation_replayer.sink_data[i] dumpfn(sink_data_json, path) +def export_sinks_to_json(simulation_replayer, path): + sinks_json = {} + for i in simulation_replayer.sinks: # Only molecules that pass sink_filter are in sinks + mol = simulation_replayer.network_loader.mol_entries[i] + sinks_json[mol.entry_id] = simulation_replayer.sink_data[i] + + dumpfn(sinks_json, path) + def export_species_report_to_json(network_loader, path): data = {} for i in range(network_loader.number_of_species): @@ -1260,3 +1296,26 @@ def sink_report( report_generator.emit_newline() report_generator.finished() + + +def final_state_report( + simulation_replayer, + final_state_report_path +): + final_state = [] + for species_index, value in enumerate(simulation_replayer.expected_final_state): + if value > 0.0: + final_state.append({"index": species_index, "value": value}) + sorted_final_state = sorted(final_state, key=lambda x: -x["value"]) + + report_generator = ReportGenerator( + simulation_replayer.network_loader.mol_entries, + final_state_report_path, + rebuild_mol_pictures=False) + + for entry in sorted_final_state: + report_generator.emit_text("amount: " + str(entry["value"])) + report_generator.emit_molecule(entry["index"]) + report_generator.emit_newline() + report_generator.finished() + diff --git a/HiPRGen/mol_entry.py b/HiPRGen/mol_entry.py index ce1dadd..de7ec59 100644 --- a/HiPRGen/mol_entry.py +++ b/HiPRGen/mol_entry.py @@ -3,8 +3,11 @@ import networkx as nx import numpy as np +import json +from ase import Atoms +from pymatgen.io.ase import AseAtomsAdaptor from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError -from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender +from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender#, oxygen_edge_extender from pymatgen.core.structure import Molecule from networkx.algorithms.graph_hashing import weisfeiler_lehman_graph_hash from HiPRGen.constants import ROOM_TEMP, metals @@ -12,13 +15,9 @@ class FragmentComplex: - def __init__( - self, - number_of_fragments, - number_of_bonds_broken, - bonds_broken, - fragment_hashes): + self, number_of_fragments, number_of_bonds_broken, bonds_broken, fragment_hashes + ): self.number_of_fragments = number_of_fragments self.number_of_bonds_broken = number_of_bonds_broken @@ -26,7 +25,6 @@ def __init__( self.fragment_hashes = fragment_hashes - class MoleculeEntry: """ A molecule entry class to provide easy access to Molecule properties. @@ -54,7 +52,7 @@ def __init__( electron_affinity, ionization_energy, spin_multiplicity, - partial_spins_nbo + partial_spins_nbo, ): self.energy = energy self.enthalpy = enthalpy @@ -69,10 +67,10 @@ def __init__( self.star_hashes = {} self.fragment_data = [] - if not mol_graph: mol_graph = MoleculeGraph.with_local_env_strategy(molecule, OpenBabelNN()) self.mol_graph = metal_edge_extender(mol_graph) + # self.mol_graph = oxygen_edge_extender(mol_graph) else: self.mol_graph = mol_graph @@ -85,9 +83,7 @@ def __init__( self.graph = self.mol_graph.graph.to_undirected() self.species = [str(s) for s in self.molecule.species] - self.m_inds = [ - i for i, x in enumerate(self.species) if x in metals - ] + self.m_inds = [i for i, x in enumerate(self.species) if x in metals] # penalty gets used in the non local part of species filtering. # certain species filters will increase penalty rather than explicitly filtering @@ -97,23 +93,17 @@ def __init__( self.covalent_graph = copy.deepcopy(self.graph) self.covalent_graph.remove_nodes_from(self.m_inds) - self.formula = self.molecule.composition.alphabetical_formula self.charge = self.molecule.charge self.num_atoms = len(self.molecule) - self.atom_locations = [ - site.coords for site in self.molecule] - + self.atom_locations = [site.coords for site in self.molecule] self.free_energy = self.get_free_energy() self.non_metal_atoms = [ - i for i in range(self.num_atoms) - if self.species[i] not in metals] - - - + i for i in range(self.num_atoms) if self.species[i] not in metals + ] @classmethod def from_dataset_entry( @@ -154,19 +144,17 @@ def from_dataset_entry( thermo == "rrho_shifted" and doc["thermo"]["shifted_rrho_eV"] is not None ): - energy = ( - doc["thermo"]["shifted_rrho_eV"]["electronic_energy"] * 0.0367493 - ) - enthalpy = doc["thermo"]["shifted_rrho_eV"]["total_enthalpy"] * 23.061 - entropy = doc["thermo"]["shifted_rrho_eV"]["total_entropy"] * 23061 + energy = doc["thermo"]["shifted_rrho_eV"]["electronic_energy"] + enthalpy = doc["thermo"]["shifted_rrho_eV"]["total_enthalpy"] + entropy = doc["thermo"]["shifted_rrho_eV"]["total_entropy"] elif thermo == "qrrho" and doc["thermo"]["quasi_rrho_eV"] is not None: - energy = doc["thermo"]["quasi_rrho_eV"]["electronic_energy"] * 0.0367493 - enthalpy = doc["thermo"]["quasi_rrho_eV"]["total_enthalpy"] * 23.061 - entropy = doc["thermo"]["quasi_rrho_eV"]["total_entropy"] * 23061 + energy = doc["thermo"]["quasi_rrho_eV"]["electronic_energy"] + enthalpy = doc["thermo"]["quasi_rrho_eV"]["total_enthalpy"] + entropy = doc["thermo"]["quasi_rrho_eV"]["total_entropy"] else: - energy = doc["thermo"]["raw"]["electronic_energy_Ha"] - enthalpy = doc["thermo"]["raw"]["total_enthalpy_kcal/mol"] - entropy = doc["thermo"]["raw"]["total_entropy_cal/molK"] + energy = doc["thermo"]["raw"]["electronic_energy_Ha"] * 27.21139 + enthalpy = doc["thermo"]["raw"]["total_enthalpy_kcal/mol"] * 0.0433641 + entropy = doc["thermo"]["raw"]["total_entropy_cal/molK"] * 0.0000433641 entry_id = doc["molecule_id"] @@ -175,26 +163,25 @@ def from_dataset_entry( else: mol_graph = MoleculeGraph.from_dict(doc["molecule_graph"]) - partial_charges_resp = doc['partial_charges']['resp'] - partial_charges_mulliken = doc['partial_charges']['mulliken'] - spin_multiplicity = doc['spin_multiplicity'] - + partial_charges_resp = doc["partial_charges"]["resp"] + partial_charges_mulliken = doc["partial_charges"]["mulliken"] + spin_multiplicity = doc["spin_multiplicity"] - if doc['number_atoms'] == 1: - partial_charges_nbo = doc['partial_charges']['mulliken'] - partial_spins_nbo = doc['partial_spins']['mulliken'] + if doc["number_atoms"] == 1: + partial_charges_nbo = doc["partial_charges"]["mulliken"] + partial_spins_nbo = doc["partial_spins"]["mulliken"] else: - partial_charges_nbo = doc['partial_charges']['nbo'] - partial_spins_nbo = doc['partial_spins']['nbo'] + partial_charges_nbo = doc["partial_charges"]["nbo"] + partial_spins_nbo = doc["partial_spins"]["nbo"] electron_affinity_eV = None ionization_energy_eV = None - if 'redox' in doc: - if 'electron_affinity_eV' in doc['redox']: - electron_affinity_eV = doc['redox']['electron_affinity_eV'] + if "redox" in doc: + if "electron_affinity_eV" in doc["redox"]: + electron_affinity_eV = doc["redox"]["electron_affinity_eV"] - if 'ionization_energy_eV' in doc['redox']: - ionization_energy_eV = doc['redox']['ionization_energy_eV'] + if "ionization_energy_eV" in doc["redox"]: + ionization_energy_eV = doc["redox"]["ionization_energy_eV"] except KeyError as e: raise Exception( @@ -202,8 +189,6 @@ def from_dataset_entry( f"attribute {e} in `doc`." ) - - return cls( molecule=molecule, energy=energy, @@ -217,10 +202,168 @@ def from_dataset_entry( electron_affinity=electron_affinity_eV, ionization_energy=ionization_energy_eV, spin_multiplicity=spin_multiplicity, - partial_spins_nbo=partial_spins_nbo + partial_spins_nbo=partial_spins_nbo, ) + @classmethod + def from_mp_doc(cls, doc: Dict): + """ + Construct a MoleculeEntry based on a document generated by emmet for + the Materials Project. + :param doc: A dict representation of an emmet document (SummaryDoc) + :return: MoleculeEntry + """ + solvent_key = None + if isinstance(doc["molecule"], Molecule): + molecule = doc["molecule"] + else: + molecule = Molecule.from_dict(doc["molecule"]) # type: ignore + if isinstance(doc["electronic_energy"], float): + energy = doc["electronic_energy"] + enthalpy = doc["total_enthalpy"] + entropy = doc["total_entropy"] + else: + solvent_key = list(doc["electronic_energy"].keys())[0] + energy = doc["electronic_energy"][solvent_key] + enthalpy = doc["total_enthalpy"][solvent_key] + entropy = doc["total_entropy"][solvent_key] + entry_id = doc["molecule_id"] + if "nbo" in doc["molecule_graph"]: + if isinstance(doc["molecule_graph"]["nbo"], MoleculeGraph): + mol_graph = doc["molecule_graph"]["nbo"] + else: + mol_graph = MoleculeGraph.from_dict(doc["molecule_graph"]["nbo"]) + elif "OpenBabelNN + metal_edge_extender" in doc["molecule_graph"]: + if isinstance( + doc["molecule_graph"]["OpenBabelNN + metal_edge_extender"], + MoleculeGraph, + ): + mol_graph = doc["molecule_graph"]["OpenBabelNN + metal_edge_extender"] + else: + mol_graph = MoleculeGraph.from_dict( + doc["molecule_graph"]["OpenBabelNN + metal_edge_extender"] + ) + elif solvent_key is not None: + if "OpenBabelNN + metal_edge_extender" in doc["molecule_graph"][solvent_key]: + if isinstance( + doc["molecule_graph"][solvent_key]["OpenBabelNN + metal_edge_extender"], + MoleculeGraph, + ): + mol_graph = doc["molecule_graph"][solvent_key]["OpenBabelNN + metal_edge_extender"] + else: + mol_graph = MoleculeGraph.from_dict( + doc["molecule_graph"][solvent_key]["OpenBabelNN + metal_edge_extender"] + ) + + if solvent_key is not None: + partial_charges_resp = doc["partial_charges"][solvent_key]["resp"] + if "mulliken" in doc["partial_charges"][solvent_key]: + partial_charges_mulliken = doc["partial_charges"][solvent_key]["mulliken"] + else: + partial_charges_mulliken = None + if "nbo" in doc["partial_charges"][solvent_key]: + partial_charges_nbo = doc["partial_charges"][solvent_key]["nbo"] + else: + partial_charges_nbo = None + else: + partial_charges_resp = doc["partial_charges"]["resp"] + if "mulliken" in doc["partial_charges"]: + partial_charges_mulliken = doc["partial_charges"]["mulliken"] + else: + partial_charges_mulliken = None + if "nbo" in doc["partial_charges"]: + partial_charges_nbo = doc["partial_charges"]["nbo"] + else: + partial_charges_nbo = None + if doc.get("electron_affinity", None) is None: + electron_affinity = 0.0 + else: + electron_affinity = doc["electron_affinity"] + if doc.get("ionization_energy", None) is None: + ionization_energy = 0.0 + else: + ionization_energy = doc["ionization_energy"] + spin_multiplicity = doc["spin_multiplicity"] + if int(spin_multiplicity) != 1 and "nbo" in doc["partial_spins"]: + partial_spins_nbo = None + else: + partial_spins_nbo = None + + return cls( + molecule=molecule, + energy=energy, + enthalpy=enthalpy, + entropy=entropy, + entry_id=entry_id, + mol_graph=mol_graph, + partial_charges_resp=partial_charges_resp, + partial_charges_mulliken=partial_charges_mulliken, + partial_charges_nbo=partial_charges_nbo, + electron_affinity=electron_affinity, + ionization_energy=ionization_energy, + spin_multiplicity=spin_multiplicity, + partial_spins_nbo=partial_spins_nbo, + ) + + @classmethod + def from_quacc_entry(cls, doc: Dict): + """ + Initialize a MoleculeEntry from a document in the bfo datasets. + + Args: + doc: Dictionary representing an entry from bfo quacc + """ + + def decode_ndarray(data): + dtype = data['__ndarray__'][1] + values = np.array(data['__ndarray__'][2], dtype=dtype) + return values.reshape(data['__ndarray__'][0]) + def init_ase_atoms_from_dict(doc): + decoded_data = json.loads(doc['atoms']['atoms_json']) + numbers = decode_ndarray(decoded_data['numbers']) + positions = decode_ndarray(decoded_data['positions']) + charges = decode_ndarray(decoded_data['initial_charges']) + magmoms = decode_ndarray(decoded_data['initial_magmoms']) + cell = decode_ndarray(decoded_data['cell']) + pbc = decode_ndarray(decoded_data['pbc']) + # Initialize the ASE Atoms object + atoms = Atoms(numbers=numbers, positions=positions, charges=charges, magmoms=magmoms, cell=cell, pbc=pbc) + return(atoms) + + atoms = init_ase_atoms_from_dict(doc) + molecule = AseAtomsAdaptor.get_molecule(atoms) + energy = doc["energy"] #eV + enthalpy = doc["enthalpy"] #eV + entropy = doc["entropy"] #eV/K + + entry_id = doc["name"] + mol_gr = MoleculeGraph.with_local_env_strategy(molecule, OpenBabelNN()) + mol_graph = metal_edge_extender(mol_gr, cutoff=3.4, metals=None,coordinators=("O")) + + partial_charges_resp = None + partial_charges_mulliken = None + partial_charges_nbo = None + partial_spins_nbo = None + spin_multiplicity = None + electron_affinity_eV = None + ionization_energy_eV = None + + return cls( + molecule=molecule, + energy=energy, + enthalpy=enthalpy, + entropy=entropy, + entry_id=entry_id, + mol_graph=mol_graph, + partial_charges_resp=partial_charges_resp, + partial_charges_mulliken=partial_charges_mulliken, + partial_charges_nbo=partial_charges_nbo, + electron_affinity=electron_affinity_eV, + ionization_energy=ionization_energy_eV, + spin_multiplicity=spin_multiplicity, + partial_spins_nbo=partial_spins_nbo, + ) def get_free_energy(self, temperature: float = ROOM_TEMP) -> Optional[float]: """ @@ -228,11 +371,7 @@ def get_free_energy(self, temperature: float = ROOM_TEMP) -> Optional[float]: """ if self.enthalpy is not None and self.entropy is not None: # TODO: fix these hard coded vals - return ( - self.energy * 27.21139 - + 0.0433641 * self.enthalpy - - temperature * self.entropy * 0.0000433641 - ) + return self.energy + self.enthalpy - temperature * self.entropy else: return None @@ -244,9 +383,9 @@ def __repr__(self): ] energies = [ - ("Energy", "Hartree", self.energy), - ("Enthalpy", "kcal/mol", self.enthalpy), - ("Entropy", "cal/mol.K", self.entropy), + ("Energy", "eV", self.energy), + ("Enthalpy", "eV", self.enthalpy), + ("Entropy", "eV/K", self.entropy), ("Free Energy (298.15 K)", "eV", self.get_free_energy()), ] for name, unit, value in energies: diff --git a/HiPRGen/network_loader.py b/HiPRGen/network_loader.py index e2f8dbd..9d9e221 100644 --- a/HiPRGen/network_loader.py +++ b/HiPRGen/network_loader.py @@ -55,11 +55,13 @@ def __init__( self.number_of_species = metadata[0] self.number_of_reactions = metadata[1] - if initial_state_database: self.initial_state_con = sqlite3.connect(initial_state_database) self.reactions = {} + self.trajectories = {} + self.initial_state_dict = {} + self.initial_state_array = {} def get_all_redox_reactions(self): redox_reactions = [] @@ -94,6 +96,7 @@ def get_all_coordination_reactions(self, metal_id): return coordination_reactions + def get_all_decoordination_reactions(self, metal_id): decoordination_reactions = [] cur = self.rn_con.cursor() @@ -157,27 +160,8 @@ def index_to_reaction(self, reaction_index): self.reactions[reaction_index] = reaction return reaction - def load_trajectories(self): - - cur = self.initial_state_con.cursor() - - # trajectories[seed][step] = (reaction_id, time) - trajectories = {} - for row in cur.execute(sql_get_trajectory): - seed = row[0] - step = row[1] - reaction_id = row[2] - time = row[3] - - if seed not in trajectories: - trajectories[seed] = {} - - trajectories[seed][step] = (reaction_id, time) - self.trajectories = trajectories - - - def load_initial_state(self): + def load_initial_state_and_trajectories(self): cur = self.initial_state_con.cursor() initial_state_dict = {} @@ -193,6 +177,28 @@ def load_initial_state(self): for i in range(self.number_of_species): initial_state_array[i] = initial_state_dict[i] + if self.initial_state_dict == {}: + self.initial_state_dict = initial_state_dict + else: + for i in range(self.number_of_species): + if initial_state_dict[i] > self.initial_state_dict[i]: + self.initial_state_dict[i] = initial_state_dict[i] + + for row in cur.execute(sql_get_trajectory): + seed = row[0] + step = row[1] + reaction_id = row[2] + time = row[3] + + if seed not in self.trajectories: + self.trajectories[seed] = {} + self.initial_state_array[seed] = initial_state_array + + self.trajectories[seed][step] = (reaction_id, time) + + - self.initial_state_dict = initial_state_dict - self.initial_state_array = initial_state_array + def set_initial_state_db(self, initial_state_database): + # NOTE: switching to a new initial state database and loading in trajectory + # info from it will only work if the new database has different seeds! + self.initial_state_con = sqlite3.connect(initial_state_database) diff --git a/HiPRGen/reaction_filter.py b/HiPRGen/reaction_filter.py index fcc4888..8dae7ed 100644 --- a/HiPRGen/reaction_filter.py +++ b/HiPRGen/reaction_filter.py @@ -15,7 +15,7 @@ ) """ -Phases 3 & 4 run in paralell using MPI +Phases 3 & 4 run in parallel using MPI Phase 3: reaction gen and filtering input: a bucket labeled by atom count diff --git a/HiPRGen/reaction_questions.py b/HiPRGen/reaction_questions.py index ad47d48..36e145a 100644 --- a/HiPRGen/reaction_questions.py +++ b/HiPRGen/reaction_questions.py @@ -2,6 +2,7 @@ from HiPRGen.mol_entry import MoleculeEntry from functools import partial import itertools +import copy import networkx as nx from networkx.algorithms.graph_hashing import weisfeiler_lehman_graph_hash from HiPRGen.constants import Terminal, ROOM_TEMP, KB, PLANCK, m_formulas @@ -54,23 +55,21 @@ class Terminal(Enum): KEEP = 1 DISCARD = -1 """ hydrogen_graph = nx.MultiGraph() -hydrogen_graph.add_node(0, specie='H') -hydrogen_hash = weisfeiler_lehman_graph_hash( - hydrogen_graph, - node_attr='specie') +hydrogen_graph.add_node(0, specie="H") +hydrogen_hash = weisfeiler_lehman_graph_hash(hydrogen_graph, node_attr="specie") fluorine_graph = nx.MultiGraph() -fluorine_graph.add_node(0, specie='F') -fluorine_hash = weisfeiler_lehman_graph_hash( - fluorine_graph, - node_attr='specie') +fluorine_graph.add_node(0, specie="F") +fluorine_hash = weisfeiler_lehman_graph_hash(fluorine_graph, node_attr="specie") + +carbon_graph = nx.MultiGraph() +carbon_graph.add_node(0, specie="C") +carbon_hash = weisfeiler_lehman_graph_hash(carbon_graph, node_attr="specie") + def run_decision_tree( - reaction, - mol_entries, - params, - decision_tree, - decision_pathway=None): + reaction, mol_entries, params, decision_tree, decision_pathway=None +): node = decision_tree while type(node) == list: @@ -89,7 +88,6 @@ def run_decision_tree( node = next_node - if type(node) == Terminal: if decision_pathway is not None: decision_pathway.append(node) @@ -107,72 +105,118 @@ def run_decision_tree( """) - def default_rate(dG_barrier, params): - kT = KB * params['temperature'] + kT = KB * params["temperature"] max_rate = kT / PLANCK - rate = max_rate * math.exp(- dG_barrier / kT) + rate = max_rate * math.exp(-dG_barrier / kT) return rate -class dG_above_threshold(MSONable): - def __init__(self, threshold, free_energy_type, constant_barrier): +class dG_above_threshold(MSONable): + def __init__(self, threshold, free_energy_type, constant_barrier, barrier_factor=0): self.threshold = threshold self.free_energy_type = free_energy_type self.constant_barrier = constant_barrier + self.barrier_factor = barrier_factor - if free_energy_type == 'free_energy': - self.get_free_energy = lambda mol: mol.free_energy - elif free_energy_type == 'solvation_free_energy': - self.get_free_energy = lambda mol: mol.solvation_free_energy + if free_energy_type == "free_energy": + self.get_free_energy = lambda mol, temperature: mol.get_free_energy(temperature) + elif free_energy_type == "solvation_free_energy": + self.get_free_energy = lambda mol, temperature: mol.solvation_correction + mol.get_free_energy(temperature) else: raise Exception("unrecognized free energy type") def __str__(self): - return ( - self.free_energy_type + - " dG is above threshold=" + - str(self.threshold)) + return self.free_energy_type + " dG is above threshold=" + str(self.threshold) def __call__(self, reaction, mol_entries, params): - dG = 0.0 # positive dCharge means electrons are lost dCharge = 0.0 - for i in range(reaction['number_of_reactants']): - reactant_index = reaction['reactants'][i] + for i in range(reaction["number_of_reactants"]): + reactant_index = reaction["reactants"][i] mol = mol_entries[reactant_index] - dG -= self.get_free_energy(mol) + dG -= self.get_free_energy(mol, params["temperature"]) dCharge -= mol.charge - for j in range(reaction['number_of_products']): - product_index = reaction['products'][j] + for j in range(reaction["number_of_products"]): + product_index = reaction["products"][j] mol = mol_entries[product_index] - dG += self.get_free_energy(mol) + dG += self.get_free_energy(mol, params["temperature"]) dCharge += mol.charge - dG += dCharge * params['electron_free_energy'] + dG += dCharge * params["electron_free_energy"] if dG > self.threshold: + reaction["dG"] = dG + if self.barrier_factor == 0: + barrier = self.constant_barrier + else: + barrier = reaction["dG"] * self.barrier_factor + reaction["dG_barrier"] = barrier + reaction["rate"] = default_rate(barrier, params) return True else: - reaction['dG'] = dG + reaction["dG"] = dG if dG < 0: barrier = self.constant_barrier else: barrier = dG + self.constant_barrier - reaction['dG_barrier'] = barrier - reaction['rate'] = default_rate(barrier, params) + reaction["dG_barrier"] = barrier + reaction["rate"] = default_rate(barrier, params) return False -class is_redox_reaction(MSONable): +class dG_below_threshold(MSONable): + def __init__(self, threshold, free_energy_type, constant_barrier): + + self.threshold = threshold + self.free_energy_type = free_energy_type + self.constant_barrier = constant_barrier + + if free_energy_type == "free_energy": + self.get_free_energy = lambda mol, temperature: mol.get_free_energy(temperature) + elif free_energy_type == "solvation_free_energy": + self.get_free_energy = lambda mol, temperature: mol.solvation_correction + mol.get_free_energy(temperature) + else: + raise Exception("unrecognized free energy type") + + def __str__(self): + return self.free_energy_type + " dG is below threshold=" + str(self.threshold) + + def __call__(self, reaction, mol_entries, params): + dG = 0.0 + + # positive dCharge means electrons are lost + dCharge = 0.0 + + for i in range(reaction["number_of_reactants"]): + reactant_index = reaction["reactants"][i] + mol = mol_entries[reactant_index] + dG -= self.get_free_energy(mol, params["temperature"]) + dCharge -= mol.charge + + for j in range(reaction["number_of_products"]): + product_index = reaction["products"][j] + mol = mol_entries[product_index] + dG += self.get_free_energy(mol, params["temperature"]) + dCharge += mol.charge + + dG += dCharge * params["electron_free_energy"] + + if dG < self.threshold: + return True + else: + return False + + +class is_redox_reaction(MSONable): def __init__(self): pass @@ -183,24 +227,64 @@ def __call__(self, reaction, mol_entries, params): # positive dCharge means electrons are lost dCharge = 0.0 - for i in range(reaction['number_of_reactants']): - reactant_index = reaction['reactants'][i] + for i in range(reaction["number_of_reactants"]): + reactant_index = reaction["reactants"][i] mol = mol_entries[reactant_index] dCharge -= mol.charge - for j in range(reaction['number_of_products']): - product_index = reaction['products'][j] + for j in range(reaction["number_of_products"]): + product_index = reaction["products"][j] mol = mol_entries[product_index] dCharge += mol.charge if dCharge == 0: - reaction['is_redox'] = False + reaction["is_redox"] = False return False else: - reaction['is_redox'] = True + reaction["is_redox"] = True return True +class add_electron_species(MSONable): + def __init__(self): + pass + + def __str__(self): + return "add electron species" + + def __call__(self, reaction, mol_entries, params): + if "electron_species" in params: + # positive dCharge means electrons are lost + dCharge = 0.0 + + if reaction["number_of_reactants"] != 1: + return False + + if reaction["number_of_products"] != 1: + return False + + dCharge -= mol_entries[reaction["reactants"][0]].charge + dCharge += mol_entries[reaction["products"][0]].charge + + if dCharge > 0: + reaction["products"] = ( + reaction["products"][0], + params["electron_species"], + ) + reaction["number_of_products"] = 2 + elif dCharge < 0: + reaction["reactants"] = ( + reaction["reactants"][0], + params["electron_species"], + ) + reaction["number_of_reactants"] = 2 + else: + pass + return False + else: + return False + + class too_many_reactants_or_products(MSONable): def __init__(self): pass @@ -208,10 +292,36 @@ def __init__(self): def __str__(self): return "too many reactants or products" + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] != 1 or reaction["number_of_products"] != 1: + return True + else: + return False + + +class more_than_one_reactant(MSONable): + def __init__(self): + pass + + def __str__(self): + return "more than one reactant" - def __call__(self, reaction, mols, params): - if (reaction['number_of_reactants'] != 1 or - reaction['number_of_products'] != 1): + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] != 1: + return True + else: + return False + + +class only_one_product(MSONable): + def __init__(self): + pass + + def __str__(self): + return "only one product" + + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_products"] == 1: return True else: return False @@ -222,10 +332,12 @@ def __init__(self): pass def __call__(self, reaction, mol_entries, params): - if (reaction['number_of_reactants'] == 1 and - reaction['number_of_products'] == 1 and - (mol_entries[reaction['reactants'][0]].formula in m_formulas) and - (mol_entries[reaction['products'][0]].formula in m_formulas)): + if ( + reaction["number_of_reactants"] == 1 + and reaction["number_of_products"] == 1 + and (mol_entries[reaction["reactants"][0]].formula in m_formulas) + and (mol_entries[reaction["products"][0]].formula in m_formulas) + ): return True else: @@ -242,13 +354,13 @@ def __str__(self): def __call__(self, reaction, mol_entries, params): dCharge = 0.0 - for i in range(reaction['number_of_reactants']): - reactant_index = reaction['reactants'][i] + for i in range(reaction["number_of_reactants"]): + reactant_index = reaction["reactants"][i] mol = mol_entries[reactant_index] dCharge -= mol.charge - for j in range(reaction['number_of_products']): - product_index = reaction['products'][j] + for j in range(reaction["number_of_products"]): + product_index = reaction["products"][j] mol = mol_entries[product_index] dCharge += mol.charge @@ -258,8 +370,7 @@ def __call__(self, reaction, mol_entries, params): return False - -def marcus_barrier(reaction, mols, params): +def marcus_barrier(reaction, mol_entries, params): """ Okay, so Marcus Theory.The math works out like so.∆G* = λ/4 (1 + @@ -279,8 +390,8 @@ def marcus_barrier(reaction, mols, params): the relative dielectric (18.5 for EC/EMC). """ - reactant = mols[reaction['reactants'][0]] - product = mols[reaction['products'][0]] + reactant = mol_entries[reaction["reactants"][0]] + product = mol_entries[reaction["products"][0]] dCharge = product.charge - reactant.charge n = 1.415 # index of refraction; variable eps = 18.5 # dielectric constant; variable @@ -288,12 +399,14 @@ def marcus_barrier(reaction, mols, params): r = 6.0 # in Angstrom R = 7.5 # in Angstrom - eps_0 = 8.85419 * 10 ** -12 # vacuum permittivity - e = 1.602 * 10 ** -19 # fundamental charge + eps_0 = 8.85419 * 10**-12 # vacuum permittivity + e = 1.602 * 10**-19 # fundamental charge l_outer = e / (8 * math.pi * eps_0) - l_outer *= (1 / r - 1/(2 * R)) * 10 ** 10 # Converting to SI units; factor of 2 is because of different definitions of the distance to electrode - l_outer *= (1 / n ** 2 - 1 / eps) + l_outer *= ( + 1 / r - 1 / (2 * R) + ) * 10**10 # Converting to SI units; factor of 2 is because of different definitions of the distance to electrode + l_outer *= 1 / n**2 - 1 / eps if dCharge == -1: vals = [reactant.electron_affinity, product.ionization_energy] @@ -305,29 +418,31 @@ def marcus_barrier(reaction, mols, params): vals_filtered = [v for v in vals if v is not None] l_inner = sum(vals_filtered) / len(vals_filtered) - if l_inner < 0: l_inner = 0 l = l_inner + l_outer - - dG = product.free_energy - reactant.free_energy + dCharge * params['electron_free_energy'] + dG = ( + product.free_energy + - reactant.free_energy + + dCharge * params["electron_free_energy"] + ) dG_barrier = l / 4 * (1 + dG / l) ** 2 - reaction['marcus_barrier'] = dG_barrier + reaction["marcus_barrier"] = dG_barrier return False -class reactant_and_product_not_isomorphic(MSONable): +class reactant_and_product_not_isomorphic(MSONable): def __init__(self): pass def __str__(self): return "reactants and products are not covalent isomorphic" - def __call__(self, reaction, mols, params): - reactant = mols[reaction['reactants'][0]] - product = mols[reaction['products'][0]] + def __call__(self, reaction, mol_entries, params): + reactant = mol_entries[reaction["reactants"][0]] + product = mol_entries[reaction["products"][0]] if reactant.covalent_hash != product.covalent_hash: return True else: @@ -335,16 +450,16 @@ def __call__(self, reaction, mols, params): class reaction_default_true(MSONable): - def __init__(self): pass def __str__(self): return "default true" - def __call__(self, reaction, mols, params): + def __call__(self, reaction, mol_entries, params): return True + class star_count_diff_above_threshold(MSONable): """ if you want to filter out break-one-form-one reactions, the @@ -357,14 +472,14 @@ def __init__(self, threshold): def __str__(self): return "star count diff above threshold=" + str(self.threshold) - def __call__(self, reaction, mols, params): + def __call__(self, reaction, mol_entries, params): reactant_stars = {} product_stars = {} tags = set() - for i in range(reaction['number_of_reactants']): - reactant_index = reaction['reactants'][i] - mol = mols[reactant_index] + for i in range(reaction["number_of_reactants"]): + reactant_index = reaction["reactants"][i] + mol = mol_entries[reactant_index] for h in mol.star_hashes.values(): tags.add(h) if h in reactant_stars: @@ -372,9 +487,9 @@ def __call__(self, reaction, mols, params): else: reactant_stars[h] = 1 - for j in range(reaction['number_of_products']): - product_index = reaction['products'][j] - mol = mols[product_index] + for j in range(reaction["number_of_products"]): + product_index = reaction["products"][j] + mol = mol_entries[product_index] for h in mol.star_hashes.values(): tags.add(h) if h in product_stars: @@ -385,35 +500,158 @@ def __call__(self, reaction, mols, params): count = 0 for tag in tags: - count += abs(reactant_stars.get(tag,0) - product_stars.get(tag,0)) + count += abs(reactant_stars.get(tag, 0) - product_stars.get(tag, 0)) if count > self.threshold: return True else: return False -class reaction_is_covalent_decomposable(MSONable): + +class reaction_is_charge_transfer(MSONable): def __init__(self): pass def __str__(self): - return "reaction is covalent decomposable" + return "reaction is charge transfer" + + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 2 and reaction["number_of_products"] == 2: + + reactant_total_hashes = set() + reactant_hash_list = [] + for i in range(reaction["number_of_reactants"]): + reactant_id = reaction["reactants"][i] + reactant = mol_entries[reactant_id] + reactant_total_hashes.add(reactant.covalent_hash) + reactant_hash_list.append(reactant.covalent_hash) + + product_total_hashes = set() + product_hash_list = [] + for i in range(reaction["number_of_products"]): + product_id = reaction["products"][i] + product = mol_entries[product_id] + product_total_hashes.add(product.covalent_hash) + product_hash_list.append(product.covalent_hash) + + if len(reactant_total_hashes.intersection(product_total_hashes)) == 2: + return True + elif len(reactant_total_hashes.intersection(product_total_hashes)) == 1 and reactant_hash_list[0] == reactant_hash_list[1] and product_hash_list[0] == product_hash_list[1]: + return True + else: + return False + + return False + + +class reaction_is_covalent_charge_decomposable(MSONable): # Remove A + B -> A + C, where A on both + # sides has the same charge + def __init__(self): + pass - def __call__(self, reaction, mols, params): + def __str__(self): + return "reaction is covalent charge decomposable" + + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 2 and reaction["number_of_products"] == 2: + + reactant_charge_hashes = set() + for i in range(reaction["number_of_reactants"]): + reactant_id = reaction["reactants"][i] + reactant = mol_entries[reactant_id] + reactant_charge_hashes.add(reactant.covalent_hash + "_"+ str(reactant.charge)) + + product_charge_hashes = set() + for i in range(reaction["number_of_products"]): + product_id = reaction["products"][i] + product = mol_entries[product_id] + product_charge_hashes.add(product.covalent_hash + "_" + str(product.charge)) + + if len(reactant_charge_hashes.intersection(product_charge_hashes)) == 1: + return True + + return False + + +class reaction_is_coupled_electron_fragment_transfer(MSONable): # Remove A + B+ -> C+ + B + + def __init__(self): + pass + + def __str__(self): + return "reaction is coupled electron fragment transfer" + + def __call__(self, reaction, mol_entries, params): if (reaction['number_of_reactants'] == 2 and reaction['number_of_products'] == 2): + reactants = [] + reactant_charge_hashes = set() + reactant_hashes = set() + for i in range(reaction["number_of_reactants"]): + reactant_id = reaction["reactants"][i] + # print("reactant_id", reactant_id) + reactant = mol_entries[reactant_id] + reactants.append(reactant) + reactant_hashes.add(reactant.covalent_hash) + reactant_charge_hashes.add(reactant.covalent_hash + "_"+ str(reactant.charge)) + + product_charge_hashes = set() + product_hashes = set() + for i in range(reaction["number_of_products"]): + product_id = reaction["products"][i] + # print("product_id", product_id) + product = mol_entries[product_id] + product_hashes.add(product.covalent_hash) + product_charge_hashes.add(product.covalent_hash + "_" + str(product.charge)) + + if len(reactant_charge_hashes.intersection(product_charge_hashes)) == 0 and len(reactant_hashes.intersection(product_hashes)) > 0: + bigger_reactant = None + smaller_hash = None + try: + comp_diff = reactants[0].molecule.composition - reactants[1].molecule.composition + bigger_reactant = 0 + smaller_hash = reactants[1].covalent_hash + except ValueError: + try: + comp_diff = reactants[1].molecule.composition - reactants[0].molecule.composition + bigger_reactant = 1 + smaller_hash = reactants[0].covalent_hash + except ValueError: + return True + # print("bigger_reactant", bigger_reactant) + for frag_complex in reactants[bigger_reactant].fragment_data: + if smaller_hash in frag_complex.fragment_hashes: + # print("hash found!") + # print(huh) + return False + return True + + + return False + +class reaction_is_covalent_decomposable(MSONable): # Remove A + B -> A + C, even if A has different + # charges on each side AND removes charge tranfer + # e.g. A+ + B -> A + B+ + def __init__(self): + pass + + def __str__(self): + return "reaction is covalent decomposable" + + def __call__(self, reaction, mol_entries, params): + if (reaction['number_of_reactants'] == 2 and + reaction['number_of_products'] == 2): reactant_total_hashes = set() for i in range(reaction['number_of_reactants']): reactant_id = reaction['reactants'][i] - reactant = mols[reactant_id] + reactant = mol_entries[reactant_id] reactant_total_hashes.add(reactant.covalent_hash) - product_total_hashes = set() for i in range(reaction['number_of_products']): product_id = reaction['products'][i] - product = mols[product_id] + product = mol_entries[product_id] product_total_hashes.add(product.covalent_hash) if len(reactant_total_hashes.intersection(product_total_hashes)) > 0: @@ -424,6 +662,114 @@ def __call__(self, reaction, mols, params): return False +class reaction_is_separable(MSONable): # remove A + B -> C + D if there are 2 pairs of same compositions + # then we represent the reaction as A -> C and B -> D + def __init__(self): + pass + + def __str__(self): + return "reaction is separable into two" + + def __call__(self, reaction, mol_entries, params): + if (reaction['number_of_reactants'] == 2 and + reaction['number_of_products'] == 2): + reactant_comps = [] + for i in range(reaction['number_of_reactants']): + reactant_id = reaction['reactants'][i] + reactant = mol_entries[reactant_id] + reactant_comps.append(reactant.molecule.composition) + product_comps = [] + for i in range(reaction['number_of_products']): + product_id = reaction['products'][i] + product = mol_entries[product_id] + product_comps.append(product.molecule.composition) + comp_diff = [(int(product_comps[0] == reactant_comps[0]), int(product_comps[1] == reactant_comps[1])), + (int(product_comps[1] == reactant_comps[0]), int(product_comps[0] == reactant_comps[1]))] + if (1,1) in comp_diff: # there are 2 pairs of same compositions + return True + else: + return False + + return False + + +class reaction_is_radical_separation(MSONable): + def __init__(self): + pass + + def __str__(self): + return "reaction is radical separation" + + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 1 and reaction["number_of_products"] == 2: + reactant_spin = mol_entries[reaction["reactants"][0]].spin_multiplicity + if reactant_spin == 1: + prod0_spin = mol_entries[reaction["products"][0]].spin_multiplicity + if prod0_spin != 1: + return True + return False + + +class reaction_is_charge_separation(MSONable): + def __init__(self): + pass + + def __str__(self): + return "reaction is charge separation" + + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 1 and reaction["number_of_products"] == 2: + reactant_charge = mol_entries[reaction["reactants"][0]].charge + prod0_charge = mol_entries[reaction["products"][0]].charge + prod1_charge = mol_entries[reaction["products"][1]].charge + if abs(prod0_charge) > abs(reactant_charge) or abs(prod1_charge) > abs(reactant_charge): + return True + elif reaction["number_of_reactants"] == 2 and reaction["number_of_products"] == 2: + reactant0_charge = mol_entries[reaction["reactants"][0]].charge + reactant1_charge = mol_entries[reaction["reactants"][1]].charge + prod0_charge = mol_entries[reaction["products"][0]].charge + prod1_charge = mol_entries[reaction["products"][1]].charge + if reactant0_charge == 0 and reactant1_charge == 0 and (abs(prod0_charge) > 0 or abs(prod1_charge)) > 0: + return True + return False + + +class reactants_are_both_anions_or_both_cations(MSONable): + def __init__(self): + pass + + def __str__(self): + return "reactants are both anions or both cations" + + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 2: + reactant0_charge = mol_entries[reaction["reactants"][0]].charge + reactant1_charge = mol_entries[reaction["reactants"][1]].charge + if reactant0_charge > 0 and reactant1_charge > 0: + return True + elif reactant0_charge < 0 and reactant1_charge < 0: + return True + return False + + +class two_closed_shell_reactants_and_two_open_shell_products(MSONable): + def __init__(self): + pass + + def __str__(self): + return "two closed shell reactants and two open shell products" + + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 2 and reaction["number_of_products"] == 2: + reactant0_spin = mol_entries[reaction["reactants"][0]].spin_multiplicity + reactant1_spin = mol_entries[reaction["reactants"][1]].spin_multiplicity + product0_spin = mol_entries[reaction["products"][0]].spin_multiplicity + product1_spin = mol_entries[reaction["products"][1]].spin_multiplicity + if reactant0_spin == 1 and reactant1_spin == 1 and product0_spin > 1 and product1_spin > 1: + return True + return False + + class metal_coordination_passthrough(MSONable): def __init__(self): pass @@ -431,70 +777,107 @@ def __init__(self): def __str__(self): return "metal coordination passthrough" - def __call__(self, reaction, mols, params): + def __call__(self, reaction, mol_entries, params): - for i in range(reaction['number_of_reactants']): - reactant_id = reaction['reactants'][i] - reactant = mols[reactant_id] + for i in range(reaction["number_of_reactants"]): + reactant_id = reaction["reactants"][i] + reactant = mol_entries[reactant_id] if reactant.formula in m_formulas: return True - for i in range(reaction['number_of_products']): - product_id = reaction['products'][i] - product = mols[product_id] + for i in range(reaction["number_of_products"]): + product_id = reaction["products"][i] + product = mol_entries[product_id] if product.formula in m_formulas: return True return False -class fragment_matching_found(MSONable): +class compositions_preclude_h_transfer(MSONable): def __init__(self): pass def __str__(self): - return "fragment matching found" + return "compositions preclude h transfer" - def __call__(self, reaction, mols, params): + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] != 2 or reaction["number_of_products"] != 2: + return True - reactant_fragment_indices_list = [] - product_fragment_indices_list = [] + reactant_0 = mol_entries[reaction["reactants"][0]] + reactant_dictionary = reactant_0.molecule.composition.as_dict() + + product_compositions = [] + for i in range(reaction["number_of_products"]): + product = mol_entries[reaction["products"][i]] + product_compositions.append(product.molecule.composition.as_dict()) + + for product_dictionary in product_compositions: + new_dict = {} + all_elements = set(reactant_dictionary.keys()).union(set(product_dictionary.keys())) + for elem in all_elements: + diff = abs(reactant_dictionary.get(elem, 0.0) - product_dictionary.get(elem, 0.0)) + if diff != 0.0: + new_dict[elem] = diff + if "H" in new_dict: + if len(new_dict.keys()) == 1: + if new_dict["H"] == 1.0: + return False - if reaction['number_of_reactants'] == 1: - reactant = mols[reaction['reactants'][0]] - for i in range(len(reactant.fragment_data)): - reactant_fragment_indices_list.append([i]) + return True - if reaction['number_of_reactants'] == 2: - reactant_0 = mols[reaction['reactants'][0]] - reactant_1 = mols[reaction['reactants'][1]] - for i in range(len(reactant_0.fragment_data)): - for j in range(len(reactant_1.fragment_data)): - if (reactant_0.fragment_data[i].number_of_bonds_broken + - reactant_1.fragment_data[j].number_of_bonds_broken <= 1): +class fragment_matching_found(MSONable): + def __init__(self): + pass - reactant_fragment_indices_list.append([i,j]) + def __str__(self): + return "fragment matching found" + + def __call__(self, reaction, mol_entries, params): + reactant_fragment_indices_list = [] + product_fragment_indices_list = [] - if reaction['number_of_products'] == 1: - product = mols[reaction['products'][0]] + if reaction["number_of_reactants"] == 1: #creates a list of the indicies pointing to FragmentComplex objects + reactant = mol_entries[reaction["reactants"][0]] #reactant is a mol_entry + for i in range(len(reactant.fragment_data)): #fragment_data is a list of FragmentComplex objects, where each + reactant_fragment_indices_list.append([i]) #FragmentComplex object is basically a dictionary with four keys + + if reaction["number_of_reactants"] == 2: + reactant_0 = mol_entries[reaction["reactants"][0]] + reactant_1 = mol_entries[reaction["reactants"][1]] + for i in range(len(reactant_0.fragment_data)): #for each fragment of one reactant + for j in range(len(reactant_1.fragment_data)): #look at each fragment of the other reactant + if ( #true only when adding fragments of one reactant with the other + reactant_0.fragment_data[i].number_of_bonds_broken #unfragmented reactant? + + reactant_1.fragment_data[j].number_of_bonds_broken + <= 2 # include b1, b2 + ): + + reactant_fragment_indices_list.append([i, j]) #append a list to the list containing fragment indicies for both reactants + + if reaction["number_of_products"] == 1: #repeat for product indicies + product = mol_entries[reaction["products"][0]] for i in range(len(product.fragment_data)): product_fragment_indices_list.append([i]) - - if reaction['number_of_products'] == 2: - product_0 = mols[reaction['products'][0]] - product_1 = mols[reaction['products'][1]] + if reaction["number_of_products"] == 2: + product_0 = mol_entries[reaction["products"][0]] + product_1 = mol_entries[reaction["products"][1]] for i in range(len(product_0.fragment_data)): for j in range(len(product_1.fragment_data)): - if (product_0.fragment_data[i].number_of_bonds_broken + - product_1.fragment_data[j].number_of_bonds_broken <= 1): - - product_fragment_indices_list.append([i,j]) + if ( + product_0.fragment_data[i].number_of_bonds_broken + + product_1.fragment_data[j].number_of_bonds_broken + <= 2 + ): + product_fragment_indices_list.append([i, j]) - for reactant_fragment_indices in reactant_fragment_indices_list: + viable_fragment_matches = [] + for reactant_fragment_indices in reactant_fragment_indices_list: #iterating over all reactant and product fragment indicies for product_fragment_indices in product_fragment_indices_list: reactant_fragment_count = 0 product_fragment_count = 0 @@ -502,16 +885,15 @@ def __call__(self, reaction, mols, params): product_bonds_broken = [] reactant_hashes = dict() - for reactant_index, frag_complex_index in enumerate( - reactant_fragment_indices): - - fragment_complex = mols[ - reaction['reactants'][reactant_index]].fragment_data[ - frag_complex_index] + for reactant_index, frag_complex_index in enumerate(reactant_fragment_indices): + fragment_complex = mol_entries[ #pulls out a fragment_complex whose index matches the above + reaction["reactants"][reactant_index] + ].fragment_data[frag_complex_index] - for bond in fragment_complex.bonds_broken: + for bond in fragment_complex.bonds_broken: #save what bonds are broken in this complex to reactant_bonds_broken reactant_bonds_broken.append( - [(reactant_index, x) for x in bond]) + [(reactant_index, x) for x in bond] #first element of tuple is which reactant, x is a integer, bond is a tuple containing two numbers denoting the edge of a molecule graph + ) for i in range(fragment_complex.number_of_fragments): reactant_fragment_count += 1 @@ -523,16 +905,15 @@ def __call__(self, reaction, mols, params): product_hashes = dict() for product_index, frag_complex_index in enumerate( - product_fragment_indices): + product_fragment_indices + ): - fragment_complex = mols[ - reaction['products'][product_index]].fragment_data[ - frag_complex_index] + fragment_complex = mol_entries[ + reaction["products"][product_index] + ].fragment_data[frag_complex_index] for bond in fragment_complex.bonds_broken: - product_bonds_broken.append( - [(product_index, x) for x in bond]) - + product_bonds_broken.append([(product_index, x) for x in bond]) for i in range(fragment_complex.number_of_fragments): product_fragment_count += 1 @@ -542,42 +923,131 @@ def __call__(self, reaction, mols, params): else: product_hashes[tag] = 1 - # don't consider fragmentations with both a ring opening and closing - if (reaction['number_of_reactants'] == 2 and - reaction['number_of_products'] == 2 and - reactant_fragment_count == 2 and - product_fragment_count == 2): + if ( + reaction["number_of_reactants"] == 2 + and reaction["number_of_products"] == 2 + and reactant_fragment_count == 2 + and product_fragment_count == 2 + ): continue - if reactant_hashes == product_hashes: - reaction['reactant_bonds_broken'] = reactant_bonds_broken - reaction['product_bonds_broken'] = product_bonds_broken - reaction['hashes'] = reactant_hashes - reaction['reactant_fragment_count'] = reactant_fragment_count - reaction['product_fragment_count'] = product_fragment_count + if hydrogen_hash in reactant_hashes: + reaction["reactant_bonds_broken"] = reactant_bonds_broken + reaction["product_bonds_broken"] = product_bonds_broken + reaction["hashes"] = reactant_hashes + reaction["reactant_fragment_count"] = reactant_fragment_count + reaction["product_fragment_count"] = product_fragment_count + return True + else: + tmp = {} + tmp["reactant_bonds_broken"] = reactant_bonds_broken + tmp["product_bonds_broken"] = product_bonds_broken + tmp["hashes"] = reactant_hashes + tmp["reactant_fragment_count"] = reactant_fragment_count + tmp["product_fragment_count"] = product_fragment_count + viable_fragment_matches.append(tmp) + + if len(viable_fragment_matches) > 0: + min_frag_size = 1000000000 + if len(viable_fragment_matches) == 1: + best_matching = viable_fragment_matches[0] + else: + for viable_match in viable_fragment_matches: + if len(viable_match["reactant_bonds_broken"]) == 0: + for reactant_index in reaction["reactants"]: + reactant = mol_entries[reactant_index] + if len(reactant.molecule) < min_frag_size: + min_frag_size = len(reactant.molecule) + best_matching = copy.deepcopy(viable_match) + else: + for l in viable_match["reactant_bonds_broken"]: + hot_reactant = mol_entries[reaction["reactants"][l[0][0]]] + hot_reactant_graph = copy.deepcopy(hot_reactant.covalent_graph) + edge = (l[0][1],l[1][1]) + hot_reactant_graph.remove_edge(*edge) + connected_components = nx.algorithms.components.connected_components(hot_reactant_graph) + for c in connected_components: + subgraph = hot_reactant_graph.subgraph(c) + # if subgraph.number_of_nodes() == 1: + # for node in subgraph: + # print(nx.get_node_attributes(hot_reactant_graph, "specie")[node]) + if subgraph.number_of_nodes() < min_frag_size: + min_frag_size = subgraph.number_of_nodes() + best_matching = copy.deepcopy(viable_match) + reaction["reactant_bonds_broken"] = best_matching["reactant_bonds_broken"] + reaction["product_bonds_broken"] = best_matching["product_bonds_broken"] + reaction["hashes"] = best_matching["hashes"] + reaction["reactant_fragment_count"] = best_matching["reactant_fragment_count"] + reaction["product_fragment_count"] = best_matching["product_fragment_count"] + return True + return False - return True +class single_reactant_single_product_not_atom_transfer(MSONable): + def __init__(self): + pass + + def __str__(self): + return "not intramolecular hydrogen/fluorine transfer" + + def __call__(self, reaction, mol_entries, params): + if ( + reaction["number_of_reactants"] == 1 + and reaction["number_of_products"] == 1 + and len(reaction["reactant_bonds_broken"]) == 1 + and len(reaction["product_bonds_broken"]) == 1 + and hydrogen_hash not in reaction["hashes"] + and fluorine_hash not in reaction["hashes"] + ): + return True return False -class single_reactant_single_product_not_atom_transfer(MSONable): +class not_h_transfer(MSONable): def __init__(self): pass def __str__(self): - return "not hydrogen transfer" + return "not intermolecular hydrogen transfer" - def __call__(self, reaction, mols, params): - if (reaction['number_of_reactants'] == 1 and - reaction['number_of_products'] == 1 and - len(reaction['reactant_bonds_broken']) == 1 and - len(reaction['product_bonds_broken']) == 1 and - hydrogen_hash not in reaction['hashes'] and - fluorine_hash not in reaction['hashes']): + def __call__(self, reaction, mol_entries, params): + if hydrogen_hash not in reaction["hashes"]: + return True + + return False + +class fragments_are_not_2A_B(MSONable): + def __init__(self): + pass + + def __str__(self): + return "fragments are not A + A + B" + + def __call__(self, reaction, mol_entries, params): + if len(reaction["hashes"].keys()) == 2: + number_of_fragments = 0 + for frag_hash in reaction["hashes"]: + number_of_fragments += reaction["hashes"][frag_hash] + if number_of_fragments == 3: + return False + else: + return True + else: + return True + + +class single_reactant_single_product(MSONable): + def __init__(self): + pass + + def __str__(self): + return "single reactant single product" + + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 1 and reaction["number_of_products"] == 1: return True return False @@ -590,20 +1060,65 @@ def __init__(self): def __str__(self): return "ring close" + def __call__(self, reaction, mol_entries, params): - def __call__(self, reaction, mols, params): + if ( + reaction["number_of_reactants"] == 1 + and reaction["number_of_products"] == 2 + and len(reaction["reactant_bonds_broken"]) == 1 + and len(reaction["product_bonds_broken"]) == 1 + and reaction["product_fragment_count"] == 2 + ): + return True + return False - if (reaction['number_of_reactants'] == 1 and - reaction['number_of_products'] == 2 and - len(reaction['reactant_bonds_broken']) == 1 and - len(reaction['product_bonds_broken']) == 1 and - reaction['product_fragment_count'] == 2): - return True +class h_abstraction_from_closed_shell_reactant(MSONable): + def __init__(self): + pass + + def __str__(self): + return "h abstraction from closed shell reactant" + + def __call__(self, reaction, mol_entries, params): + + if reaction["number_of_reactants"] == 2 and reaction["number_of_products"] == 2 and hydrogen_hash in reaction["hashes"]: + hot_reactant_ind = reaction["reactant_bonds_broken"][0][0][0] + cold_reactant_ind = 0 + if hot_reactant_ind == 0: + cold_reactant_ind = 1 + hot_product_ind = reaction["product_bonds_broken"][0][0][0] + hot_reactant = mol_entries[reaction["reactants"][hot_reactant_ind]] + cold_reactant = mol_entries[reaction["reactants"][cold_reactant_ind]] + hot_product = mol_entries[reaction["products"][hot_product_ind]] + if hot_reactant.spin_multiplicity == 1: + if hot_product.charge - cold_reactant.charge == 0: + return True return False +class h_minus_abstraction(MSONable): + def __init__(self): + pass + + def __str__(self): + return "h minus abstraction" + + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 2 and reaction["number_of_products"] == 2 and hydrogen_hash in reaction["hashes"]: + hot_reactant_ind = reaction["reactant_bonds_broken"][0][0][0] + cold_reactant_ind = 0 + if hot_reactant_ind == 0: + cold_reactant_ind = 1 + hot_product_ind = reaction["product_bonds_broken"][0][0][0] + cold_reactant = mol_entries[reaction["reactants"][cold_reactant_ind]] + hot_product = mol_entries[reaction["products"][hot_product_ind]] + if hot_product.charge - cold_reactant.charge == -1: + return True + + return False + class concerted_metal_coordination(MSONable): def __init__(self): @@ -612,28 +1127,28 @@ def __init__(self): def __str__(self): return "concerted metal coordination" - def __call__(self, reaction, mols, params): - - if (reaction['number_of_reactants'] == 2 and - reaction['number_of_products'] == 2): - - reactant_0 = mols[reaction['reactants'][0]] - reactant_1 = mols[reaction['reactants'][1]] - product_0 = mols[reaction['products'][0]] - product_1 = mols[reaction['products'][1]] + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 2 and reaction["number_of_products"] == 2: + reactant_0 = mol_entries[reaction["reactants"][0]] + reactant_1 = mol_entries[reaction["reactants"][1]] + product_0 = mol_entries[reaction["products"][0]] + product_1 = mol_entries[reaction["products"][1]] - if (reactant_0.formula in m_formulas or - reactant_1.formula in m_formulas or - product_0.formula in m_formulas or - product_1.formula in m_formulas): + if ( + reactant_0.formula in m_formulas + or reactant_1.formula in m_formulas + or product_0.formula in m_formulas + or product_1.formula in m_formulas + ): return True else: return False return False + class concerted_metal_coordination_one_product(MSONable): def __init__(self): pass @@ -641,31 +1156,28 @@ def __init__(self): def __str__(self): return "concerted metal coordination one product" + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 2 and reaction["number_of_products"] == 1: - def __call__(self, reaction, mols, params): - - if (reaction['number_of_reactants'] == 2 and - reaction['number_of_products'] == 1): + reactant_0 = mol_entries[reaction["reactants"][0]] + reactant_1 = mol_entries[reaction["reactants"][1]] + product = mol_entries[reaction["products"][0]] - reactant_0 = mols[reaction['reactants'][0]] - reactant_1 = mols[reaction['reactants'][1]] - product = mols[reaction['products'][0]] + reactant_covalent_hashes = set( + [reactant_0.covalent_hash, reactant_1.covalent_hash] + ) - reactant_covalent_hashes = set([ - reactant_0.covalent_hash, - reactant_1.covalent_hash]) - - if ((reactant_0.formula in m_formulas or - reactant_1.formula in m_formulas) and - product.covalent_hash not in reactant_covalent_hashes - ): + if ( + reactant_0.formula in m_formulas or reactant_1.formula in m_formulas + ) and product.covalent_hash not in reactant_covalent_hashes: return True else: return False return False + class concerted_metal_coordination_one_reactant(MSONable): def __init__(self): pass @@ -673,25 +1185,21 @@ def __init__(self): def __str__(self): return "concerted metal coordination one reactant" + def __call__(self, reaction, mol_entries, params): + if reaction["number_of_reactants"] == 1 and reaction["number_of_products"] == 2: - def __call__(self, reaction, mols, params): - - if (reaction['number_of_reactants'] == 1 and - reaction['number_of_products'] == 2): - - product_0 = mols[reaction['products'][0]] - product_1 = mols[reaction['products'][1]] - reactant = mols[reaction['reactants'][0]] + product_0 = mol_entries[reaction["products"][0]] #use this to get a mol entry + product_1 = mol_entries[reaction["products"][1]] + reactant = mol_entries[reaction["reactants"][0]] - product_covalent_hashes = set([ - product_0.covalent_hash, - product_1.covalent_hash]) + product_covalent_hashes = set( + [product_0.covalent_hash, product_1.covalent_hash] + ) - if ((product_0.formula in m_formulas or - product_1.formula in m_formulas) and - reactant.covalent_hash not in product_covalent_hashes - ): + if ( + product_0.formula in m_formulas or product_1.formula in m_formulas + ) and reactant.covalent_hash not in product_covalent_hashes: return True else: return False @@ -706,20 +1214,22 @@ def __init__(self): def __str__(self): return "single reactant with a ring, break two" - def __call__(self, reaction, mols, params): - if (reaction["number_of_reactants"] == 1 and - reaction["number_of_products"] == 2 and - mols[reaction["reactants"][0]].has_covalent_ring): - - reactant = mols[reaction["reactants"][0]] - product_1 = mols[reaction["products"][0]] - product_2 = mols[reaction["products"][1]] + def __call__(self, reaction, mol_entries, params): + if ( + reaction["number_of_reactants"] == 1 + and reaction["number_of_products"] == 2 + and mol_entries[reaction["reactants"][0]].has_covalent_ring + ): + + reactant = mol_entries[reaction["reactants"][0]] + product_1 = mol_entries[reaction["products"][0]] + product_2 = mol_entries[reaction["products"][1]] for fragment_complex in reactant.ring_fragment_data: - if (set(fragment_complex.fragment_hashes) == - set([product_1.covalent_hash, product_2.covalent_hash])): + if set(fragment_complex.fragment_hashes) == set( + [product_1.covalent_hash, product_2.covalent_hash] + ): return True - return False @@ -730,60 +1240,352 @@ def __init__(self): def __str__(self): return "single product with a ring, form two" - def __call__(self, reaction, mols, params): - if (reaction["number_of_reactants"] == 2 and - reaction["number_of_products"] == 1 and - mols[reaction["products"][0]].has_covalent_ring): - - product = mols[reaction["products"][0]] - reactant_1 = mols[reaction["reactants"][0]] - reactant_2 = mols[reaction["reactants"][1]] + def __call__(self, reaction, mol_entries, params): + if ( + reaction["number_of_reactants"] == 2 + and reaction["number_of_products"] == 1 + and mol_entries[reaction["products"][0]].has_covalent_ring + ): + + product = mol_entries[reaction["products"][0]] + reactant_1 = mol_entries[reaction["reactants"][0]] + reactant_2 = mol_entries[reaction["reactants"][1]] for fragment_complex in product.ring_fragment_data: - if (set(fragment_complex.fragment_hashes) == - set([reactant_1.covalent_hash, reactant_2.covalent_hash])): + if set(fragment_complex.fragment_hashes) == set( + [reactant_1.covalent_hash, reactant_2.covalent_hash] + ): return True - return False +class reaction_is_hindered(MSONable): + def __init__(self): + pass -default_reaction_decision_tree = [ + def __str__(self): + return "reaction is hindered" - (metal_metal_reaction(), Terminal.DISCARD), - # redox branch - (is_redox_reaction(), [ + def __call__(self, reaction, mol_entries, params): - (too_many_reactants_or_products(), Terminal.DISCARD), - (dcharge_too_large(), Terminal.DISCARD), - (reactant_and_product_not_isomorphic(), Terminal.DISCARD), - (dG_above_threshold(0.0, "free_energy", 0.0), Terminal.DISCARD), - (reaction_default_true(), Terminal.KEEP) - ]), + hot_reactant_atoms = [] + + for l in reaction["reactant_bonds_broken"]: #finds the indicies for the atoms in the broken bond + for t in l: + hot_reactant = mol_entries[reaction["reactants"][t[0]]] + hot_reactant_atoms.append(t[1]) + + hot_product_atoms = [] + + for l in reaction["product_bonds_broken"]: #finds the indicies for the atoms in the formed bond + for t in l: + hot_product = mol_entries[reaction["products"][t[0]]] + hot_product_atoms.append(t[1]) + + reaction_methyl_test = [] + reactant_num_carbon_neighbors = 0 + for atom in hot_reactant_atoms: + reactant_num_hydrogens = 0 + if hot_reactant.mol_graph.get_coordination_of_site(atom) == 4: #only care about sp3 hybidized carbons + neighbor_list = hot_reactant.mol_graph.get_connected_sites(atom) + for neighbor in neighbor_list: + neighbor_index = neighbor[2] + if hot_reactant.mol_graph.get_coordination_of_site(neighbor_index) == 4: #if neighbor is also sp3 hybridized + reactant_num_carbon_neighbors += 1 #we consider it to affect hindrance + elif hot_reactant.mol_graph.get_coordination_of_site(neighbor_index) == 1: + reactant_num_hydrogens += 1 + if reactant_num_hydrogens == 3: + reaction_methyl_test.append(atom) + + product_num_carbon_neighbors = 0 + for atom in hot_product_atoms: #repeat for products + product_num_hydrogens = 0 + if hot_product.mol_graph.get_coordination_of_site(atom) == 4: + neighbor_list = hot_product.mol_graph.get_connected_sites(atom) + for neighbor in neighbor_list: + neighbor_index = neighbor[2] + if hot_product.mol_graph.get_coordination_of_site(neighbor_index) == 4: + product_num_carbon_neighbors += 1 + elif hot_product.mol_graph.get_coordination_of_site(neighbor_index) == 1: + product_num_hydrogens += 1 + if product_num_hydrogens == 3: + reaction_methyl_test.append(atom) + + if reactant_num_carbon_neighbors >= 3 and product_num_carbon_neighbors >= 3 and len(reaction_methyl_test) < 2: #6 was chosen as the cutoff to prevent tertiary/quaternary carbons from reacting + return True - (dG_above_threshold(0.0, "solvation_free_energy", 0.0), Terminal.DISCARD), + return False +default_reaction_decision_tree = [ + (metal_metal_reaction(), Terminal.DISCARD), + # redox branch + ( + is_redox_reaction(), + [ + (too_many_reactants_or_products(), Terminal.DISCARD), + (dcharge_too_large(), Terminal.DISCARD), + (reactant_and_product_not_isomorphic(), Terminal.DISCARD), + (dG_above_threshold(0.0, "free_energy", 0.0), Terminal.DISCARD), + (reaction_default_true(), Terminal.KEEP), + ], + ), + (dG_above_threshold(0.0, "solvation_free_energy", 0.0), Terminal.DISCARD), # (single_reactant_with_ring_break_two(), Terminal.KEEP), # (single_product_with_ring_form_two(), Terminal.KEEP), - (star_count_diff_above_threshold(6), Terminal.DISCARD), - (reaction_is_covalent_decomposable(), Terminal.DISCARD), - (concerted_metal_coordination(), Terminal.DISCARD), - (concerted_metal_coordination_one_product(), Terminal.DISCARD), - (concerted_metal_coordination_one_reactant(), Terminal.DISCARD), - (metal_coordination_passthrough(), Terminal.KEEP), - - (fragment_matching_found(), [ - (single_reactant_single_product_not_atom_transfer(), Terminal.DISCARD), - (single_reactant_double_product_ring_close(), Terminal.DISCARD), - (reaction_default_true(), Terminal.KEEP)] + ( + fragment_matching_found(), + [ + (single_reactant_single_product_not_atom_transfer(), Terminal.DISCARD), + (single_reactant_double_product_ring_close(), Terminal.DISCARD), + (reaction_default_true(), Terminal.KEEP), + ], ), + (reaction_default_true(), Terminal.DISCARD), +] - (reaction_default_true(), Terminal.DISCARD) - ] +bfo_reaction_decision_tree = [ + (metal_metal_reaction(), Terminal.DISCARD), + # redox branch + (is_redox_reaction(), Terminal.DISCARD), + (dG_above_threshold(5.0, "free_energy", 0.0), Terminal.DISCARD), # look # introduce loops + (reaction_is_covalent_decomposable(), Terminal.DISCARD), # should remove A + B -> A + C + (reaction_is_separable(), Terminal.DISCARD), # should remove A + A -> B + C and any reaction separable by composition + #(single_reactant_with_ring_break_two(), Terminal.KEEP), #break2 # -> look if can remove + #(single_product_with_ring_form_two(), Terminal.KEEP), #form2 # -> look if can remove + (star_count_diff_above_threshold(8), Terminal.DISCARD), # 6 --> 8 # total: 4 distinct bonds can be broken and formed # symmetry can mess it up (similar bonds - more bonds) + # (concerted_metal_coordination(), Terminal.DISCARD), # look # when 1 fragment is single metal # does not change anything + # (concerted_metal_coordination_one_product(), Terminal.DISCARD), + # (concerted_metal_coordination_one_reactant(), Terminal.DISCARD), + (metal_coordination_passthrough(), Terminal.KEEP), + (fragment_matching_found(), Terminal.KEEP), + #( + # fragment_matching_found(), + # [ + # #(single_reactant_single_product_not_atom_transfer(), Terminal.DISCARD), # always false + # #(single_reactant_double_product_ring_close(), Terminal.DISCARD), # always false + # (reaction_default_true(), Terminal.KEEP), + # ], + #), + (reaction_default_true(), Terminal.DISCARD), +] + +bfo_logging_reaction_decision_tree = [ + (metal_metal_reaction(), Terminal.DISCARD), + # redox branch + (is_redox_reaction(), Terminal.DISCARD), + (dG_above_threshold(5.0, "free_energy", 0.0), Terminal.DISCARD), # look # introduce loops + (reaction_is_covalent_decomposable(), Terminal.DISCARD), # should remove A + B -> A + C + (reaction_is_separable(), Terminal.DISCARD), # should remove A + A -> B + C and any reaction separable by composition + #(single_reactant_with_ring_break_two(), Terminal.KEEP), #break2 # -> look if can remove + #(single_product_with_ring_form_two(), Terminal.KEEP), #form2 # -> look if can remove + (star_count_diff_above_threshold(8), Terminal.DISCARD), # 6 --> 8 # total: 4 distinct bonds can be broken and formed # symmetry can mess it up (similar bonds - more bonds) + # (concerted_metal_coordination(), Terminal.DISCARD), # look # when 1 fragment is single metal # does not change anything + # (concerted_metal_coordination_one_product(), Terminal.DISCARD), + # (concerted_metal_coordination_one_reactant(), Terminal.DISCARD), + (metal_coordination_passthrough(), Terminal.DISCARD), + (fragment_matching_found(), Terminal.DISCARD), + #( + # fragment_matching_found(), + # [ + # #(single_reactant_single_product_not_atom_transfer(), Terminal.DISCARD), # always false + # #(single_reactant_double_product_ring_close(), Terminal.DISCARD), # always false + # (reaction_default_true(), Terminal.KEEP), + # ], + #), + (reaction_default_true(), Terminal.KEEP), +] + + +co2_reaction_decision_tree = [ + ( + is_redox_reaction(), + [ + (too_many_reactants_or_products(), Terminal.DISCARD), + (dcharge_too_large(), Terminal.DISCARD), + (reactant_and_product_not_isomorphic(), Terminal.DISCARD), + (dG_above_threshold(0.0, "free_energy", 0.0), Terminal.DISCARD), + (reaction_default_true(), Terminal.KEEP), + ], + ), + (dG_above_threshold(0.0, "free_energy", 0.0), Terminal.DISCARD), + (star_count_diff_above_threshold(6), Terminal.DISCARD), + (reaction_is_covalent_decomposable(), Terminal.DISCARD), + ( + fragment_matching_found(), + [ + (single_reactant_single_product_not_atom_transfer(), Terminal.DISCARD), + (single_reactant_double_product_ring_close(), Terminal.DISCARD), + (reaction_default_true(), Terminal.KEEP), + ], + ), + (reaction_default_true(), Terminal.DISCARD), +] + + +euvl_phase1_reaction_decision_tree = [ + ( + is_redox_reaction(), + [ + (too_many_reactants_or_products(), Terminal.DISCARD), + (dcharge_too_large(), Terminal.DISCARD), + (reactant_and_product_not_isomorphic(), Terminal.DISCARD), + (add_electron_species(), Terminal.DISCARD), + (dG_above_threshold(-float("inf"), "free_energy", 0.0), Terminal.KEEP), + (reaction_default_true(), Terminal.DISCARD), + ], + ), + (dG_below_threshold(0.0, "free_energy", 0.0), Terminal.DISCARD), + ( + more_than_one_reactant(), + [ + (only_one_product(), Terminal.DISCARD), + (reactants_are_both_anions_or_both_cations(), Terminal.DISCARD), + (two_closed_shell_reactants_and_two_open_shell_products(), Terminal.DISCARD), + (reaction_is_charge_separation(), Terminal.DISCARD), + (reaction_is_covalent_charge_decomposable(), Terminal.DISCARD), + (reaction_is_coupled_electron_fragment_transfer(), Terminal.DISCARD), + (star_count_diff_above_threshold(6), Terminal.DISCARD), + (compositions_preclude_h_transfer(), Terminal.DISCARD), + ( + fragment_matching_found(), + [ + (not_h_transfer(), Terminal.DISCARD), + (h_abstraction_from_closed_shell_reactant(), Terminal.DISCARD), + (h_minus_abstraction(), Terminal.DISCARD), + (dG_above_threshold(0.0, "free_energy", 0.0, 0.1), Terminal.KEEP), + (reaction_default_true(), Terminal.DISCARD), + ], + ), + (reaction_default_true(), Terminal.DISCARD), + ], + ), + (single_reactant_single_product(), Terminal.DISCARD), + (star_count_diff_above_threshold(4), Terminal.DISCARD), + (reaction_is_radical_separation(), Terminal.DISCARD), + (reaction_is_charge_separation(), Terminal.DISCARD), + ( + fragment_matching_found(), + [ + (single_reactant_double_product_ring_close(), Terminal.DISCARD), + (dG_above_threshold(0.0, "free_energy", 0.0), Terminal.KEEP), + (reaction_default_true(), Terminal.DISCARD), + ], + ), + + (reaction_default_true(), Terminal.DISCARD), +] + + +euvl_phase1_reaction_logging_tree = [ + ( + is_redox_reaction(), + [ + (too_many_reactants_or_products(), Terminal.DISCARD), + (dcharge_too_large(), Terminal.DISCARD), + (reactant_and_product_not_isomorphic(), Terminal.DISCARD), + (add_electron_species(), Terminal.DISCARD), + (dG_above_threshold(-float("inf"), "free_energy", 0.0), Terminal.DISCARD), + (reaction_default_true(), Terminal.DISCARD), + ], + ), + (dG_below_threshold(0.0, "free_energy", 0.0), Terminal.DISCARD), + ( + more_than_one_reactant(), + [ + (only_one_product(), Terminal.DISCARD), + (reactants_are_both_anions_or_both_cations(), Terminal.DISCARD), + (two_closed_shell_reactants_and_two_open_shell_products(), Terminal.DISCARD), + (reaction_is_charge_separation(), Terminal.DISCARD), + (reaction_is_covalent_charge_decomposable(), Terminal.DISCARD), + (reaction_is_coupled_electron_fragment_transfer(), Terminal.DISCARD), + (star_count_diff_above_threshold(6), Terminal.DISCARD), + (compositions_preclude_h_transfer(), Terminal.DISCARD), + ( + fragment_matching_found(), + [ + (not_h_transfer(), Terminal.DISCARD), + (h_abstraction_from_closed_shell_reactant(), Terminal.DISCARD), + (h_minus_abstraction(), Terminal.DISCARD), + (dG_above_threshold(0.0, "free_energy", 0.0, 0.1), Terminal.DISCARD), + (reaction_default_true(), Terminal.DISCARD), + ], + ), + (reaction_default_true(), Terminal.DISCARD), + ], + ), + (single_reactant_single_product(), Terminal.DISCARD), + (star_count_diff_above_threshold(4), Terminal.DISCARD), + (reaction_is_radical_separation(), Terminal.DISCARD), + (reaction_is_charge_separation(), Terminal.DISCARD), + ( + fragment_matching_found(), + [ + (single_reactant_double_product_ring_close(), Terminal.DISCARD), + (dG_above_threshold(0.0, "free_energy", 0.0), Terminal.DISCARD), + (reaction_default_true(), Terminal.DISCARD), + ], + ), + + (reaction_default_true(), Terminal.DISCARD), +] + +euvl_phase2_reaction_decision_tree = [ + (is_redox_reaction(), Terminal.DISCARD), + (dG_above_threshold(0.0, "free_energy", 0.0), Terminal.DISCARD), + (reactants_are_both_anions_or_both_cations(), Terminal.DISCARD), + (reaction_is_charge_transfer(), Terminal.KEEP), + (reaction_is_covalent_charge_decomposable(), Terminal.DISCARD), + (reaction_is_coupled_electron_fragment_transfer(), Terminal.DISCARD), + (star_count_diff_above_threshold(6), Terminal.DISCARD), + ( + fragment_matching_found(), + [ + (single_reactant_single_product_not_atom_transfer(), Terminal.DISCARD), + (single_reactant_double_product_ring_close(), Terminal.DISCARD), + (reaction_is_hindered(), Terminal.DISCARD), + ( + reaction_is_covalent_decomposable(), + [ + (fragments_are_not_2A_B(), Terminal.DISCARD), + (reaction_default_true(), Terminal.KEEP), + ], + ), + (reaction_default_true(), Terminal.KEEP), + ], + ), + (reaction_default_true(), Terminal.DISCARD), +] + +euvl_phase2_logging_tree = [ + (is_redox_reaction(), Terminal.DISCARD), + (dG_above_threshold(0.0, "free_energy", 0.0), Terminal.DISCARD), + (reactants_are_both_anions_or_both_cations(), Terminal.DISCARD), + (reaction_is_charge_transfer(), Terminal.DISCARD), + (reaction_is_covalent_charge_decomposable(), Terminal.DISCARD), + (reaction_is_coupled_electron_fragment_transfer(), Terminal.DISCARD), + (star_count_diff_above_threshold(6), Terminal.DISCARD), + ( + fragment_matching_found(), + [ + (single_reactant_single_product_not_atom_transfer(), Terminal.DISCARD), + (single_reactant_double_product_ring_close(), Terminal.DISCARD), + (reaction_is_hindered(), Terminal.DISCARD), + ( + reaction_is_covalent_decomposable(), + [ + (fragments_are_not_2A_B(), Terminal.DISCARD), + (reaction_default_true(), Terminal.KEEP), + ], + ), + (reaction_default_true(), Terminal.DISCARD), + ], + ), + (reaction_default_true(), Terminal.DISCARD), +] \ No newline at end of file diff --git a/HiPRGen/report_generator.py b/HiPRGen/report_generator.py index b55b8cb..66fedf5 100644 --- a/HiPRGen/report_generator.py +++ b/HiPRGen/report_generator.py @@ -6,7 +6,7 @@ atom_colors = { "H": "gray", "C": "black", - "Li": "purple", + "Bi": "purple", "B": "orange", "N": "blue", "O": "red", @@ -14,9 +14,13 @@ "Mg": "green", "P": "darkorange", "S": "yellow", - "Cl": "chartreuse" + "Cl": "chartreuse", + "E": "pink", + "Br": "darkred", + "I": "purple4", } + def visualize_molecule_entry(molecule_entry, path): """ visualize a molecule using graphviz and @@ -25,20 +29,20 @@ def visualize_molecule_entry(molecule_entry, path): graph = deepcopy(molecule_entry.graph) - nx.set_node_attributes(graph, "filled", "style") nx.set_node_attributes(graph, "circle", "shape") - nx.set_node_attributes(graph, "0.2", "width") + if molecule_entry.species[0] == "E": + nx.set_node_attributes(graph, "0.5", "width") + else: + nx.set_node_attributes(graph, "0.2", "width") nx.set_node_attributes(graph, "8.0", "fontsize") nx.set_node_attributes(graph, "white", "fontcolor") nx.set_node_attributes(graph, "true", "fixedsize") - nx.set_node_attributes( graph, - dict(enumerate([atom_colors[a] - for a in molecule_entry.species])), - "color" + dict(enumerate([atom_colors[a] for a in molecule_entry.species])), + "color", ) charge = molecule_entry.charge @@ -61,33 +65,28 @@ def visualize_molecules(mol_entries, folder): folder.mkdir() for index, molecule_entry in enumerate(mol_entries): - visualize_molecule_entry( - molecule_entry, - folder.joinpath(str(index) + ".pdf")) - + visualize_molecule_entry(molecule_entry, folder.joinpath(str(index) + ".pdf")) class ReportGenerator: - def __init__( - self, - mol_entries, - report_file_path, - mol_pictures_folder_name='mol_pictures', - rebuild_mol_pictures=True + self, + mol_entries, + report_file_path, + mol_pictures_folder_name="mol_pictures", + rebuild_mol_pictures=True, ): self.report_file_path = Path(report_file_path) self.mol_pictures_folder_name = mol_pictures_folder_name self.mol_pictures_folder = self.report_file_path.parent.joinpath( - mol_pictures_folder_name) - + mol_pictures_folder_name + ) if rebuild_mol_pictures: visualize_molecules(mol_entries, self.mol_pictures_folder) self.mol_entries = mol_entries - self.f = self.report_file_path.open(mode='w') - + self.f = self.report_file_path.open(mode="w") # write in header self.f.write("\\documentclass{article}\n") @@ -108,27 +107,27 @@ def emit_molecule(self, species_index, include_index=True): self.f.write( "\\raisebox{-.5\\height}{" - + "\\includegraphics[scale=0.2]{" - + self.mol_pictures_folder_name + '/' + + "\\includegraphics[scale=0.15]{" + + self.mol_pictures_folder_name + + "/" + str(species_index) + ".pdf}}\n" ) def emit_newline(self): - self.f.write( - "\n\\vspace{1cm}\n") + self.f.write("\n\\vspace{1cm}\n") def emit_newpage(self): self.f.write("\\newpage\n\n\n") def emit_verbatim(self, s): - self.f.write('\\begin{verbatim}\n') + self.f.write("\\begin{verbatim}\n") self.f.write(s) - self.f.write('\n') - self.f.write('\\end{verbatim}\n') + self.f.write("\n") + self.f.write("\\end{verbatim}\n") - def emit_text(self,s): - self.f.write('\n\n' + s + '\n\n') + def emit_text(self, s): + self.f.write("\n\n" + s + "\n\n") def emit_initial_state(self, initial_state): self.emit_text("initial state:") @@ -139,13 +138,10 @@ def emit_initial_state(self, initial_state): self.emit_molecule(species_id) self.emit_newline() - def emit_reaction(self, reaction, label=None): - reactants_filtered = [i for i in reaction['reactants'] - if i != -1] + reactants_filtered = [i for i in reaction["reactants"] if i != -1] - products_filtered = [i for i in reaction['products'] - if i != -1] + products_filtered = [i for i in reaction["products"] if i != -1] self.f.write("$$\n") if label is not None: @@ -161,15 +157,16 @@ def emit_reaction(self, reaction, label=None): self.emit_molecule(reactant_index) - if 'dG' in reaction: + if "dG" in reaction: self.f.write( "\\xrightarrow[" - + ("%.2f" % reaction["dG_barrier"]) + - "]{" + - ("%.2f" % reaction["dG"]) + "}\n") + + ("%.2f" % reaction["dG_barrier"]) + + "]{" + + ("%.2f" % reaction["dG"]) + + "}\n" + ) else: - self.f.write( - "\\xrightarrow{}\n") + self.f.write("\\xrightarrow{}\n") first = True for product_index in products_filtered: @@ -184,14 +181,14 @@ def emit_reaction(self, reaction, label=None): self.f.write("\n\n\n") def emit_bond_breakage(self, reaction): - if 'reactant_bonds_broken' in reaction: + if "reactant_bonds_broken" in reaction: self.f.write("reactant bonds broken:") - for bond in reaction['reactant_bonds_broken']: + for bond in reaction["reactant_bonds_broken"]: self.emit_verbatim(str(bond)) - if 'product_bonds_broken' in reaction: + if "product_bonds_broken" in reaction: self.f.write("product bonds broken:") - for bond in reaction['product_bonds_broken']: + for bond in reaction["product_bonds_broken"]: self.emit_verbatim(str(bond)) self.f.write("\n\n\n") diff --git a/HiPRGen/species_filter.py b/HiPRGen/species_filter.py index 14b4563..32b1618 100644 --- a/HiPRGen/species_filter.py +++ b/HiPRGen/species_filter.py @@ -10,6 +10,11 @@ from networkx.algorithms.graph_hashing import weisfeiler_lehman_graph_hash import networkx.algorithms.isomorphism as iso from HiPRGen.report_generator import ReportGenerator +from pymatgen.core.periodic_table import DummySpecies +from pymatgen.core.sites import Site +from pymatgen.core.structure import Molecule +from pymatgen.analysis.graphs import MoleculeGraph + """ Phase 1: species filtering input: a list of dataset entries @@ -21,6 +26,7 @@ The input dataset entries will often contain isomorphic molecules. Identifying such isomorphisms doesn't fit into the species decision tree, so we have it as a preprocessing phase. """ + def sort_into_tags(mols): isomorphism_buckets = {} for mol in mols: @@ -44,11 +50,10 @@ def really_covalent_isomorphic(mol1, mol2): return nx.is_isomorphic( mol1.covalent_graph, mol2.covalent_graph, - node_match = iso.categorical_node_match('specie', None) + node_match=iso.categorical_node_match("specie", None), ) - def groupby(equivalence_relation, xs): """ warning: this has slightly different semantics than @@ -71,19 +76,17 @@ def groupby(equivalence_relation, xs): def log_message(string): - print( - '[' + strftime('%H:%M:%S', localtime()) + ']', - string) + print("[" + strftime("%H:%M:%S", localtime()) + "]", string) def species_filter( - dataset_entries, - mol_entries_pickle_location, - species_report, - species_decision_tree, - coordimer_weight, - species_logging_decision_tree=Terminal.DISCARD, - generate_unfiltered_mol_pictures=False + dataset_entries, + mol_entries_pickle_location, + species_report, + species_decision_tree, + coordimer_weight, + species_logging_decision_tree=Terminal.DISCARD, + generate_unfiltered_mol_pictures=False, ): """ @@ -94,17 +97,26 @@ def species_filter( log_message("starting species filter") log_message("loading molecule entries from json") - mol_entries_unfiltered = [ - MoleculeEntry.from_dataset_entry(e) for e in dataset_entries ] - - + if "label" in dataset_entries[0].keys(): + mol_entries_unfiltered = [MoleculeEntry.from_quacc_entry(e) for e in dataset_entries] + log_message("Quacc entries passed") + elif "has_props" in dataset_entries[0].keys(): + mol_entries_unfiltered = [MoleculeEntry.from_mp_doc(e) for e in dataset_entries] + log_message("MP doc entries passed") + else: + log_message("dataset entries passed") + mol_entries_unfiltered = [ + MoleculeEntry.from_dataset_entry(e) for e in dataset_entries + ] + + log_message("found " + str(len(mol_entries_unfiltered)) + " molecule entries") log_message("generating unfiltered mol pictures") report_generator = ReportGenerator( mol_entries_unfiltered, species_report, - mol_pictures_folder_name='mol_pictures_unfiltered', - rebuild_mol_pictures=generate_unfiltered_mol_pictures + mol_pictures_folder_name="mol_pictures_unfiltered", + rebuild_mol_pictures=generate_unfiltered_mol_pictures, ) report_generator.emit_text("species report") @@ -125,31 +137,30 @@ def species_filter( if run_decision_tree(mol, species_logging_decision_tree): report_generator.emit_verbatim( - '\n'.join([str(f) for f in decision_pathway])) + "\n".join([str(f) for f in decision_pathway]) + ) report_generator.emit_text("number: " + str(i)) report_generator.emit_text("entry id: " + mol.entry_id) - report_generator.emit_text("uncorrected free energy: " + - str(mol.free_energy)) - report_generator.emit_text( - "number of coordination bonds: " + - str(mol.number_of_coordination_bonds)) + "uncorrected free energy: " + str(mol.free_energy) + ) - report_generator.emit_text( - "corrected free energy: " + - str(mol.solvation_free_energy)) + # report_generator.emit_text( + # "number of coordination bonds: " + str(mol.number_of_coordination_bonds) + # ) - report_generator.emit_text( - "formula: " + mol.formula) + # report_generator.emit_text( + # "corrected free energy: " + str(mol.solvation_free_energy) + # ) + + report_generator.emit_text("formula: " + mol.formula) report_generator.emit_molecule(i, include_index=False) report_generator.emit_newline() - report_generator.finished() - # python doesn't have shared memory. That means that every worker during # reaction filtering must maintain its own copy of the molecules. # for this reason, it is good to remove attributes that are only used @@ -165,36 +176,60 @@ def species_filter( # currently, take lowest energy mol in each iso class log_message("applying non local filters") - def collapse_isomorphism_group(g): - lowest_energy_coordimer = min(g,key=coordimer_weight) + lowest_energy_coordimer = min(g, key=coordimer_weight) return lowest_energy_coordimer - mol_entries = [] for tag_group in sort_into_tags(mol_entries_filtered).values(): for iso_group in groupby(really_covalent_isomorphic, tag_group): - mol_entries.append( - collapse_isomorphism_group(iso_group)) - + mol_entries.append(collapse_isomorphism_group(iso_group)) log_message("assigning indices") for i, e in enumerate(mol_entries): e.ind = i - log_message("creating molecule entry pickle") # ideally we would serialize mol_entries to a json # some of the auxilary_data we compute # has frozen set keys, so doesn't seralize well into json format. # pickles work better in this setting - with open(mol_entries_pickle_location, 'wb') as f: + with open(mol_entries_pickle_location, "wb") as f: pickle.dump(mol_entries, f) - log_message("species filtering finished. " + - str(len(mol_entries)) + - " species") + log_message("species filtering finished. " + str(len(mol_entries)) + " species") + + return mol_entries + +def add_electron_species( + mol_entries, mol_entries_pickle_location, electron_free_energy +): + e_site = Site( + DummySpecies("E", oxidation_state=None, properties=None), [0.0, 0.0, 0.0] + ) + e_mol = Molecule.from_sites([e_site]) + e_mol.set_charge_and_spin(-1, 2) + e_graph = MoleculeGraph.with_empty_graph(molecule=e_mol) + electron_entry = MoleculeEntry( + molecule=e_mol, + energy=electron_free_energy, + enthalpy=0, + entropy=0, + entry_id=None, + mol_graph=e_graph, + partial_charges_resp=None, + partial_charges_mulliken=None, + partial_charges_nbo=None, + electron_affinity=None, + ionization_energy=None, + spin_multiplicity=None, + partial_spins_nbo=None, + ) + electron_entry.ind = len(mol_entries) + mol_entries.append(electron_entry) + with open(mol_entries_pickle_location, "wb") as f: + pickle.dump(mol_entries, f) return mol_entries diff --git a/HiPRGen/species_questions.py b/HiPRGen/species_questions.py index 462313a..ba62679 100644 --- a/HiPRGen/species_questions.py +++ b/HiPRGen/species_questions.py @@ -7,6 +7,7 @@ import numpy as np from monty.json import MSONable from itertools import combinations +from collections import Counter """ species decision tree: @@ -28,9 +29,8 @@ class Terminal(Enum): Once a Terminal node is reached, it tells us whether to keep or discard the species. """ -def run_decision_tree(mol_entry, - decision_tree, - decision_pathway=None): + +def run_decision_tree(mol_entry, decision_tree, decision_pathway=None): node = decision_tree @@ -45,18 +45,15 @@ def run_decision_tree(mol_entry, if decision_pathway is not None: decision_pathway.append(question) - next_node = new_node break node = next_node - if type(node) == Terminal: if decision_pathway is not None: decision_pathway.append(node) - if node == Terminal.KEEP: return True else: @@ -68,6 +65,7 @@ def run_decision_tree(mol_entry, class metal_ion_filter(MSONable): "only allow positively charged metal ions" + def __init__(self): pass @@ -77,6 +75,7 @@ def __call__(self, mol_entry): else: return False + class mol_not_connected(MSONable): def __init__(self): pass @@ -84,12 +83,13 @@ def __init__(self): def __call__(self, mol): return not nx.is_connected(mol.graph) + class spin_multiplicity_filter(MSONable): def __init__(self, threshold): self.threshold = threshold def __call__(self, mol): - if (mol.spin_multiplicity == 2): + if mol.spin_multiplicity == 2: num_partial_spins_above_threshold = 0 for i in range(mol.num_atoms): if mol.partial_spins_nbo[i] > self.threshold: @@ -100,6 +100,7 @@ def __call__(self, mol): return False + class positive_penalty(MSONable): def __init__(self): pass @@ -110,81 +111,130 @@ def __call__(self, mol): else: return False + class add_star_hashes(MSONable): def __init__(self): pass def __call__(self, mol): - for i in range(mol.num_atoms): - if i not in mol.m_inds: - neighborhood = nx.generators.ego.ego_graph( - mol.covalent_graph, - i, - 1, - undirected=True) - - mol.star_hashes[i] = weisfeiler_lehman_graph_hash( - neighborhood, - node_attr='specie') + for i in range(mol.num_atoms): #iterates over all atoms in a molecule + if i not in mol.m_inds: #ignoring metal atoms + neighborhood = nx.generators.ego.ego_graph( #generates an ego graph named neighborhood, with atom i at the + mol.covalent_graph, i, 1, undirected=True #center, with the nodes of the graph being the atoms i is + ) #covalently bonded to + + mol.star_hashes[i] = weisfeiler_lehman_graph_hash( #star_hashes is a dictionary, and this adds an entry to it + neighborhood, node_attr="specie" #with the atom index, i, as the key and a graph_hash (string) + ) #as the value return False -class add_unbroken_fragment(MSONable): + +class add_unbroken_fragment(MSONable): #aka adds unfragmented molecule as a "fragment complex" def __init__(self): pass def __call__(self, mol): if mol.formula in m_formulas: return False - - fragment_complex = FragmentComplex( - 1, - 0, - [], - [mol.covalent_hash]) + fragment_complex = FragmentComplex(1, 0, [], [mol.covalent_hash]) mol.fragment_data.append(fragment_complex) return False -class add_single_bond_fragments(MSONable): - def __init__(self): - pass +class add_single_bond_fragments(MSONable): #called for all species that have passed through filtration + def __init__(self, allow_ring_opening=True): + self.allow_ring_opening = allow_ring_opening def __call__(self, mol): if mol.formula in m_formulas: return False - - - for edge in mol.covalent_graph.edges: - fragments = [] + for edge in mol.covalent_graph.edges: #iterates through each bond in a molecule graph by iterating through a list of tuples + fragment_hashes = [] h = copy.deepcopy(mol.covalent_graph) - h.remove_edge(*edge) - connected_components = nx.algorithms.components.connected_components(h) + h.remove_edge(*edge) #"breaks a bond" in the molecule graph + connected_components = nx.algorithms.components.connected_components(h) #generates a set of nodes for each "fragment" for c in connected_components: - subgraph = h.subgraph(c) + subgraph = h.subgraph(c) #generates a subgraph from one set of nodes (this is a fragment graph) + + fragment_hash = weisfeiler_lehman_graph_hash( #saves the hash of this graph + subgraph, node_attr="specie" + ) + + fragment_hashes.append(fragment_hash) #adds each fragment hash to the fragment hash list + + equivalent_fragments_already_found = False + for fragment_complex in mol.fragment_data: + if len(fragment_hashes) == len(fragment_complex.fragment_hashes): + if set(fragment_hashes) == set(fragment_complex.fragment_hashes): + equivalent_fragments_already_found = True + + if not equivalent_fragments_already_found: + + if len(fragment_hashes) == 1 and not self.allow_ring_opening: + pass + else: + + fragment_complex = FragmentComplex( #saves a FragmentComplex object after both fragment_hashes have been + len(fragment_hashes), 1, [edge[0:2]], fragment_hashes #added to the list of fragments with len(fragments) fragments, 1 bond broken, the identity + ) #of the bond broken (as a list containing one tuple), and the list of fragment hashes + + mol.fragment_data.append(fragment_complex) #append the above FragmentComplex object to the molecule's fragment_data list + + return False + + +class add_two_bond_fragments(MSONable): + def __init__(self, allow_ring_opening=True): + self.allow_ring_opening = allow_ring_opening + + def __call__(self, mol): + + if mol.formula in m_formulas: + return False + + for edge1 in mol.covalent_graph.edges: + for edge2 in mol.covalent_graph.edges: + if edge1 != edge2: # not breaking the same bond twice and the two bonds are not connected # A B and B C - check if it is in intersection - fragment_hash = weisfeiler_lehman_graph_hash( - subgraph, - node_attr='specie') + fragment_hashes = [] + h = copy.deepcopy(mol.covalent_graph) + h.remove_edge(*edge1) + h.remove_edge(*edge2) + connected_components = nx.algorithms.components.connected_components(h) - fragments.append(fragment_hash) + for c in connected_components: + subgraph = h.subgraph(c) + fragment_hash = weisfeiler_lehman_graph_hash(subgraph, node_attr="specie") + fragment_hashes.append(fragment_hash) # can have 1, 2, or 3 fragments, allow all - fragment_complex = FragmentComplex( - len(fragments), - 1, - [edge[0:2]], - fragments) + equivalent_fragments_already_found = False + for fragment_complex in mol.fragment_data: + if len(fragment_hashes) == len(fragment_complex.fragment_hashes): + #if set(fragment_hashes) == set(fragment_complex.fragment_hashes): # A A B same set as A B B - fix + if dict(Counter(fragment_hashes)) == dict(Counter(fragment_complex.fragment_hashes)): # fix dict: key = hash, value = number , compare them + equivalent_fragments_already_found = True - mol.fragment_data.append(fragment_complex) + if not equivalent_fragments_already_found: + + if len(fragment_hashes) != 3 and not self.allow_ring_opening: # 2 bonds could lead to 1, 2, or 3 fragments + pass + else: + + fragment_complex = FragmentComplex( + len(fragment_hashes), 2, [edge1[0:2], edge2[0:2]], fragment_hashes # we've broken 2 bonds # edge[0:2], should have 2 frag hashes + ) + mol.fragment_data.append(fragment_complex) return False + class has_covalent_ring(MSONable): def __init__(self): pass @@ -215,21 +265,22 @@ def __call__(self, mol): h.remove_edge(*edge) if nx.is_connected(h): ring_edges[edge] = { - 'modified_graph' : h, - 'node_set' : set([edge[0],edge[1]]) + "modified_graph": h, + "node_set": set([edge[0], edge[1]]), } + for ring_edge_1, ring_edge_2 in combinations(ring_edges, 2): - for ring_edge_1, ring_edge_2 in combinations(ring_edges,2): - - if ring_edges[ring_edge_1]['node_set'].isdisjoint( - ring_edges[ring_edge_2]['node_set']): + if ring_edges[ring_edge_1]["node_set"].isdisjoint( + ring_edges[ring_edge_2]["node_set"] + ): - - potential_edges = [ (ring_edge_1[0], ring_edge_2[0],0), - (ring_edge_1[0], ring_edge_2[1],0), - (ring_edge_1[1], ring_edge_2[0],0), - (ring_edge_1[1], ring_edge_2[1],0) ] + potential_edges = [ + (ring_edge_1[0], ring_edge_2[0], 0), + (ring_edge_1[0], ring_edge_2[1], 0), + (ring_edge_1[1], ring_edge_2[0], 0), + (ring_edge_1[1], ring_edge_2[1], 0), + ] one_bond_away = False for ring_edge_3 in ring_edges: @@ -237,21 +288,22 @@ def __call__(self, mol): one_bond_away = True if one_bond_away: - h = copy.deepcopy(ring_edges[ring_edge_1]['modified_graph']) + h = copy.deepcopy(ring_edges[ring_edge_1]["modified_graph"]) h.remove_edge(*ring_edge_2) if nx.is_connected(h): continue else: fragments = [] - connected_components = nx.algorithms.components.connected_components(h) + connected_components = ( + nx.algorithms.components.connected_components(h) + ) for c in connected_components: subgraph = h.subgraph(c) fragment_hash = weisfeiler_lehman_graph_hash( - subgraph, - node_attr='specie') - + subgraph, node_attr="specie" + ) fragments.append(fragment_hash) @@ -259,7 +311,8 @@ def __call__(self, mol): len(fragments), 2, [ring_edge_1[0:2], ring_edge_2[0:2]], - fragments) + fragments, + ) mol.ring_fragment_data.append(fragment_complex) @@ -278,6 +331,24 @@ def __call__(self, mol): return not nx.is_connected(mol.covalent_graph) +class h_atom_filter(MSONable): + def __init__(self): + pass + + def __call__(self, mol): + # if mol is H+, H0, or H- + return mol.formula == "H1" + + +class oh_plus_filter(MSONable): + def __init__(self): + pass + + def __call__(self, mol): + # if mol is OH+ + return mol.formula == "H1 O1" and mol.charge == 1 + + class fix_hydrogen_bonding(MSONable): def __init__(self): pass @@ -285,7 +356,7 @@ def __init__(self): def __call__(self, mol): if mol.num_atoms > 1: for i in range(mol.num_atoms): - if mol.species[i] == 'H': + if mol.species[i] == "H": adjacent_atoms = [] @@ -297,14 +368,15 @@ def __call__(self, mol): else: adjacent_atom = bond[0] - displacement = (mol.atom_locations[adjacent_atom] - - mol.atom_locations[i]) + displacement = ( + mol.atom_locations[adjacent_atom] + - mol.atom_locations[i] + ) dist = np.inner(displacement, displacement) adjacent_atoms.append((adjacent_atom, dist)) - closest_atom, _ = min(adjacent_atoms, key=lambda pair: pair[1]) for adjacent_atom, _ in adjacent_atoms: @@ -313,8 +385,6 @@ def __call__(self, mol): if adjacent_atom in mol.covalent_graph: mol.covalent_graph.remove_edge(i, adjacent_atom) - - return False @@ -326,15 +396,17 @@ def __call__(self, mol): if mol.formula not in m_formulas: - if (len(metals.intersection(set(mol.species))) > 0 and - mol.number_of_coordination_bonds == 0): + if ( + len(metals.intersection(set(mol.species))) > 0 + and mol.number_of_coordination_bonds == 0 + ): return True return False -class set_solvation_free_energy(MSONable): +class set_solvation_correction(MSONable): """ metal atoms coordinate with the surrounding solvent. We need to correct free energy to take this into account. The correction is @@ -369,27 +441,26 @@ def __call__(self, mol): for j in range(mol.num_atoms): if j != i: - displacement_vector = ( - mol.atom_locations[j] - - mol.atom_locations[i]) - if (np.inner(displacement_vector, displacement_vector) - < radius ** 2 and ( - mol.partial_charges_resp[j] < 0 or - mol.partial_charges_mulliken[j] < 0 or - mol.partial_charges_nbo[j] < 0)): - if not mol.graph.has_edge(i,j): - mol.graph.add_edge(i,j) + displacement_vector = mol.atom_locations[j] - mol.atom_locations[i] + if np.inner( + displacement_vector, displacement_vector + ) < radius**2 and ( + mol.partial_charges_resp[j] < 0 + or mol.partial_charges_mulliken[j] < 0 + or mol.partial_charges_nbo[j] < 0 + ): + if not mol.graph.has_edge(i, j): + mol.graph.add_edge(i, j) coordination_partners.append(j) number_of_coordination_bonds = len(coordination_partners) mol.number_of_coordination_bonds += number_of_coordination_bonds - correction += self.solvation_env[ - "solvation_correction"][species_charge] * ( - self.solvation_env[ - "max_number_of_coordination_bonds"][species_charge] - - number_of_coordination_bonds) + correction += self.solvation_env["solvation_correction"][species_charge] * ( + self.solvation_env["max_number_of_coordination_bonds"][species_charge] + - number_of_coordination_bonds + ) - mol.solvation_free_energy = correction + mol.free_energy + mol.solvation_correction = correction return False @@ -402,13 +473,11 @@ def __call__(self, mol): def compute_graph_hashes(mol): - mol.total_hash = weisfeiler_lehman_graph_hash( - mol.graph, - node_attr='specie') + mol.total_hash = weisfeiler_lehman_graph_hash(mol.graph, node_attr="specie") mol.covalent_hash = weisfeiler_lehman_graph_hash( - mol.covalent_graph, - node_attr='specie') + mol.covalent_graph, node_attr="specie" + ) return False @@ -420,12 +489,12 @@ def __init__(self, cutoff): def __call__(self, mol): for i in mol.m_inds: - if (mol.species[i] in metals and - mol.partial_charges_nbo[i] < self.cutoff): + if mol.species[i] in metals and mol.partial_charges_nbo[i] < self.cutoff: return True return False + class charge_too_big(MSONable): def __init__(self): pass @@ -437,12 +506,13 @@ def __call__(self, mol): else: return False + # any species filter which modifies bonding has to come before # any filter checking for connectivity (which includes the metal-centric complex filter) li_species_decision_tree = [ (fix_hydrogen_bonding(), Terminal.KEEP), - (set_solvation_free_energy(li_ec), Terminal.KEEP), + (set_solvation_correction(li_ec), Terminal.KEEP), (charge_too_big(), Terminal.DISCARD), (neutral_metal_filter(0.1), Terminal.DISCARD), (compute_graph_hashes, Terminal.KEEP), @@ -458,12 +528,12 @@ def __call__(self, mol): # (covalent_ring_fragments(), Terminal.KEEP), # (species_default_true(), Terminal.KEEP) # ]), - (species_default_true(), Terminal.KEEP) - ] + (species_default_true(), Terminal.KEEP), +] mg_species_decision_tree = [ (fix_hydrogen_bonding(), Terminal.KEEP), - (set_solvation_free_energy(mg_g2), Terminal.KEEP), + (set_solvation_correction(mg_g2), Terminal.KEEP), (neutral_metal_filter(0.5), Terminal.DISCARD), (compute_graph_hashes, Terminal.KEEP), (metal_ion_filter(), Terminal.DISCARD), @@ -473,6 +543,40 @@ def __call__(self, mol): (add_star_hashes(), Terminal.KEEP), (add_unbroken_fragment(), Terminal.KEEP), (add_single_bond_fragments(), Terminal.KEEP), - (species_default_true(), Terminal.KEEP) - ] + (species_default_true(), Terminal.KEEP), +] + +nonmetal_species_decision_tree = [ + (fix_hydrogen_bonding(), Terminal.KEEP), + (compute_graph_hashes, Terminal.KEEP), + (add_star_hashes(), Terminal.KEEP), + (add_unbroken_fragment(), Terminal.KEEP), + (add_single_bond_fragments(allow_ring_opening=False), Terminal.KEEP), + (species_default_true(), Terminal.KEEP), +] + +euvl_species_decision_tree = [ + (fix_hydrogen_bonding(), Terminal.KEEP), + (h_atom_filter(), Terminal.DISCARD), + (oh_plus_filter(), Terminal.DISCARD), + (compute_graph_hashes, Terminal.KEEP), + (add_star_hashes(), Terminal.KEEP), + (add_unbroken_fragment(), Terminal.KEEP), + (add_single_bond_fragments(allow_ring_opening=False), Terminal.KEEP), + (species_default_true(), Terminal.KEEP), +] + +bfo_species_decision_tree = [ + (compute_graph_hashes, Terminal.KEEP), # added covalent hashes + (add_star_hashes(), Terminal.KEEP), + (add_unbroken_fragment(), Terminal.KEEP), + (add_single_bond_fragments(allow_ring_opening=True), Terminal.KEEP), + (add_two_bond_fragments(allow_ring_opening=True), Terminal.KEEP), + #(has_covalent_ring(), [ + # (covalent_ring_fragments(), Terminal.KEEP), # covered with 2 bond fragments + # (species_default_true(), Terminal.KEEP) + #]), + (species_default_true(), Terminal.KEEP), + +] \ No newline at end of file diff --git a/HiPRGen/test_species.txt b/HiPRGen/test_species.txt new file mode 100644 index 0000000..22b431e --- /dev/null +++ b/HiPRGen/test_species.txt @@ -0,0 +1,45 @@ +PHS neutral-1d64d1a96b5db50b9fdf583dc18f90cf-C10H14O1-0-1 +tBA-0aade5ee5263fd1ad77490688fb37d0e-C10H20O2-0-1 +TPS-94be97269b03e361ba1b344f48f19e44-C18H15S1-1-1 +HONF-31c2af8f1605817c400250991fe7fefe-C4F9H1O3S1-0-1 +TPS CS fragment-bc3641376a32020a0345549009577712-C12H10S1-0-1 +tBaH+-2c137c7f62959d051173f4c02a854944-C10H21O2-1-1 +benzene-a502ffe15bce2adb300daebdd27f0aa0-C6H6-0-1 +TPS CS fragmentH+-2f65c8c819c26044f8a1b94755ad77b1-C12H11S1-1-1 +SO3-06ec8edf4209e7e492b8e563b71afbeb-O3S1-0-1 +ONFminus-f357352f5dd5488b54d50242d228ed6d-C4F9O3S1-m1-1 +PHSminusHrad-df1b0273442db364220e3662c74307eb-C10H13O1-0-2 +PHSminusOHrad-82ca46cecd8439a6d7fbd87eea2c54b9-C10H13-0-2 +TBOCminustertradical-0701a0edad7058c8168456de1c92e8e0-C6H11O2-0-2 +TBOCminustertradical+H+-a4c65f243bb0eef36b5ee0a359560871-C6H12O2-0-1 +556-b753e8d3829ebe4c1b93bf339690d319-C16H19S1-1-1 +222-affe6041ffe648433daa714b2d39dd72-C15H28O4-0-1 +524-00dc803a2a2dd2005acbb5d51b71a7d7-C9H17O2-0-2 +CH3dot-5f85470c393edc87393085bba5b03428-C1H3-0-2 +CO2-6abc9e860814179fef28aabbe09d1571-C1O2-0-1 +1260-aa3de124b222759aaea1463f6143873b-C23H26S1-0-1 +1258-93d061fd43eaf14c5fc8c73be52da15b-C23H26S1-0-1 +610-eea050c031d211549457abfc44b469a9-C4H10-0-1 +-62e08d5119480b03357cc679f310168d-C10H14O1-0-1 +-ace426ad373f83a93c83458cf66b8866-C6H5-1-1 +-d7c3b045b53266f82e25ae3098e29d4f-C18H14S1-0-1 +-2f4051ef4b3969cbf0d7a51a3d57959e-C4H9-1-1 +-443639a41f47d07b41b9f1b4150e7e7b-C10H15O1-m1-1 +-3bd4ab1135b39ff25d94beb51dd6c503-C13H13S1-1-1 +-aab0ea89ff9b4e27da78126a6c80cbf0-H2O1-0-1 +-367103e07e78cd55a4b80413679fda7e-H1O1-0-2 +-3ce8bce066bf652195a8784f7b4f04af-C10H19O2-0-2 +-edad4c3a7b053b636810e3cb94f17981-C10H15O1-1-1 +-3464f250ed90621ea6a9588d1705d205-C6H12O1-0-1 +-22ad4d4343667554c075f68e93c5c419-C4H9O1-0-2 +-24bbd018781f482c1635b08033fdf846-C4H10O1-0-1 +-414f98c42405835d32167a01608750ef-C4H8-m1-2 +-2f7e19a6344da517348e59f408a1aa99-C4H8-0-1 +-5d58a6a0200f85eff7a5f9f805a8e35f-C4H8-1-2 +-206ec2213d7388c5e8bf2cff81dedac7-C3H6O1-m1-2 +-9e7acc5b302a48411607db0a9234396f-C3H6O1-0-1 +-f4194a8bb7a342bbab4eece7c3820fa8-C3H6O1-1-2 +-ce487751a2c5c0b104116e3240cf5042-C6H12O1-m1-2 +-9480763ced3710477010a038211b937f-C6H12O1-0-1 +-a07777285e002c40f6d2107272819986-C6H12O1-1-2 +-646e41d216c60e02a2f50b62e29b8b88-C18H16S1-0-1 diff --git a/README.md b/README.md index 3223286..e1656de 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,10 @@ +CRN branch + HiPRGen (**Hi**_gh_ **P**_erformance_ **R**_eaction_ **Gen**_eration_) is a python module for constructing reaction networks via exhaustive reaction enumeration and filtering decision trees with the capacity to be applied to systems with hundreds of billions of possible reactions. HiPRGen is built on top of [MPI4py](https://mpi4py.readthedocs.io/en/stable/) which facilitates multi-node parallelism. -### Installation +### Running locally HiPRGen depends on `pymatgen`, `openbabel`, `pygraphviz`, `pycairo` and `mpi4py`. In our experience, the Conda version of MPI4py does not work consistently, so we use the [nix package manager](https://nixos.org/) to get HiPRGen running on a wide range of systems. Instructions for installing nix can be found [here](https://nixos.org/download.html). @@ -40,29 +42,61 @@ On the LRC cluster, an environment where HiPRGen can be run is set up as follows ``` cd $HOME + +source ~/miniconda3/etc/profile.d/conda.sh +conda activate + module load python/3.8.2-gcc -pip3 install --user mpi4py pymatgen -wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -bash Miniconda3-latest-Linux-x86_64.sh +module load gcc/7.4.0 +module load openmpi/4.0.1-gcc +pip3 install --user mpi4py -# load miniconda -source ./.bashrc +conda create -n hiprgen python=3.8 -y +conda activate hiprgen +conda install -c conda-forge openbabel -y +conda install -c conda-forge pygraphviz -y +#conda install -c conda-forge pymatgen -y +conda install -c conda-forge pycairo -y -conda create -n HiPRGen_RNMC python=3.8 -conda activate HiPRGen_RNMC -conda install -c conda-forge openbabel pygraphviz pymatgen pycairo +cd +git clone https://github.com/ViktoriiaBaib/HiPRGen.git +cd HiPRGen +git checkout vik_crn +cd -git clone https://github.com/BlauGroup/HiPRGen.git git clone https://github.com/BlauGroup/RNMC.git cd RNMC module load gsl -CC=g++ ./build.sh -export PATH=$PATH:$PROJ/RNMC/build -cd ../HiPRGen +CXX=g++ ./build.sh +export PATH=$PATH:$HOME/RNMC/build + +cd + +#additional packages + +conda install -c conda-forge matplotlib -y +conda install -c conda-forge numpy -y +pip install ruamel.yaml==0.17.21 +pip install pymatgen==2023.3.10 +pip install ase==3.22.1 python test.py 2 ``` +#### Running + +After activating environment, reload modules to avoid errors: +``` +module load python/3.8.2-gcc +module load gcc/7.4.0 +module load openmpi/4.0.1-gcc + +cd RNMC +module load gsl +CXX=g++ ./build.sh # otherwise get FileNotFoundError: [Errno 2] No such file or directory: 'GMC' +export PATH=$PATH:$HOME/RNMC/build +``` + ### Tests Once you are in an environment where HiPRGen is installed, the tests can be run with `python test.py 4`. This will run the tests using 4 threads, though you could use as many threads as your machine allows to speed up the execution. Running the tests will populate working directories in `scratch`. Note that `test.py` is heavily commented to explain how to use HiPRGen. With at least 4 threads, the tests should take less than five minutes to run. Along with a variety of other information, the following lines will be printed to standard output to confirm that the tests have passed: diff --git a/data/bfo_hiprgen_dataset.json b/data/bfo_hiprgen_dataset.json new file mode 100644 index 0000000..3494794 --- /dev/null +++ b/data/bfo_hiprgen_dataset.json @@ -0,0 +1 @@ +[{"_id": {"@module": "bson.objectid", "@class": "ObjectId", "oid": "65430474b744ca91ae8aaf0f"}, "label": "bfo_hiprgen_dataset", "name": "2609_graph455_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0", "atoms": {"@module": "ase.atoms", "@class": "Atoms", "atoms_json": "{\"numbers\": {\"__ndarray__\": [[13], \"int64\", [83, 7, 8, 8, 8, 7, 8, 8, 8, 7, 8, 8, 8]]}, \"positions\": {\"__ndarray__\": [[13, 3], \"float64\", [0.4577185478327527, -0.5966112870190736, 0.7159708308396675, -1.0642070255606748, 1.553999152491728, 1.740874623649266, -0.18146608186589178, 1.0679959405921167, 2.4888655609655803, -1.174096665837259, 0.9810552783646123, 0.5812525309254182, -1.7694802381046641, 2.4718115240600995, 2.035991650841635, -0.8948970922840186, -1.1018198920169235, -1.713425108394775, 0.17935853690504946, -0.39675409762140973, -1.5324493374764925, -1.35793046398169, -1.6348040114205415, -0.6754906023675, -1.3763739453758468, -1.2110318223929168, -2.801161826951724, 2.7536486885479703, 0.756524017783442, -0.22647519474721262, 2.7780356238004833, -0.4979136222407524, -0.24872279957359528, 1.6650046359586652, 1.2738421651540264, 0.2554571809351588, 3.6427524899651225, 1.4564682742655928, -0.6094100086454265]]}, \"initial_charges\": {\"__ndarray__\": [[13], \"float64\", [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]}, \"initial_magmoms\": {\"__ndarray__\": [[13], \"float64\", [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]}, \"cell\": {\"__ndarray__\": [[3, 3], \"float64\", [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]}, \"pbc\": {\"__ndarray__\": [[3], \"bool\", [false, false, false]]}, \"info\": {\"_id\": \"5f4d880af83e7c0cd92138b47b971dab\"}, \"__ase_objtype__\": \"atoms\"}"}, "energy": -28727.58611708652, "entropy": 0.004921257751687283, "enthalpy": 1.6748696566734218}, {"_id": {"@module": "bson.objectid", "@class": "ObjectId", "oid": "65430474b744ca91ae8aaf10"}, "label": "bfo_hiprgen_dataset", "name": "0210_graph621_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0", "atoms": {"@module": "ase.atoms", "@class": "Atoms", "atoms_json": "{\"numbers\": {\"__ndarray__\": [[26], \"int64\", [83, 7, 8, 8, 8, 7, 8, 8, 8, 6, 8, 6, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8]]}, \"positions\": {\"__ndarray__\": [[26, 3], \"float64\", [0.3288750023136141, -0.06180734335472562, 0.10244825545117338, 1.3102693958531257, -0.4648735785408582, 2.714880895630165, 2.159397062109056, -0.3644948646245007, 1.7995849227078673, 0.07574770657628549, -0.3324481843045297, 2.340648615006211, 1.5769861205575337, -0.6699650982094659, 3.863635198496387, -2.4729559170514723, -0.1244270243356553, 0.5007595849105414, 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"bson.objectid", "@class": "ObjectId", "oid": "65430474b744ca91ae8aaf11"}, "label": "bfo_hiprgen_dataset", "name": "0210_graph620_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0", "atoms": {"@module": "ase.atoms", "@class": "Atoms", "atoms_json": "{\"numbers\": {\"__ndarray__\": [[26], \"int64\", [83, 7, 8, 8, 8, 7, 8, 8, 8, 6, 8, 6, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8]]}, \"positions\": {\"__ndarray__\": [[26, 3], \"float64\", [-0.37112456397747523, -0.11787374509895762, -0.2684061520416769, -1.4441224923433822, 2.473232464868568, 0.41855147999527653, -0.6496280335539771, 2.344617025341591, -0.5596380139273158, -1.7367477275350718, 1.3983020384594445, 1.03482376305983, -1.89669661962084, 3.5379138751887766, 0.7483071754896707, -2.0275987152145376, -1.7553082001722173, 1.4989844808940083, -2.526259383822556, -1.4826604682773217, 0.3844514477653066, -0.8303585939762889, -1.3302066489544908, 1.7057582807207217, -2.6064456498963677, -2.3800773038110017, 2.3516465733189063, 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"ionization_energy": null, "ie_task_id": null, "reduction_free_energy": {"DIELECTRIC=3,00": -6.163125297982333}, "red_mpcule_id": {"DIELECTRIC=3,00": "9480763ced3710477010a038211b937f-C6H12O1-0-1"}, "oxidation_free_energy": null, "ox_mpcule_id": null, "reduction_potentials": {"DIELECTRIC=3,00": {"H": 1.7231252979823326, "Li": 4.763125297982333, "Mg": 4.1031252979823325, "Ca": 4.563125297982333}}, "oxidation_potentials": null, "has_props": ["bonding", "vibration", "thermo", "partial_spins", "redox", "orbitals", "partial_charges"], "_bt": {"@module": "datetime", "@class": "datetime", "string": "2023-03-29 19:23:25.167000"}}] \ No newline at end of file diff --git a/data/json2xyz.py b/data/json2xyz.py new file mode 100644 index 0000000..f9302be --- /dev/null +++ b/data/json2xyz.py @@ -0,0 +1,38 @@ +from monty.serialization import loadfn +import json +from ase import Atoms +from ase.io import write +import numpy as np + +def decode_ndarray(data): + dtype = data['__ndarray__'][1] + values = np.array(data['__ndarray__'][2], dtype=dtype) + return values.reshape(data['__ndarray__'][0]) + +def init_ase_atoms_from_dict(doc): + decoded_data = json.loads(doc['atoms']['atoms_json']) + numbers = decode_ndarray(decoded_data['numbers']) + positions = decode_ndarray(decoded_data['positions']) + charges = decode_ndarray(decoded_data['initial_charges']) + magmoms = decode_ndarray(decoded_data['initial_magmoms']) + cell = decode_ndarray(decoded_data['cell']) + pbc = decode_ndarray(decoded_data['pbc']) + # Initialize the ASE Atoms object + atoms = Atoms(numbers=numbers, positions=positions, charges=charges, magmoms=magmoms, cell=cell, pbc=pbc) + return(atoms) + +def get_free_energy(doc): + return doc["energy"]+doc["enthalpy"]-298.15*doc["entropy"] + +mol_json = "bfo_hiprgen_dataset.json" + +database_entries = loadfn(mol_json) + +for doc in database_entries: + #if "graph463" not in doc["name"]: + # continue + #atoms = init_ase_atoms_from_dict(doc) + #free_energy = get_free_energy(doc) + #write("tmp_xyz/"+doc["name"]+".xyz", atoms) + #print(free_energy, "\t" ,doc["name"]) + print(doc["name"]) diff --git a/data/log_new.txt b/data/log_new.txt new file mode 100644 index 0000000..faef7cd --- /dev/null +++ b/data/log_new.txt @@ -0,0 +1,235 @@ +2609_graph455_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +0210_graph621_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0 +0210_graph620_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0 +2809_graph610_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +2609_graph27_cn5_pentagonal_planar_2_nunpairedes_0_charge_0 +2809_graph473_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +2809_graph476_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +2809_graph397_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0 +2809_graph463_cn6_octahedral_0_nunpairedes_0_charge_0 +2809_graph364_cn5_square_pyramidal_0_nunpairedes_0_charge_0 +2809_graph383_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0 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+"ind1002_graph1002_cn6_pentagonal_pyramidal_3_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_octahedral_0_nunpairedes_0_charge_0", +"ind1000_graph1000_cn7_am_c3_7H2O_c0_2_nunpairedes_0_charge_0", +"2609_graph0_cn5_trigonal_bipyramidal_1_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0", +"2609_graph0_cn5_square_pyramidal_0_nunpairedes_0_charge_0" diff --git a/data/log_old.txt b/data/log_old.txt new file mode 100644 index 0000000..26ed0c5 --- /dev/null +++ b/data/log_old.txt @@ -0,0 +1,207 @@ +2609_graph455_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +0210_graph621_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0 +0210_graph620_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0 +2809_graph610_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +2609_graph27_cn5_pentagonal_planar_2_nunpairedes_0_charge_0 +2809_graph473_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +2809_graph476_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 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+ind107_graph773_cn6_hexagonal_planar_0_nunpairedes_0_charge_0 +ind106_graph766_cn5_square_pyramidal_0_nunpairedes_0_charge_0 +ind11_graph32_cn5_trigonal_bipyramidal_1_nunpairedes_0_charge_0 +ind15_graph55_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +ind12_graph47_cn5_square_pyramidal_0_nunpairedes_0_charge_0 +ind13_graph48_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +ind108_graph782_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +ind109_graph807_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0 +ind14_graph51_cn5_trigonal_bipyramidal_2_nunpairedes_0_charge_0 +0210_graph329_cn6_hexagonal_planar_8_nunpairedes_0_charge_0 +0210_graph82_cn6_pentagonal_pyramidal_1_nunpairedes_0_charge_0 +0210_graph226_cn5_square_pyramidal_2_nunpairedes_0_charge_0 +2809_graph221_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0 +2809_graph93_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0 +0210_graph226_cn5_square_pyramidal_5_nunpairedes_0_charge_0 +0210_graph111_cn6_octahedral_0_nunpairedes_0_charge_0 +0210_graph583_cn6_trigonal_prismatic_1_nunpairedes_0_charge_0 +0210_graph581_cn6_trigonal_prismatic_8_nunpairedes_0_charge_0 +0210_graph584_cn6_trigonal_prismatic_1_nunpairedes_0_charge_0 +0210_graph9_cn5_trigonal_bipyramidal_6_nunpairedes_0_charge_0 +0210_graph5_cn5_square_pyramidal_2_nunpairedes_0_charge_0 +0210_graph226_cn5_pentagonal_planar_4_nunpairedes_0_charge_0 +0210_graph757_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0 +0210_graph759_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0 +0210_graph758_cn6_pentagonal_pyramidal_1_nunpairedes_0_charge_0 +0210_graph236_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0 +ind102_graph714_cn5_trigonal_bipyramidal_1_nunpairedes_0_charge_0 +ind100_graph630_cn6_hexagonal_planar_0_nunpairedes_0_charge_0 +ind1_graph1_cn6_octahedral_0_nunpairedes_0_charge_0 +ind101_graph690_cn5_square_pyramidal_0_nunpairedes_0_charge_0 +0210_graph387_cn6_hexagonal_planar_6_nunpairedes_0_charge_0 +0210_graph387_cn6_hexagonal_planar_0_nunpairedes_0_charge_0 +0210_graph387_cn6_hexagonal_planar_1_nunpairedes_0_charge_0 +0210_graph113_cn6_pentagonal_pyramidal_5_nunpairedes_0_charge_0 +0210_graph113_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0 +0210_graph113_cn6_pentagonal_pyramidal_2_nunpairedes_0_charge_0 +2809_graph97_cn6_pentagonal_pyramidal_9_nunpairedes_0_charge_0 +2609_graph0_cn5_trigonal_bipyramidal_1_nunpairedes_0_charge_0 +2609_graph0_cn5_square_pyramidal_0_nunpairedes_0_charge_0 +0210_graph89_cn6_hexagonal_planar_1_nunpairedes_0_charge_0 +0210_graph119_cn6_trigonal_prismatic_2_nunpairedes_0_charge_0 +no3_ion_opt +hno3_opt +moe_ion_opt +moe_opt diff --git a/data/make_test_data.py b/data/make_test_data.py new file mode 100644 index 0000000..36f4065 --- /dev/null +++ b/data/make_test_data.py @@ -0,0 +1,66 @@ +import json + +fname = "bfo_hiprgen_dataset" + +# Open and read the JSON file +with open(fname+".json", 'r') as f: + data = json.load(f) +#for i in range(len(data)): +# print(i, data[i]["name"]) +# Select the 1st, 4th, 5th, and 9th items from the list +#selected_items = [data[1], data[4], data[5], data[12]] +#for i in range(len(selected_items)): +# print(i, selected_items[i]["name"]) +#Select by name +names = ["2809_graph773_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0", +"0210_graph620_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0", +"2809_graph397_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0", +"2809_graph476_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0", +"ind95_graph610_cn5_trigonal_bipyramidal_0_nunpairedes_0_charge_0", +"2609_graph207_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0", +"ind44_graph207_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0", +"_graph70_", "_graph82_", "_graph69_", "_graph306_", +"2809_graph149_cn6_hexagonal_planar_0_nunpairedes_0_charge_0", +"_graph1_", "_graph32_", +"ind71_graph356_cn6_trigonal_prismatic_4_nunpairedes_0_charge_0", +"_graph218_", "_graph463_", +"no3_ion_opt", "hno3_opt", "moe_ion_opt", "moe_opt", +"0210_graph387_cn6_hexagonal_planar_6_nunpairedes_0_charge_0", +"0210_graph387_cn6_hexagonal_planar_0_nunpairedes_0_charge_0", +"0210_graph113_cn6_pentagonal_pyramidal_2_nunpairedes_0_charge_0", +"0210_graph119_cn6_hexagonal_planar_4_nunpairedes_0_charge_0", +"0210_graph113_cn6_pentagonal_pyramidal_5_nunpairedes_0_charge_0", +"0210_graph387_cn6_hexagonal_planar_1_nunpairedes_0_charge_0", +"0210_graph113_cn6_pentagonal_pyramidal_0_nunpairedes_0_charge_0", +"2809_graph97_cn6_pentagonal_pyramidal_9_nunpairedes_0_charge_0", +"0210_graph89_cn6_hexagonal_planar_1_nunpairedes_0_charge_0", +"ind1003_graph1003_cn7_capped_trigonal_prismatic_6_nunpairedes_0_charge_0", +"ind1003_graph1003_cn7_capped_octahedral_5_nunpairedes_0_charge_0", +"ind1003_graph1003_cn7_capped_octahedral_1_nunpairedes_0_charge_0", +"ind1003_graph1003_cn7_capped_octahedral_6_nunpairedes_0_charge_0", +"ind1000_graph1000_cn7_capped_trigonal_prismatic_0_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_pentagonal_pyramidal_2_nunpairedes_0_charge_0", +"ind1000_graph1000_cn7_capped_octahedral_2_nunpairedes_0_charge_0", +"ind1000_graph1000_cn7_hexagonal_pyramidal_0_nunpairedes_0_charge_0", +"ind1000_graph1000_cn7_am_c3_7H2O_c0_0_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_trigonal_prismatic_4_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_trigonal_prismatic_3_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_trigonal_prismatic_1_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_trigonal_prismatic_2_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_pentagonal_pyramidal_3_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_octahedral_0_nunpairedes_0_charge_0", +"ind1000_graph1000_cn7_am_c3_7H2O_c0_2_nunpairedes_0_charge_0", +"2609_graph0_cn5_trigonal_bipyramidal_1_nunpairedes_0_charge_0", +"ind1002_graph1002_cn6_trigonal_prismatic_0_nunpairedes_0_charge_0", +"2609_graph0_cn5_square_pyramidal_0_nunpairedes_0_charge_0"] +# Save the selected items to a new JSON file +selected_items = [] +for i,doc in enumerate(data): + for name in names: + if name in doc["name"]: + selected_items.append(doc) + print(i, doc["name"]) +with open(fname+"_test.json", 'w') as f: + json.dump(selected_items, f, indent=4) + +print("Data has been saved to new test json") diff --git a/data/tmp_xyz/2.xyz b/data/tmp_xyz/2.xyz new file mode 100644 index 0000000..af03b43 --- /dev/null +++ b/data/tmp_xyz/2.xyz @@ -0,0 +1,39 @@ +37 +Properties=species:S:1:pos:R:3:initial_magmoms:R:1:initial_charges:R:1 pbc="F F F" +Bi -1.12562622 0.51725098 1.05504142 0.00000000 0.00000000 +C 1.35304123 -0.05978592 3.56046697 0.00000000 0.00000000 +O 0.21872793 -0.70225519 3.00314982 0.00000000 0.00000000 +C 0.49987761 -1.99189092 2.47252139 0.00000000 0.00000000 +C -0.75219319 -2.46122802 1.76233970 0.00000000 0.00000000 +O -1.12652158 -1.59559407 0.72359399 0.00000000 0.00000000 +H 1.73553809 -0.63894583 4.41368625 0.00000000 0.00000000 +H 1.03693162 0.93001095 3.90563502 0.00000000 0.00000000 +H 2.13953748 0.05155212 2.80136537 0.00000000 0.00000000 +H 0.77593779 -2.68190581 3.28623500 0.00000000 0.00000000 +H 1.33958978 -1.91650209 1.76178685 0.00000000 0.00000000 +H -1.55966342 -2.56867404 2.51061747 0.00000000 0.00000000 +H -0.55741240 -3.46494602 1.34920619 0.00000000 0.00000000 +C 1.32160235 -0.12560309 -3.52126115 0.00000000 0.00000000 +O 0.30479618 -0.43411908 -2.60124026 0.00000000 0.00000000 +C -0.97254864 -0.01656522 -3.03168738 0.00000000 0.00000000 +C -1.97881016 -0.20152045 -1.91524361 0.00000000 0.00000000 +O -1.86287957 0.78289015 -0.91864351 0.00000000 0.00000000 +H 1.14519442 -0.61573795 -4.49416078 0.00000000 0.00000000 +H 2.27048618 -0.48285916 -3.10660782 0.00000000 0.00000000 +H 1.38957257 0.96350237 -3.68856326 0.00000000 0.00000000 +H -1.28355432 -0.60299020 -3.91669403 0.00000000 0.00000000 +H -0.94401834 1.04920874 -3.32651033 0.00000000 0.00000000 +H -1.86066832 -1.21791466 -1.50574126 0.00000000 0.00000000 +H -2.98699938 -0.14134699 -2.36243151 0.00000000 0.00000000 +C -0.73229162 4.21982062 1.42152823 0.00000000 0.00000000 +O -0.36679473 3.10936023 0.62614780 0.00000000 0.00000000 +C 1.01603601 3.06070372 0.30148706 0.00000000 0.00000000 +C 1.27101723 1.71691379 -0.34982040 0.00000000 0.00000000 +O 0.92295115 0.66360229 0.51212014 0.00000000 0.00000000 +H -0.53539727 5.16098335 0.88600294 0.00000000 0.00000000 +H -0.17147458 4.22319674 2.36936294 0.00000000 0.00000000 +H -1.80382294 4.13997088 1.63246155 0.00000000 0.00000000 +H 1.61224285 3.15957800 1.22506661 0.00000000 0.00000000 +H 1.27587876 3.88924636 -0.37863118 0.00000000 0.00000000 +H 2.34265624 1.64254959 -0.59718947 0.00000000 0.00000000 +H 0.70665428 1.65765870 -1.29489884 0.00000000 0.00000000 diff --git a/data/tmp_xyz/2609_graph463_cn6_octahedral_0_nunpairedes_0_charge_0.xyz b/data/tmp_xyz/2609_graph463_cn6_octahedral_0_nunpairedes_0_charge_0.xyz new file mode 100644 index 0000000..10d80ef --- /dev/null +++ b/data/tmp_xyz/2609_graph463_cn6_octahedral_0_nunpairedes_0_charge_0.xyz @@ -0,0 +1,39 @@ +37 +Properties=species:S:1:pos:R:3:initial_magmoms:R:1:initial_charges:R:1 pbc="F F F" +Bi -0.93636113 0.59422207 0.90446935 0.00000000 0.00000000 +C 1.91328313 -0.07419590 2.99367180 0.00000000 0.00000000 +O 0.58976110 -0.57938674 2.89986096 0.00000000 0.00000000 +C 0.52652432 -1.96599780 2.56021713 0.00000000 0.00000000 +C 0.44112720 -2.13902119 1.05449853 0.00000000 0.00000000 +O -0.68705248 -1.48872435 0.53292100 0.00000000 0.00000000 +H 2.46022558 -0.59657551 3.79203389 0.00000000 0.00000000 +H 1.84006729 0.98908183 3.24507345 0.00000000 0.00000000 +H 2.45150248 -0.18270322 2.04165374 0.00000000 0.00000000 +H -0.38485611 -2.36069442 3.02828399 0.00000000 0.00000000 +H 1.39657400 -2.49599038 2.97853169 0.00000000 0.00000000 +H 0.37458993 -3.21754841 0.83202550 0.00000000 0.00000000 +H 1.36903897 -1.76477560 0.58529168 0.00000000 0.00000000 +C 0.08649484 -1.66748047 -2.64432317 0.00000000 0.00000000 +O -1.29163048 -1.43248030 -2.83990938 0.00000000 0.00000000 +C -1.60221627 -0.10550693 -3.21234135 0.00000000 0.00000000 +C -1.21149073 0.95589134 -2.19497351 0.00000000 0.00000000 +O -1.89818559 0.82503714 -0.97808477 0.00000000 0.00000000 +H 0.66874174 -1.34689989 -3.52610261 0.00000000 0.00000000 +H 0.21704043 -2.74602575 -2.50365691 0.00000000 0.00000000 +H 0.46489114 -1.15140406 -1.75034988 0.00000000 0.00000000 +H -2.68858270 -0.08150023 -3.37014670 0.00000000 0.00000000 +H -1.10897999 0.14305085 -4.17241601 0.00000000 0.00000000 +H -1.44722072 1.93351941 -2.65771599 0.00000000 0.00000000 +H -0.11927388 0.93959016 -2.04686987 0.00000000 0.00000000 +C -1.43545088 4.04975986 0.00615711 0.00000000 0.00000000 +O -0.40843019 3.20495931 0.49493783 0.00000000 0.00000000 +C 0.78042687 3.23472337 -0.28212689 0.00000000 0.00000000 +C 1.65645054 2.10174073 0.21088117 0.00000000 0.00000000 +O 1.01494677 0.85503278 0.12188244 0.00000000 0.00000000 +H -1.10830400 5.09987564 0.02337694 0.00000000 0.00000000 +H -2.30412035 3.92765419 0.66077835 0.00000000 0.00000000 +H -1.71107160 3.76810004 -1.02094577 0.00000000 0.00000000 +H 1.28949362 4.20485698 -0.16399616 0.00000000 0.00000000 +H 0.52816142 3.09590740 -1.34602404 0.00000000 0.00000000 +H 1.96616760 2.32334521 1.24858308 0.00000000 0.00000000 +H 2.57180024 2.07690426 -0.40213902 0.00000000 0.00000000 diff --git a/data/tmp_xyz/ind85_graph463_cn6_octahedral_0_nunpairedes_0_charge_0.xyz b/data/tmp_xyz/ind85_graph463_cn6_octahedral_0_nunpairedes_0_charge_0.xyz new file mode 100644 index 0000000..0c3018d --- /dev/null +++ b/data/tmp_xyz/ind85_graph463_cn6_octahedral_0_nunpairedes_0_charge_0.xyz @@ -0,0 +1,39 @@ +37 +Properties=species:S:1:pos:R:3:initial_magmoms:R:1:initial_charges:R:1 pbc="F F F" +Bi -0.23814277 0.68158269 -0.45260953 0.00000000 0.00000000 +C 1.10188602 -2.47369534 -0.93234296 0.00000000 0.00000000 +O 0.01386499 -1.89642546 -0.22015028 0.00000000 0.00000000 +C -0.02811321 -2.24369594 1.16103724 0.00000000 0.00000000 +C 0.67089665 -1.15215764 1.95276773 0.00000000 0.00000000 +O 0.12012405 0.08501838 1.62775057 0.00000000 0.00000000 +H 0.95111966 -3.56037540 -1.00605438 0.00000000 0.00000000 +H 2.05754419 -2.26309790 -0.43315164 0.00000000 0.00000000 +H 1.10154770 -2.01901352 -1.92503266 0.00000000 0.00000000 +H 0.42743592 -3.23247218 1.31789151 0.00000000 0.00000000 +H -1.08943392 -2.28551527 1.43995341 0.00000000 0.00000000 +H 1.75766881 -1.18607210 1.73650176 0.00000000 0.00000000 +H 0.55121437 -1.36286204 3.03030469 0.00000000 0.00000000 +C -3.65519857 0.15734373 -0.36760789 0.00000000 0.00000000 +O -2.55129181 -0.71809531 -0.53918891 0.00000000 0.00000000 +C -2.51586983 -1.36508933 -1.81619297 0.00000000 0.00000000 +C -1.78131894 -0.50333947 -2.83405613 0.00000000 0.00000000 +O -0.46846595 -0.23200809 -2.44139801 0.00000000 0.00000000 +H -4.59660033 -0.41034211 -0.38170574 0.00000000 0.00000000 +H -3.69051609 0.92829158 -1.15233479 0.00000000 0.00000000 +H -3.54010978 0.64507966 0.60670772 0.00000000 0.00000000 +H -3.54236657 -1.58692282 -2.14749012 0.00000000 0.00000000 +H -1.97229439 -2.30362288 -1.66386073 0.00000000 0.00000000 +H -2.36461970 0.42522990 -3.00446573 0.00000000 0.00000000 +H -1.78877696 -1.04629830 -3.79657401 0.00000000 0.00000000 +C 1.08939465 3.15149677 1.76195955 0.00000000 0.00000000 +O 1.22469078 2.93938144 0.36412325 0.00000000 0.00000000 +C 2.55183655 2.60512998 -0.04010527 0.00000000 0.00000000 +C 2.73652391 1.09818683 -0.03632118 0.00000000 0.00000000 +O 1.82605255 0.47968862 -0.90814191 0.00000000 0.00000000 +H 1.67189183 4.03291478 2.06793983 0.00000000 0.00000000 +H 1.41429471 2.27097269 2.33304766 0.00000000 0.00000000 +H 0.02787609 3.32899106 1.96476841 0.00000000 0.00000000 +H 3.28507120 3.10204973 0.61453483 0.00000000 0.00000000 +H 2.67439304 2.98888122 -1.06144199 0.00000000 0.00000000 +H 2.63018587 0.72062285 0.99688403 0.00000000 0.00000000 +H 3.76395526 0.86714917 -0.36367540 0.00000000 0.00000000 diff --git a/euvl_phase1_test/.DS_Store b/euvl_phase1_test/.DS_Store new file mode 100644 index 0000000..5008ddf Binary files /dev/null and b/euvl_phase1_test/.DS_Store differ diff --git a/euvl_phase1_test/buckets.sqlite b/euvl_phase1_test/buckets.sqlite new file mode 100644 index 0000000..161da27 Binary files /dev/null and b/euvl_phase1_test/buckets.sqlite differ diff --git a/euvl_phase1_test/dispatcher_payload.json b/euvl_phase1_test/dispatcher_payload.json new file mode 100644 index 0000000..11567c6 --- /dev/null +++ b/euvl_phase1_test/dispatcher_payload.json @@ -0,0 +1 @@ +{"@module": "HiPRGen.reaction_filter_payloads", "@class": "DispatcherPayload", "@version": null, "bucket_db_file": "./scratch/euvl_phase1_test/buckets.sqlite", "reaction_network_db_file": "./scratch/euvl_phase1_test/rn.sqlite", "report_file": "./scratch/euvl_phase1_test/reaction_report.tex", "commit_frequency": 1000, "checkpoint_interval": 10} \ No newline at end of file diff --git a/euvl_phase1_test/final_state_report.tex b/euvl_phase1_test/final_state_report.tex new file mode 100644 index 0000000..0ac3e4c --- /dev/null +++ b/euvl_phase1_test/final_state_report.tex @@ -0,0 +1,568 @@ +\documentclass{article} +\usepackage{graphicx} +\usepackage[margin=1cm]{geometry} +\usepackage{amsmath} +\pagenumbering{gobble} +\begin{document} +\setlength\parindent{0pt} + + +amount: 25.301 + +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} + +\vspace{1cm} + + +amount: 18.044 + +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} + +\vspace{1cm} + + +amount: 13.554 + +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} + +\vspace{1cm} + + +amount: 13.07 + +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} + +\vspace{1cm} + + +amount: 4.953 + +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} + +\vspace{1cm} + + +amount: 4.895 + +14 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+\usepackage[margin=1cm]{geometry} +\usepackage{amsmath} +\pagenumbering{gobble} +\begin{document} +\setlength\parindent{0pt} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.23]{2.26} +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.00]{0.05} +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.07]{0.73} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.19]{1.94} +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.06]{0.60} +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 3), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.14]{1.41} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.12]{1.22} +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.09]{0.89} +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.01]{0.05} +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +\xrightarrow[0.10]{1.03} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +\xrightarrow[0.02]{0.18} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.20]{2.01} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.41]{4.14} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.27]{2.70} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.06]{0.57} +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 3), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} +\xrightarrow[0.25]{2.53} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.33]{3.32} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.39]{3.88} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.11]{1.08} +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.05]{0.52} +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.37]{3.69} +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.16]{1.61} +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.23]{2.27} +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.25]{2.52} +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.11]{1.05} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.11]{1.10} +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.22]{2.22} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.08]{0.79} +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.33]{3.30} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.11]{1.07} +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.25]{2.45} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.18]{1.75} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.03]{0.29} +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.15]{1.46} +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.02]{0.16} +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.02]{0.24} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.24]{2.43} +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.09]{0.92} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.25]{2.53} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.32]{3.20} +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.21]{2.06} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.04]{0.38} +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.13]{1.26} +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.09]{0.94} +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.14]{1.36} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.26]{2.62} +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.36]{3.58} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.24]{2.35} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.16]{1.59} +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.09]{0.89} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.03]{0.26} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.13]{1.27} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.05]{0.50} +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.05]{0.50} +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.14]{1.36} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.02]{0.19} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.20]{2.05} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.05]{0.53} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.12]{1.18} +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.17]{1.69} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.02]{0.18} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.14]{1.38} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.25]{2.54} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.03]{0.33} +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.06]{0.57} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.11]{1.13} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.05]{0.47} +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.14]{1.42} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +\xrightarrow[0.04]{0.40} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.12]{1.15} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +\xrightarrow[0.09]{0.92} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} +\xrightarrow[0.15]{1.51} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.15]{1.46} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.13]{1.27} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} +\xrightarrow[0.24]{2.36} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.10]{1.02} +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.23]{2.31} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.01]{0.10} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.14]{1.39} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.28]{2.80} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.10]{0.99} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.14]{1.43} +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.07]{0.71} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.21]{2.12} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.03]{0.30} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.02]{0.17} +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.23]{2.30} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.04]{0.35} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.11]{1.13} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.11]{1.07} +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.21]{2.12} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.10]{0.95} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.18]{1.76} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.26]{2.61} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.07]{0.70} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +\xrightarrow[0.01]{0.09} +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.11]{1.14} +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.14]{1.45} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.19]{1.93} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +\xrightarrow[0.08]{0.78} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.00]{0.01} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.08]{0.76} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +\xrightarrow[0.04]{0.35} +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +\xrightarrow[0.00]{0.02} +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +\xrightarrow[0.08]{0.83} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +96 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/96.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 5)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.37]{3.75} +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.08]{0.82} +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} ++ +96 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/96.pdf}} +\xrightarrow[0.14]{1.44} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +\xrightarrow[0.02]{0.20} +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 3), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +\xrightarrow[0.04]{0.39} +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +\xrightarrow[0.08]{0.76} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.22]{2.24} +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.07]{0.69} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.12]{1.24} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +78 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/78.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.13]{1.29} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.50]{4.95} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +77 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/77.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.12]{1.18} +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.10]{0.95} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.20]{2.03} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} +\xrightarrow[0.01]{0.08} +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.33]{3.31} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.06]{0.57} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +\xrightarrow[0.10]{0.96} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +\xrightarrow[0.12]{1.17} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.15]{1.51} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +\xrightarrow[0.06]{0.58} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.26]{2.58} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.31]{3.10} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.05]{0.49} +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} +\xrightarrow[0.08]{0.79} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.33]{3.27} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.47]{4.71} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.06]{0.57} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.17]{1.73} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.19]{1.94} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.24]{2.39} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.01]{0.10} +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.11]{1.14} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.15]{1.47} +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.09]{0.86} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +96 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/96.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.13]{1.26} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +\xrightarrow[0.05]{0.45} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +78 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/78.pdf}} +\xrightarrow[0.54]{5.39} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.03]{0.31} +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.21]{2.08} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +78 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/78.pdf}} +\xrightarrow[0.42]{4.22} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.11]{1.12} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.29]{2.93} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +\xrightarrow[0.06]{0.57} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.17]{1.67} +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.05]{0.48} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.19]{1.86} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.32]{3.18} +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.20]{2.00} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.01]{0.08} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.20]{1.97} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.06]{0.57} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.16]{1.57} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.04]{0.41} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +\xrightarrow[0.09]{0.88} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +\xrightarrow[0.16]{1.56} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.21]{2.15} +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +\xrightarrow[0.04]{0.43} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.01]{0.11} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +\xrightarrow[0.06]{0.61} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +\xrightarrow[0.10]{1.03} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +\xrightarrow[0.13]{1.29} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +\xrightarrow[0.18]{1.77} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +77 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/77.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.08]{0.85} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.13]{1.30} +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.30]{3.00} +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.28]{2.82} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.10]{0.96} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.17]{1.70} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.03]{0.30} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} +\xrightarrow[0.07]{0.70} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.08]{0.84} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.37]{3.75} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.07]{0.75} +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} +\xrightarrow[0.04]{0.40} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +78 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/78.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +\xrightarrow[0.19]{1.86} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} +\xrightarrow[0.65]{6.49} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +\xrightarrow[0.06]{0.57} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +\xrightarrow[0.04]{0.43} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} +\xrightarrow[0.28]{2.81} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +\xrightarrow[0.40]{3.96} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.18]{1.83} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +96 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/96.pdf}} +\xrightarrow[0.03]{0.31} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.30]{3.04} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +\xrightarrow[0.37]{3.70} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.05]{0.51} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.01]{0.11} +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +\xrightarrow[0.39]{3.90} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.06]{0.65} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.04]{0.38} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.27]{2.70} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.15]{1.53} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} +\xrightarrow[0.02]{0.17} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} +\xrightarrow[0.55]{5.55} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.45]{4.48} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.02]{0.24} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.18]{1.78} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.52]{5.17} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.07]{0.70} +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +\xrightarrow[0.38]{3.79} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +\xrightarrow[0.50]{4.98} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +\xrightarrow[0.41]{4.13} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.13]{1.31} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} +\xrightarrow[0.58]{5.79} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.20]{2.00} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.08]{0.81} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} +\xrightarrow[0.13]{1.27} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.25]{2.46} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} +\xrightarrow[0.33]{3.26} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.06]{0.62} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} +\xrightarrow[0.71]{7.06} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.16]{1.61} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.01]{0.08} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.17]{1.66} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} +\xrightarrow[0.08]{0.83} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +\xrightarrow[0.26]{2.57} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +\xrightarrow[0.05]{0.52} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.15]{1.47} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +\xrightarrow[0.47]{4.68} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.07]{0.67} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +\xrightarrow[0.05]{0.46} +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.20]{1.97} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +\xrightarrow[0.02]{0.22} +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.31]{3.11} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.43]{4.27} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +78 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/78.pdf}} ++ +96 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/96.pdf}} +\xrightarrow[0.45]{4.53} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +\xrightarrow[0.13]{1.28} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.16]{1.64} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.01]{0.10} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.05]{0.54} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.01]{0.12} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.07]{0.68} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.10]{1.04} +78 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/78.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.02]{0.25} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +96 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/96.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.16]{1.62} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.27]{2.65} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.12]{1.22} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.31]{3.10} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.10]{0.98} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.09]{0.89} +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.39]{3.92} +77 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/77.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.35]{3.50} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.03]{0.28} +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.18]{1.79} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +\xrightarrow[0.06]{0.58} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.03]{0.33} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.08]{0.84} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.48]{4.77} +77 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/77.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.02]{0.25} +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.11]{1.07} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.38]{3.80} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.02]{0.15} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.42]{4.25} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.21]{2.13} +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +\xrightarrow[0.31]{3.12} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.07]{0.66} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.06]{0.60} +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.10]{1.00} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.12]{1.24} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.29]{2.93} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 3), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.24]{2.41} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.06]{0.61} +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.15]{1.51} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.03]{0.35} +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.00]{0.00} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +\xrightarrow[0.03]{0.32} +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.06]{0.57} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.10]{1.02} +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.01]{0.10} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.05]{0.55} +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.14]{1.42} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} ++ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} +\xrightarrow[0.20]{2.02} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.21]{2.07} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.20]{2.04} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.35]{3.46} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.06]{0.56} +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} ++ +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} +\xrightarrow[0.17]{1.69} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.19]{1.88} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.05]{0.52} +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.04]{0.42} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.04]{0.42} +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.33]{3.26} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.09]{0.87} +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +\xrightarrow[0.05]{0.52} +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.03]{0.27} +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +\xrightarrow[0.13]{1.30} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.07]{0.71} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.18]{1.79} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.21]{2.10} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.26]{2.58} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.00]{0.05} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.06]{0.56} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} +\xrightarrow[0.45]{4.47} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.08]{0.76} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.05]{0.50} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.15]{1.52} +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.12]{1.23} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} ++ +78 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/78.pdf}} +\xrightarrow[0.48]{4.78} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.13]{1.32} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.07]{0.65} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.26]{2.62} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.13]{1.34} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.21]{2.08} +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.02]{0.19} +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.34]{3.38} +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.18]{1.84} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.03]{0.26} +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.18]{1.78} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +\xrightarrow[0.03]{0.25} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +\xrightarrow[0.01]{0.06} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +\xrightarrow[0.03]{0.31} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.15]{1.52} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +\xrightarrow[0.61]{6.10} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +3 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/3.pdf}} ++ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +\xrightarrow[0.27]{2.71} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.14]{1.40} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +\xrightarrow[0.36]{3.64} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +\xrightarrow[0.18]{1.80} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +5 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/5.pdf}} ++ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} +\xrightarrow[0.00]{0.03} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +\xrightarrow[0.10]{1.03} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.35]{3.50} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +3 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/3.pdf}} ++ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} +\xrightarrow[0.06]{0.63} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} +\xrightarrow[0.03]{0.26} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.03]{0.29} +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} +\xrightarrow[0.18]{1.82} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 10), (1, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +3 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/3.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +\xrightarrow[0.01]{0.06} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.00]{0.02} +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 3), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +\xrightarrow[0.14]{1.42} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.06]{0.57} +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +\xrightarrow[0.05]{0.52} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.17]{1.70} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.02]{0.22} +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.28]{2.80} +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} ++ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +\xrightarrow[0.16]{1.63} +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} ++ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.04]{0.39} +3 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/3.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.15]{1.47} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 3), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +\xrightarrow[0.30]{3.02} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.06]{0.57} +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +\xrightarrow[0.09]{0.90} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +\xrightarrow[0.16]{1.58} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.06]{0.59} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +\xrightarrow[0.08]{0.79} +3 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/3.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.06]{0.59} +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} +\xrightarrow[0.02]{0.17} +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.20]{1.96} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.11]{1.07} +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.15]{1.49} +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +\xrightarrow[0.02]{0.18} +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.02]{0.22} +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +\xrightarrow[0.09]{0.87} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.02]{0.16} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.16]{1.62} +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +\xrightarrow[0.06]{0.56} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.06]{0.61} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.23]{2.30} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +\xrightarrow[0.08]{0.75} +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} +\xrightarrow[0.07]{0.72} +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +\xrightarrow[0.02]{0.17} +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +\xrightarrow[0.04]{0.40} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +\xrightarrow[0.12]{1.25} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} +\xrightarrow[0.04]{0.42} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} +\xrightarrow[0.21]{2.15} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.01]{0.13} +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.06]{0.57} +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 12), (1, 25)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +\xrightarrow[0.37]{3.68} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.08]{0.77} +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.05]{0.54} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 12), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +96 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/96.pdf}} +\xrightarrow[0.04]{0.41} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} +\xrightarrow[0.17]{1.69} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} +\xrightarrow[0.11]{1.14} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.10]{1.00} +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +\xrightarrow[0.04]{0.42} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} ++ +96 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/96.pdf}} +\xrightarrow[0.13]{1.26} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.06]{0.63} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 9), (1, 10)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} +\xrightarrow[0.00]{0.03} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 23)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.21]{2.12} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +\xrightarrow[0.54]{5.37} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} +\xrightarrow[0.03]{0.30} +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 32)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +\xrightarrow[0.09]{0.90} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +\xrightarrow[0.05]{0.47} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 1), (1, 32)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +\xrightarrow[0.06]{0.57} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.26]{2.63} +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 25)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.20]{2.04} +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.03]{0.25} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 34)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.04]{0.40} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} ++ +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} +\xrightarrow[0.23]{2.35} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 2), (1, 17)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.18]{1.78} +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} ++ +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.09]{0.88} +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.34]{3.44} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} ++ +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.21]{2.11} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 3)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 2), (1, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +\xrightarrow[0.00]{2.10} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 2)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +\xrightarrow[0.00]{0.53} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 2)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.04]{0.38} +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +\xrightarrow[0.05]{0.55} +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +\xrightarrow[0.17]{1.66} +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.21]{2.13} +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 12), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.08]{0.83} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.14]{1.44} +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 9), (0, 10)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 2), (0, 17)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.00]{1.56} +20 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/20.pdf}} ++ +56 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/56.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 5)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.00]{2.09} +58 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/58.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 11), (0, 12)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.00]{1.58} +21 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/21.pdf}} ++ +55 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/55.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 5)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.00]{0.86} +59 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/59.pdf}} ++ +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 11), (0, 12)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.00]{2.09} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 2)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +\xrightarrow[0.00]{0.39} +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 2)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.00]{4.26} +60 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/60.pdf}} ++ +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 11), (0, 12)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.00]{2.85} +21 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/21.pdf}} ++ +57 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/57.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 5)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +51 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/51.pdf}} +\xrightarrow[0.00]{0.73} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +55 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/55.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 23)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +52 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/52.pdf}} +\xrightarrow[0.00]{0.16} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +56 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/56.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 23)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.00]{0.03} +22 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/22.pdf}} ++ +56 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/56.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 2), (0, 5)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +\xrightarrow[0.00]{1.57} +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +60 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/60.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 11), (0, 12)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} +\xrightarrow[0.11]{1.12} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.16]{1.62} +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.30]{2.99} +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} ++ +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +53 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/53.pdf}} +\xrightarrow[0.00]{2.84} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +57 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/57.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 10), (0, 23)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} +\xrightarrow[0.09]{0.86} +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} ++ +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 11)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.00]{0.19} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 2)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +\xrightarrow[0.00]{2.79} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 12)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.16]{1.64} +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +24 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/24.pdf}} +\xrightarrow[0.00]{0.53} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +3 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/3.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +\xrightarrow[0.09]{0.91} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} +\xrightarrow[0.00]{0.02} +5 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/5.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 12)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.21]{2.14} +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} ++ +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +\xrightarrow[0.01]{0.14} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 1), (1, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 23)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +\xrightarrow[0.04]{0.39} +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 6)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} +\xrightarrow[0.00]{0.62} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +101 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/101.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 6)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +10 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/10.pdf}} +\xrightarrow[0.00]{1.84} +20 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/20.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 21)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} +\xrightarrow[0.00]{1.15} +55 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/55.pdf}} ++ +98 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/98.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 1), (0, 4)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} +\xrightarrow[0.00]{2.45} +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} ++ +101 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/101.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 6)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} +\xrightarrow[0.00]{0.33} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 2)] +\end{verbatim} +product bonds broken: + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.31]{3.10} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.28]{2.84} +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +\xrightarrow[0.05]{0.47} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} + + + + +\vspace{1cm} +\begin{verbatim} +more than one reactant +fragment matching found +free_energy dG is above threshold=0.0 +Terminal.KEEP +\end{verbatim} +$$ +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +\xrightarrow[0.08]{0.78} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} +$$ + + +reactant bonds broken:\begin{verbatim} +[(1, 0), (1, 1)] +\end{verbatim} +product bonds broken:\begin{verbatim} +[(0, 0), (0, 13)] +\end{verbatim} + + + + +\vspace{1cm} +\end{document} \ No newline at end of file diff --git a/euvl_phase1_test/reaction_tally.tex b/euvl_phase1_test/reaction_tally.tex new file mode 100644 index 0000000..b2d5024 --- /dev/null +++ b/euvl_phase1_test/reaction_tally.tex @@ -0,0 +1,1921 @@ +\documentclass{article} +\usepackage{graphicx} +\usepackage[margin=1cm]{geometry} +\usepackage{amsmath} +\pagenumbering{gobble} +\begin{document} +\setlength\parindent{0pt} + + +reaction tally report + + + +total number of reactions: 563 + + + +number of reactions which fired: 192 + + + +total number of species: 104 + + + +number of species observed: 74 + + + +4362 occourances of: + +$$ +459: +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-0.30} +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +$$ + + + +\vspace{1cm} + + +3601 occourances of: + +$$ +461: +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.00]{8.00} +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +$$ + + + +\vspace{1cm} + + +3564 occourances of: + +$$ +269: +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +\xrightarrow[0.00]{0.00} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + + +\vspace{1cm} + + +2794 occourances of: + +$$ +460: +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-0.45} +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + + +\vspace{1cm} + + +2430 occourances of: + +$$ +462: +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.00]{6.63} +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +$$ + + + +\vspace{1cm} + + +2315 occourances of: + +$$ +509: +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-2.93} +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} +$$ + + + +\vspace{1cm} + + +2282 occourances of: + +$$ +517: +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +\xrightarrow[0.00]{2.79} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + + +\vspace{1cm} + + +2165 occourances of: + +$$ +418: +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} +\xrightarrow[0.00]{6.90} +84 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/84.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +$$ + + + +\vspace{1cm} + + +1964 occourances of: + +$$ +510: +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} +\xrightarrow[0.00]{9.31} +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +$$ + + + +\vspace{1cm} + + +1831 occourances of: + +$$ +273: +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.01]{0.10} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +$$ + + + +\vspace{1cm} + + +1652 occourances of: + +$$ +256: +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.02]{0.15} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + + +\vspace{1cm} + + +1101 occourances of: + +$$ +289: +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.03]{0.27} +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + + +\vspace{1cm} + + +1046 occourances of: + +$$ +521: +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} +\xrightarrow[0.00]{0.02} +5 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/5.pdf}} ++ +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} +$$ + + + +\vspace{1cm} + + +965 occourances of: + +$$ +311: +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.03]{0.26} +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + + +\vspace{1cm} + + +476 occourances of: + +$$ +488: +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.00]{0.03} +22 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/22.pdf}} ++ +56 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/56.pdf}} +$$ + + + +\vspace{1cm} + + +311 occourances of: + +$$ +322: +5 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+\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +\xrightarrow[0.01]{0.12} +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +$$ + + + +\vspace{1cm} + + +37 occourances of: + +$$ +329: +3 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/3.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +\xrightarrow[0.01]{0.06} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +$$ + + + +\vspace{1cm} + + +33 occourances of: + +$$ +524: +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +\xrightarrow[0.01]{0.14} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + + +\vspace{1cm} + + +32 occourances of: + +$$ +414: +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.00]{6.68} +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +$$ + + + +\vspace{1cm} + + +32 occourances of: + +$$ +463: +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-1.98} +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} +$$ + + + +\vspace{1cm} + + +30 occourances of: + +$$ +33: +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +\xrightarrow[0.02]{0.16} +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + + +\vspace{1cm} + + +29 occourances of: + +$$ +479: +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-4.99} +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} +$$ + + + +\vspace{1cm} + + +27 occourances of: + +$$ +552: +5 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/5.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-6.54} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} +$$ + + + +\vspace{1cm} + + +25 occourances of: + +$$ +526: +21 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/21.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-1.96} +20 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/20.pdf}} +$$ + + + +\vspace{1cm} + + +22 occourances of: + +$$ +452: +56 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/56.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-1.94} +55 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/55.pdf}} +$$ + + + +\vspace{1cm} + + +20 occourances of: + +$$ +490: +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +\xrightarrow[0.00]{1.57} +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} ++ +60 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/60.pdf}} +$$ + + + +\vspace{1cm} + + +19 occourances of: + +$$ +545: +3 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/3.pdf}} +\xrightarrow[0.00]{0.67} +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +$$ + + + +\vspace{1cm} + + +18 occourances of: + +$$ +398: +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} +\xrightarrow[0.00]{-0.10} +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +$$ + + + +\vspace{1cm} + + +18 occourances of: + +$$ +163: +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.01]{0.11} +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} +$$ + + + +\vspace{1cm} + + +17 occourances of: + +$$ +370: +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.05]{0.54} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + + +\vspace{1cm} + + +17 occourances of: + +$$ +234: +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.05]{0.54} +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + + +\vspace{1cm} + + +17 occourances of: + +$$ +96: +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.11]{1.14} +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + + +\vspace{1cm} + + +16 occourances of: + +$$ +530: +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-1.60} +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} +$$ + + + +\vspace{1cm} + + +16 occourances of: + +$$ +332: +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} ++ +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} +\xrightarrow[0.05]{0.52} +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} ++ +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} +$$ + + + +\vspace{1cm} + + +16 occourances of: + +$$ +536: +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} +\xrightarrow[0.00]{0.62} +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} ++ +101 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/101.pdf}} +$$ + + + +\vspace{1cm} + + +15 occourances of: + +$$ +4: +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} ++ +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} +\xrightarrow[0.06]{0.60} +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +$$ + + + +\vspace{1cm} + + +14 occourances of: + +$$ +528: +22 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/22.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-4.81} +21 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/21.pdf}} +$$ + + + +\vspace{1cm} + + +14 occourances of: + +$$ +309: +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.02]{0.19} +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +$$ + + + +\vspace{1cm} + + +14 occourances of: + +$$ +103: +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} +\xrightarrow[0.04]{0.35} +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} ++ +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} +$$ + + + +\vspace{1cm} + + +14 occourances of: + +$$ +454: +57 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/57.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +\xrightarrow[0.00]{-7.63} +56 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/56.pdf}} +$$ + + + +\vspace{1cm} + + +13 occourances of: + +$$ +260: +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +\xrightarrow[0.07]{0.66} +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} ++ +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} +$$ + + + +\vspace{1cm} + + +13 occourances of: + +$$ +504: +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} +\xrightarrow[0.00]{1.37} +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} ++ +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} +$$ + + + +\vspace{1cm} + + +12 occourances of: + +$$ +176: +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} ++ +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} +\xrightarrow[0.07]{0.75} +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} ++ +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} +$$ + + + +\vspace{1cm} + + +12 occourances of: + +$$ +248: +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} +\xrightarrow[0.06]{0.58} +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} ++ +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} +$$ + + + +\vspace{1cm} + + +11 occourances of: + +$$ +271: +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} ++ +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} +\xrightarrow[0.06]{0.57} +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} +$$ + + + +\vspace{1cm} + + +11 occourances of: + +$$ +295: +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} ++ +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} +\xrightarrow[0.00]{0.05} +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} ++ +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} +$$ + + + +\vspace{1cm} + + +11 occourances of: + +$$ +66: +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} ++ +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} +\xrightarrow[0.05]{0.47} +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} ++ +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} +$$ + + + +\vspace{1cm} +\end{document} \ No newline at end of file diff --git a/euvl_phase1_test/rn.sqlite b/euvl_phase1_test/rn.sqlite new file mode 100644 index 0000000..40b7008 Binary files /dev/null and b/euvl_phase1_test/rn.sqlite differ diff --git a/euvl_phase1_test/species_report.tex b/euvl_phase1_test/species_report.tex new file mode 100644 index 0000000..1588cf1 --- /dev/null +++ b/euvl_phase1_test/species_report.tex @@ -0,0 +1,1676 @@ +\documentclass{article} +\usepackage{graphicx} +\usepackage[margin=1cm]{geometry} +\usepackage{amsmath} +\pagenumbering{gobble} +\begin{document} +\setlength\parindent{0pt} + + +species report + + + +8ff2bab9dc4f026763d936962021aa43-C10F9H5O3S1-0-1 + + + +formula: C10 F9 H5 O3 S1 + + + +free energy = -51881.05943951432 eV + +0 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/0.pdf}} + +\vspace{1cm} + + +af0733dcda4cc3494970c99618faad2a-C4H9O1-m1-1 + + + +formula: C4 H9 O1 + + + +free energy = -6340.551332453043 eV + +1 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/1.pdf}} + +\vspace{1cm} + + +22ad4d4343667554c075f68e93c5c419-C4H9O1-0-2 + + + +formula: C4 H9 O1 + + + +free energy = -6337.038072173203 eV + +2 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/2.pdf}} + +\vspace{1cm} + + +db346580544213066bb82c346b1fff3a-C12H10S1-m1-2 + + + +formula: C12 H10 S1 + + + +free energy = -23437.70611996324 eV + +3 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/3.pdf}} + +\vspace{1cm} + + +bc3641376a32020a0345549009577712-C12H10S1-0-1 + + + +formula: C12 H10 S1 + + + +free energy = -23437.039385831296 eV + +4 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/4.pdf}} + +\vspace{1cm} + + +e524cbadc1649d2535bdee66942e4dba-C12H10S1-1-2 + + + +formula: C12 H10 S1 + + + +free energy = -23430.495352141443 eV + +5 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/5.pdf}} + +\vspace{1cm} + + +ebf68aa2f6d4a07641dcb570486ea86d-O3S1-m2-1 + + + +formula: O3 S1 + + + +free energy = -16981.496435199475 eV + +6 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/6.pdf}} + +\vspace{1cm} + + +4fae9656fce777fe31f204f123fa4921-O3S1-m1-2 + + + +formula: O3 S1 + + + +free energy = -16980.038738980504 eV + +7 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/7.pdf}} + +\vspace{1cm} + + +06ec8edf4209e7e492b8e563b71afbeb-O3S1-0-1 + + + +formula: O3 S1 + + + +free energy = -16976.242933424644 eV + +8 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/8.pdf}} + +\vspace{1cm} + + +9100204becf2990b58581af65fd3b696-O3S1-1-2 + + + +formula: O3 S1 + + + +free energy = -16965.25336250728 eV + +9 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/9.pdf}} + +\vspace{1cm} + + +ce02829e6764a1bba90ddba3eabc3c6a-C15H28O4-m1-2 + + + +formula: C15 H28 O4 + + + +free energy = -24191.628919694365 eV + +10 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/10.pdf}} + +\vspace{1cm} + + +affe6041ffe648433daa714b2d39dd72-C15H28O4-0-1 + + + +formula: C15 H28 O4 + + + +free energy = -24191.05630934911 eV + +11 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/11.pdf}} + +\vspace{1cm} + + +8425c6cfd18e1596203ba12ba792a30e-C15H28O4-1-2 + + + +formula: C15 H28 O4 + + + +free energy = -24182.736968514186 eV + +12 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/12.pdf}} + +\vspace{1cm} + + +89f973ce0822f0ba97d90b7b4377454f-C10H21O2-m1-1 + + + +formula: C10 H21 O2 + + + +free energy = -14799.207919582419 eV + +13 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/13.pdf}} + +\vspace{1cm} + + +8a7e8693a6998655afc6c3cd13715281-C10H21O2-0-2 + + + +formula: C10 H21 O2 + + + +free energy = -14797.527224036618 eV + +14 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/14.pdf}} + +\vspace{1cm} + + +2c137c7f62959d051173f4c02a854944-C10H21O2-1-1 + + + +formula: C10 H21 O2 + + + +free energy = -14793.836633812178 eV + +15 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/15.pdf}} + +\vspace{1cm} + + +2f65c8c819c26044f8a1b94755ad77b1-C12H11S1-1-1 + + + +formula: C12 H11 S1 + + + +free energy = -23446.885503395588 eV + +16 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/16.pdf}} + +\vspace{1cm} + + +e51d163ce60f39a477fbac74bf153e6e-C18H14S1-m1-2 + + + +formula: C18 H14 S1 + + + +free energy = -29720.276875044165 eV + +17 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/17.pdf}} + +\vspace{1cm} + + +d7c3b045b53266f82e25ae3098e29d4f-C18H14S1-0-1 + + + +formula: C18 H14 S1 + + + +free energy = -29718.678399679367 eV + +18 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/18.pdf}} + +\vspace{1cm} + + +2aa3c4ee4b19f7b7953edb0df41b416f-C18H14S1-1-2 + + + +formula: C18 H14 S1 + + + +free energy = -29713.82662078988 eV + +19 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/19.pdf}} + +\vspace{1cm} + + +bf707048f238a54366b2e58f3544e82f-C9H17O2-m1-1 + + + +formula: C9 H17 O2 + + + +free energy = -13699.256050742573 eV + +20 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/20.pdf}} + +\vspace{1cm} + + +00dc803a2a2dd2005acbb5d51b71a7d7-C9H17O2-0-2 + + + +formula: C9 H17 O2 + + + +free energy = -13697.297882450022 eV + +21 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/21.pdf}} + +\vspace{1cm} + + +ef9885d298317f560d763c1c9df88ea7-C9H17O2-1-1 + + + +formula: C9 H17 O2 + + + +free energy = -13692.483353819382 eV + +22 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/22.pdf}} + +\vspace{1cm} + + +ace47f1afdf09aea2d7a88313246cf5e-C16H19S1-0-2 + + + +formula: C16 H19 S1 + + + +free energy = -27725.461978143005 eV + +23 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/23.pdf}} + +\vspace{1cm} + + +b753e8d3829ebe4c1b93bf339690d319-C16H19S1-1-1 + + + +formula: C16 H19 S1 + + + +free energy = -27722.57399714871 eV + +24 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/24.pdf}} + +\vspace{1cm} + + +f70a294e2348dc611a45088494876955-C4H10-m1-2 + + + +formula: C4 H10 + + + +free energy = -4306.996405540511 eV + +25 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/25.pdf}} + +\vspace{1cm} + + +eea050c031d211549457abfc44b469a9-C4H10-0-1 + + + +formula: C4 H10 + + + +free energy = -4307.494049512899 eV + +26 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/26.pdf}} + +\vspace{1cm} + + +bff66d78cfd6b31ffe8f16b27ae69618-C4H10-1-2 + + + +formula: C4 H10 + + + +free energy = -4298.846498430801 eV + +27 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/27.pdf}} + +\vspace{1cm} + + +035975cc24e93e53983b067459690b02-C18H15S1-0-2 + + + +formula: C18 H15 S1 + + + +free energy = -29735.095680830127 eV + +28 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/28.pdf}} + +\vspace{1cm} + + +94be97269b03e361ba1b344f48f19e44-C18H15S1-1-1 + + + +formula: C18 H15 S1 + + + +free energy = -29732.16832442951 eV + +29 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/29.pdf}} + +\vspace{1cm} + + +03fa2887bf9301307bdf24d123f68795-C18H15S1-2-2 + + + +formula: C18 H15 S1 + + + +free energy = -29722.855017808004 eV + +30 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/30.pdf}} + +\vspace{1cm} + + +6abc9e860814179fef28aabbe09d1571-C1O2-0-1 + + + +formula: C1 O2 + + + +free energy = -5133.019132421511 eV + +31 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/31.pdf}} + +\vspace{1cm} + + +63a94c85aea3114c3e2baa7a790f2dcc-C4H9-m1-1 + + + +formula: C4 H9 + + + +free energy = -4291.406620223405 eV + +32 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/32.pdf}} + +\vspace{1cm} + + +53e9047861139aaf2a4fff70dc49d701-C4H9-0-2 + + + +formula: C4 H9 + + + +free energy = -4290.035016715747 eV + +33 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/33.pdf}} + +\vspace{1cm} + + +2f4051ef4b3969cbf0d7a51a3d57959e-C4H9-1-1 + + + +formula: C4 H9 + + + +free energy = -4284.999866720066 eV + +34 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/34.pdf}} + +\vspace{1cm} + + +c765bf785ca367e07df60e89c5fe5e8d-C23H26S1-m1-2 + + + +formula: C23 H26 S1 + + + +free energy = -35096.309034517726 eV + +35 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/35.pdf}} + +\vspace{1cm} + + +93d061fd43eaf14c5fc8c73be52da15b-C23H26S1-0-1 + + + +formula: C23 H26 S1 + + + +free energy = -35095.28371038775 eV + +36 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/36.pdf}} + +\vspace{1cm} + + +aa3de124b222759aaea1463f6143873b-C23H26S1-0-1 + + + +formula: C23 H26 S1 + + + +free energy = -35095.16063362286 eV + +37 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/37.pdf}} + +\vspace{1cm} + + +b1540153219ab9844a80bc3ef4d5b560-C23H26S1-1-2 + + + +formula: C23 H26 S1 + + + +free energy = -35090.75581420064 eV + +38 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/38.pdf}} + +\vspace{1cm} + + +4e5d4774df9d01e93db3763faa6e7914-C23H26S1-1-2 + + + +formula: C23 H26 S1 + + + +free energy = -35090.36948689221 eV + +39 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/39.pdf}} + +\vspace{1cm} + + +443639a41f47d07b41b9f1b4150e7e7b-C10H15O1-m1-1 + + + +formula: C10 H15 O1 + + + +free energy = -12656.20077055078 eV + +40 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/40.pdf}} + +\vspace{1cm} + + +3adeb22f2907b178f6b106fc59646ad1-C10H15O1-0-2 + + + +formula: C10 H15 O1 + + + +free energy = -12654.411933632726 eV + +41 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/41.pdf}} + +\vspace{1cm} + + +3222ddd6de9a68c13c9a14952aabf24e-C10H15O1-1-1 + + + +formula: C10 H15 O1 + + + +free energy = -12649.646675455047 eV + +42 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/42.pdf}} + +\vspace{1cm} + + +7365841bed8fe73e132c46960e8c23e4-H2O1-m1-2 + + + +formula: H2 O1 + + + +free energy = -2079.9357742987468 eV + +43 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/43.pdf}} + +\vspace{1cm} + + +aab0ea89ff9b4e27da78126a6c80cbf0-H2O1-0-1 + + + +formula: H2 O1 + + + +free energy = -2079.873783910513 eV + +44 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/44.pdf}} + +\vspace{1cm} + + +f157c4b8fe094772f3a425e5dfc57294-H2O1-1-2 + + + +formula: H2 O1 + + + +free energy = -2069.641064122109 eV + +45 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/45.pdf}} + +\vspace{1cm} + + +a9e891e561bce34cf4b49b6c7c2347c6-C6H11O2-m1-1 + + + +formula: C6 H11 O2 + + + +free energy = -10495.525058434632 eV + +46 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/46.pdf}} + +\vspace{1cm} + + +0701a0edad7058c8168456de1c92e8e0-C6H11O2-0-2 + + + +formula: C6 H11 O2 + + + +free energy = -10490.532211506848 eV + +47 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/47.pdf}} + +\vspace{1cm} + + +a7acbdb77305196bf789ae0c875d0f19-C6H5-m1-1 + + + +formula: C6 H5 + + + +free energy = -6301.668558148871 eV + +48 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/48.pdf}} + +\vspace{1cm} + + +c9636169ed9efe63dd613dad22c5b63f-C6H5-0-2 + + + +formula: C6 H5 + + + +free energy = -6298.918176108165 eV + +49 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/49.pdf}} + +\vspace{1cm} + + +ace426ad373f83a93c83458cf66b8866-C6H5-1-1 + + + +formula: C6 H5 + + + +free energy = -6292.336186550749 eV + +50 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/50.pdf}} + +\vspace{1cm} + + +bf845e308e61c1f4aeb1392daf2af740-C13H13S1-m1-1 + + + +formula: C13 H13 S1 + + + +free energy = -24522.92145073565 eV + +51 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/51.pdf}} + +\vspace{1cm} + + +60e63c69581d9af4f0f33039786cea50-C13H13S1-0-2 + + + +formula: C13 H13 S1 + + + +free energy = -24520.406660494013 eV + +52 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/52.pdf}} + +\vspace{1cm} + + +3bd4ab1135b39ff25d94beb51dd6c503-C13H13S1-1-1 + + + +formula: C13 H13 S1 + + + +free energy = -24515.459113537858 eV + +53 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/53.pdf}} + +\vspace{1cm} + + +3ce8bce066bf652195a8784f7b4f04af-C10H19O2-0-2 + + + +formula: C10 H19 O2 + + + +free energy = -14765.933688558556 eV + +54 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/54.pdf}} + +\vspace{1cm} + + +fb79683b7f312a9cf81ffef86594feba-C1H3-m1-1 + + + +formula: C1 H3 + + + +free energy = -1085.1504582113405 eV + +55 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/55.pdf}} + +\vspace{1cm} + + +5f85470c393edc87393085bba5b03428-C1H3-0-2 + + + +formula: C1 H3 + + + +free energy = -1083.2057568833218 eV + +56 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/56.pdf}} + +\vspace{1cm} + + +cb48ad765690f27a672c38acf77f12c2-C1H3-1-1 + + + +formula: C1 H3 + + + +free energy = -1075.5798123450227 eV + +57 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/57.pdf}} + +\vspace{1cm} + + +6203000256b3f131b82ca6c273f2fe5d-C10H13-m1-1 + + + +formula: C10 H13 + + + +free energy = -10577.002303712354 eV + +58 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/58.pdf}} + +\vspace{1cm} + + +82ca46cecd8439a6d7fbd87eea2c54b9-C10H13-0-2 + + + +formula: C10 H13 + + + +free energy = -10574.252479640065 eV + +59 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/59.pdf}} + +\vspace{1cm} + + +705bbb0e5307bd961891ae2334cee3dc-C10H13-1-1 + + + +formula: C10 H13 + + + +free energy = -10567.753851087275 eV + +60 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/60.pdf}} + +\vspace{1cm} + + +31c2af8f1605817c400250991fe7fefe-C4F9H1O3S1-0-1 + + + +formula: C4 F9 H1 O3 S1 + + + +free energy = -45596.45874412551 eV + +61 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/61.pdf}} + +\vspace{1cm} + + +2699beb3fcbcc2b0075c9dd8f7b304cb-C6H12O1-m1-2 + + + +formula: C6 H12 O1 + + + +free energy = -8461.167846444436 eV + +62 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/62.pdf}} + +\vspace{1cm} + + +3464f250ed90621ea6a9588d1705d205-C6H12O1-0-1 + + + +formula: C6 H12 O1 + + + +free energy = -8460.378491681187 eV + +63 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/63.pdf}} + +\vspace{1cm} + + +86511bda5d0f000e5685e9c2e9e7be53-C6H12O1-1-2 + + + +formula: C6 H12 O1 + + + +free energy = -8452.458390250442 eV + +64 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/64.pdf}} + +\vspace{1cm} + + +7d4d03d7557395fd35364ec1cfc6add2-C10H14O1-m1-2 + + + +formula: C10 H14 O1 + + + +free energy = -12640.406719740313 eV + +65 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/65.pdf}} + +\vspace{1cm} + + +8b8c577519e77347f52c970bc6f2bcdd-C10H14O1-m1-2 + + + +formula: C10 H14 O1 + + + +free energy = -12641.256465891402 eV + +66 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/66.pdf}} + +\vspace{1cm} + + +1d64d1a96b5db50b9fdf583dc18f90cf-C10H14O1-0-1 + + + +formula: C10 H14 O1 + + + +free energy = -12639.959950636323 eV + +67 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/67.pdf}} + +\vspace{1cm} + + +62e08d5119480b03357cc679f310168d-C10H14O1-0-1 + + + +formula: C10 H14 O1 + + + +free energy = -12639.27597622435 eV + +68 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/68.pdf}} + +\vspace{1cm} + + +e9382c788338f71391524d940b96d69e-C10H14O1-1-2 + + + +formula: C10 H14 O1 + + + +free energy = -12633.32607140473 eV + +69 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/69.pdf}} + +\vspace{1cm} + + +b1d9b641790ab43d18cb8d4637b7fae0-C10H14O1-1-2 + + + +formula: C10 H14 O1 + + + +free energy = -12632.159367732 eV + +70 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/70.pdf}} + +\vspace{1cm} + + +baa58da5bef49709d3547c41ce3f3b80-C10H20O2-m1-2 + + + +formula: C10 H20 O2 + + + +free energy = -14784.023911463151 eV + +71 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/71.pdf}} + +\vspace{1cm} + + +0aade5ee5263fd1ad77490688fb37d0e-C10H20O2-0-1 + + + +formula: C10 H20 O2 + + + +free energy = -14783.726373365138 eV + +72 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/72.pdf}} + +\vspace{1cm} + + +836983f55a91c9ab5862a0055ec0cfc7-C10H20O2-1-2 + + + +formula: C10 H20 O2 + + + +free energy = -14775.723381925452 eV + +73 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/73.pdf}} + +\vspace{1cm} + + +66beeac3fabe98289969e2e3a67dbb9b-C6H12O2-m1-2 + + + +formula: C6 H12 O2 + + + +free energy = -10508.903171007532 eV + +74 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/74.pdf}} + +\vspace{1cm} + + +a4c65f243bb0eef36b5ee0a359560871-C6H12O2-0-1 + + + +formula: C6 H12 O2 + + + +free energy = -10508.508960790188 eV + +75 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/75.pdf}} + +\vspace{1cm} + + +645243313f5f8643fd55474ab64cb472-C6H12O2-1-2 + + + +formula: C6 H12 O2 + + + +free energy = -10500.127095795115 eV + +76 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/76.pdf}} + +\vspace{1cm} + + +4631a22ef2bcb97a654a1c7308b02b01-C18H16S1-m1-2 + + + +formula: C18 H16 S1 + + + +free energy = -29752.392570521068 eV + +77 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/77.pdf}} + +\vspace{1cm} + + +646e41d216c60e02a2f50b62e29b8b88-C18H16S1-0-1 + + + +formula: C18 H16 S1 + + + +free energy = -29751.116989155034 eV + +78 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/78.pdf}} + +\vspace{1cm} + + +8ae04139e8d0f83b3debcf8914dddac0-C18H16S1-1-2 + + + +formula: C18 H16 S1 + + + +free energy = -29746.72512387199 eV + +79 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/79.pdf}} + +\vspace{1cm} + + +4e44c76f3402f4df60740ca2d259a81f-C6H6-m1-2 + + + +formula: C6 H6 + + + +free energy = -6317.511162066979 eV + +80 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/80.pdf}} + +\vspace{1cm} + + +a502ffe15bce2adb300daebdd27f0aa0-C6H6-0-1 + + + +formula: C6 H6 + + + +free energy = -6317.187206843345 eV + +81 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/81.pdf}} + +\vspace{1cm} + + +3be576635549e34409774a618e64528f-C6H6-1-2 + + + +formula: C6 H6 + + + +free energy = -6309.593168108404 eV + +82 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/82.pdf}} + +\vspace{1cm} + + +f357352f5dd5488b54d50242d228ed6d-C4F9O3S1-m1-1 + + + +formula: C4 F9 O3 S1 + + + +free energy = -45585.08102933094 eV + +83 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/83.pdf}} + +\vspace{1cm} + + +3408c7952fc067d2195bb7e61537e62c-C4F9O3S1-0-2 + + + +formula: C4 F9 O3 S1 + + + +free energy = -45578.181931710256 eV + +84 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/84.pdf}} + +\vspace{1cm} + + +317a0de8932121ca8335f53d8f14470d-H1O1-m1-1 + + + +formula: H1 O1 + + + +free energy = -2065.299026201689 eV + +85 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/85.pdf}} + +\vspace{1cm} + + +367103e07e78cd55a4b80413679fda7e-H1O1-0-2 + + + +formula: H1 O1 + + + +free energy = -2061.317161293273 eV + +86 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/86.pdf}} + +\vspace{1cm} + + +4f8d27bf6f0c6b33159db4265cc7b320-C10H13O1-m1-1 + + + +formula: C10 H13 O1 + + + +free energy = -12626.45398240735 eV + +87 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/87.pdf}} + +\vspace{1cm} + + +df1b0273442db364220e3662c74307eb-C10H13O1-0-2 + + + +formula: C10 H13 O1 + + + +free energy = -12622.941258162959 eV + +88 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/88.pdf}} + +\vspace{1cm} + + +936a8f949a3daa0870e76108ec451a95-C10H13O1-1-1 + + + +formula: C10 H13 O1 + + + +free energy = -12616.26200886817 eV + +89 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/89.pdf}} + +\vspace{1cm} + + +6b8a7a850d80cbad493217fee671819b-C4H10O1-m1-2 + + + +formula: C4 H10 O1 + + + +free energy = -6354.820208237991 eV + +90 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/90.pdf}} + +\vspace{1cm} + + +24bbd018781f482c1635b08033fdf846-C4H10O1-0-1 + + + +formula: C4 H10 O1 + + + +free energy = -6354.9536163168395 eV + +91 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/91.pdf}} + +\vspace{1cm} + + +bd9c9503f0b02c355efa8d73661b511e-C4H10O1-1-2 + + + +formula: C4 H10 O1 + + + +free energy = -6346.851033905848 eV + +92 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/92.pdf}} + +\vspace{1cm} + + +edad4c3a7b053b636810e3cb94f17981-C10H15O1-1-1 + + + +formula: C10 H15 O1 + + + +free energy = -12649.200363190526 eV + +93 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/93.pdf}} + +\vspace{1cm} + + +414f98c42405835d32167a01608750ef-C4H8-m1-2 + + + +formula: C4 H8 + + + +free energy = -4274.911027178526 eV + +94 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/94.pdf}} + +\vspace{1cm} + + +2f7e19a6344da517348e59f408a1aa99-C4H8-0-1 + + + +formula: C4 H8 + + + +free energy = -4275.013705385731 eV + +95 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/95.pdf}} + +\vspace{1cm} + + +5d58a6a0200f85eff7a5f9f805a8e35f-C4H8-1-2 + + + +formula: C4 H8 + + + +free energy = -4267.676635895219 eV + +96 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/96.pdf}} + +\vspace{1cm} + + +206ec2213d7388c5e8bf2cff81dedac7-C3H6O1-m1-2 + + + +formula: C3 H6 O1 + + + +free energy = -5254.7991961421185 eV + +97 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/97.pdf}} + +\vspace{1cm} + + +9e7acc5b302a48411607db0a9234396f-C3H6O1-0-1 + + + +formula: C3 H6 O1 + + + +free energy = -5254.247362822989 eV + +98 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/98.pdf}} + +\vspace{1cm} + + +f4194a8bb7a342bbab4eece7c3820fa8-C3H6O1-1-2 + + + +formula: C3 H6 O1 + + + +free energy = -5246.253732861297 eV + +99 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/99.pdf}} + +\vspace{1cm} + + +ce487751a2c5c0b104116e3240cf5042-C6H12O1-m1-2 + + + +formula: C6 H12 O1 + + + +free energy = -8459.259346530696 eV + +100 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/100.pdf}} + +\vspace{1cm} + + +9480763ced3710477010a038211b937f-C6H12O1-0-1 + + + +formula: C6 H12 O1 + + + +free energy = -8458.040606928937 eV + +101 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/101.pdf}} + +\vspace{1cm} + + +a07777285e002c40f6d2107272819986-C6H12O1-1-2 + + + +formula: C6 H12 O1 + + + +free energy = -8451.877481630954 eV + +102 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/102.pdf}} + +\vspace{1cm} + + +None + + + +formula: E1 + + + +free energy = 0.0 eV + +103 +\raisebox{-.5\height}{\includegraphics[scale=0.15]{mol_pictures/103.pdf}} + +\vspace{1cm} +\end{document} \ No newline at end of file diff --git a/euvl_phase1_test/worker_payload.json b/euvl_phase1_test/worker_payload.json new file mode 100644 index 0000000..88e4609 --- /dev/null +++ b/euvl_phase1_test/worker_payload.json @@ -0,0 +1 @@ +{"@module": "HiPRGen.reaction_filter_payloads", "@class": "WorkerPayload", "@version": null, "bucket_db_file": "./scratch/euvl_phase1_test/buckets.sqlite", "reaction_decision_tree": [[{"@module": "HiPRGen.reaction_questions", "@class": "is_redox_reaction", "@version": null}, [[{"@module": "HiPRGen.reaction_questions", "@class": "too_many_reactants_or_products", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}], [{"@module": "HiPRGen.reaction_questions", "@class": "dcharge_too_large", "@version": null}, {"@module": 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"@version": null, "value": -1}]], "params": {"temperature": 298.15, "electron_free_energy": 0.0, "electron_species": 103}, "logging_decision_tree": [[{"@module": "HiPRGen.reaction_questions", "@class": "is_redox_reaction", "@version": null}, [[{"@module": "HiPRGen.reaction_questions", "@class": "too_many_reactants_or_products", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}], [{"@module": "HiPRGen.reaction_questions", "@class": "dcharge_too_large", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}], [{"@module": "HiPRGen.reaction_questions", "@class": "reactant_and_product_not_isomorphic", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}], [{"@module": "HiPRGen.reaction_questions", "@class": "add_electron_species", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}], 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"HiPRGen.reaction_questions", "@class": "star_count_diff_above_threshold", "@version": null, "threshold": 4}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}], [{"@module": "HiPRGen.reaction_questions", "@class": "reaction_is_radical_separation", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}], [{"@module": "HiPRGen.reaction_questions", "@class": "reaction_is_charge_separation", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}], [{"@module": "HiPRGen.reaction_questions", "@class": "fragment_matching_found", "@version": null}, [[{"@module": "HiPRGen.reaction_questions", "@class": "single_reactant_double_product_ring_close", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}], [{"@module": "HiPRGen.reaction_questions", "@class": "dG_above_threshold", "@version": null, "threshold": 0.0, "free_energy_type": "free_energy", "constant_barrier": 0.0, "barrier_factor": 0}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": 1}], [{"@module": "HiPRGen.reaction_questions", "@class": "reaction_default_true", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}]]], [{"@module": "HiPRGen.reaction_questions", "@class": "reaction_default_true", "@version": null}, {"@module": "HiPRGen.constants", "@class": "Terminal", "@version": null, "value": -1}]]} \ No newline at end of file diff --git a/test.py b/test.py index ae911b2..255e7bb 100644 --- a/test.py +++ b/test.py @@ -3,31 +3,38 @@ import subprocess import sqlite3 import pickle +import copy - +import matplotlib.colors as mcolors from HiPRGen.network_loader import NetworkLoader from HiPRGen.initial_state import find_mol_entry_from_xyz_and_charge from monty.serialization import loadfn, dumpfn -from HiPRGen.species_filter import species_filter +from HiPRGen.species_filter import species_filter, add_electron_species from HiPRGen.bucketing import bucket from HiPRGen.report_generator import ReportGenerator from HiPRGen.initial_state import insert_initial_state from HiPRGen.constants import ROOM_TEMP, Terminal -from HiPRGen.reaction_filter_payloads import ( - DispatcherPayload, - WorkerPayload -) +from HiPRGen.reaction_filter_payloads import DispatcherPayload, WorkerPayload from HiPRGen.species_questions import ( mg_species_decision_tree, li_species_decision_tree, + nonmetal_species_decision_tree, + euvl_species_decision_tree, positive_penalty, - species_default_true + species_default_true, + bfo_species_decision_tree ) from HiPRGen.reaction_questions import ( default_reaction_decision_tree, - + bfo_reaction_decision_tree, + bfo_logging_reaction_decision_tree, + co2_reaction_decision_tree, + euvl_phase1_reaction_decision_tree, + euvl_phase1_reaction_logging_tree, + euvl_phase2_reaction_decision_tree, + euvl_phase2_logging_tree ) from HiPRGen.mc_analysis import ( @@ -35,10 +42,11 @@ species_report, Pathfinding, SimulationReplayer, - generate_pathway_report, + pathway_report, sink_report, consumption_report, - redox_report + redox_report, + final_state_report, ) # Since HiPRGen uses an end-to-end testing approach rather than testing @@ -63,10 +71,11 @@ number_of_threads = sys.argv[1] + class bcolors: - PASS = '\u001b[32;1m' - FAIL = '\u001b[31;1m' - ENDC = '\u001b[0m' + PASS = "\u001b[32;1m" + FAIL = "\u001b[31;1m" + ENDC = "\u001b[0m" # HiPRGen is organized as a pipeline, where all the relevent data is @@ -76,28 +85,27 @@ class bcolors: # set and a magnesium set. Since the lithium test set is older, we shall # document that instead of the mg test set. -if os.path.isdir('./scratch'): - subprocess.run(['rm', '-r', './scratch']) - -subprocess.run(['mkdir', './scratch']) +if os.path.isdir("./scratch"): + subprocess.run(["rm", "-r", "./scratch"]) +subprocess.run(["mkdir", "./scratch"]) def li_test(): - # folder is the where we store all our intermediate databases - folder = './scratch/li_test' - subprocess.run(['mkdir', folder ]) + folder = "./scratch/li_test" + subprocess.run(["mkdir", folder]) # The initial input to the pipeline is a list of LIBE or MADEIRA # dataset entries. We provide two examples in the data foloder. - mol_json = './data/ronald_LIBE.json' + mol_json = "./data/ronald_LIBE.json" database_entries = loadfn(mol_json) # The first step of the HiPRGen pipeline is passing the input molecules # through the species decision tree to discard molecules. species_decision_tree = li_species_decision_tree + params = {"temperature": ROOM_TEMP, "electron_free_energy": -1.4} # There is one non-local part of species filtering: we consider two # molecules to be equivalent if they have the same total charge, @@ -111,18 +119,16 @@ def li_test(): mol_entries = species_filter( database_entries, - mol_entries_pickle_location=folder + '/mol_entries.pickle', - species_report=folder + '/unfiltered_species_report.tex', + mol_entries_pickle_location=folder + "/mol_entries.pickle", + species_report=folder + "/unfiltered_species_report.tex", species_decision_tree=species_decision_tree, - coordimer_weight=lambda mol: (mol.penalty, mol.solvation_free_energy), + coordimer_weight=lambda mol: (mol.penalty, mol.solvation_correction + mol.get_free_energy(params["temperature"])), ) - # Once we have generated our molecule list, we generate the bucket database # which is how we break up the reaction filtering amongst all avaliable workers. # It gets stored in the buckets.sqlite database. - bucket(mol_entries, folder + '/buckets.sqlite') - + bucket(mol_entries, folder + "/buckets.sqlite") # Reaction filtering is paralellized using MPI, so we need to spawn # an MPI instance to run it. This is why we can't just start @@ -138,41 +144,35 @@ def li_test(): # The reaction decision trees are constructed in # HiPRGen.reaction_questions - params = { - 'temperature' : ROOM_TEMP, - 'electron_free_energy' : -1.4 - } - dispatcher_payload = DispatcherPayload( - folder + '/buckets.sqlite', - folder + '/rn.sqlite', - folder + '/reaction_report.tex' + folder + "/buckets.sqlite", + folder + "/rn.sqlite", + folder + "/reaction_report.tex", ) worker_payload = WorkerPayload( - folder + '/buckets.sqlite', + folder + "/buckets.sqlite", default_reaction_decision_tree, params, - Terminal.DISCARD + Terminal.DISCARD, ) - # The dispatcher and worker payloads are passed through the MPI barrier # as JSON blobs dispatcher_payload and worker_payload - dumpfn(dispatcher_payload, folder + '/dispatcher_payload.json') - dumpfn(worker_payload, folder + '/worker_payload.json') + dumpfn(dispatcher_payload, folder + "/dispatcher_payload.json") + dumpfn(worker_payload, folder + "/worker_payload.json") subprocess.run( [ - 'mpirun', - '--use-hwthread-cpus', - '-n', + "mpirun", + "--use-hwthread-cpus", + "-n", number_of_threads, - 'python', - 'run_network_generation.py', - folder + '/mol_entries.pickle', - folder + '/dispatcher_payload.json', - folder + '/worker_payload.json' + "python", + "run_network_generation.py", + folder + "/mol_entries.pickle", + folder + "/dispatcher_payload.json", + folder + "/worker_payload.json", ] ) @@ -181,61 +181,48 @@ def li_test(): # help find the indices of specific species to be used in the initial # condition for propagating trajectories and/or trajectory analysis. Li_plus_id = find_mol_entry_from_xyz_and_charge( - mol_entries, - './xyz_files/Li.xyz', - 1) - - EC_id = find_mol_entry_from_xyz_and_charge( - mol_entries, - './xyz_files/EC.xyz', - 0) + mol_entries, "./xyz_files/Li.xyz", 1 + ) - LEDC_id = find_mol_entry_from_xyz_and_charge( - mol_entries, - './xyz_files/LEDC.xyz', - 0) + EC_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/EC.xyz", 0) + LEDC_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/LEDC.xyz", 0) # After generating a reaction network, it is stored in rn.sqlite. We # use Monte Carlo simulation to interrogate the network, and for that # we need to define an initial condition. - initial_state = { - Li_plus_id : 30, - EC_id : 30 - } + initial_state = {Li_plus_id: 30, EC_id: 30} # The initial state and the trajectories (after simulation) are stored in # a seperate database from the network, here called initial_state.sqlite. # This facilitates running multiple independent simulations of the same # network with different initial conditions at the same time, if desired. - insert_initial_state(initial_state, mol_entries, folder + '/initial_state.sqlite') - + insert_initial_state(initial_state, mol_entries, folder + "/initial_state.sqlite") # GMC is a high performance reaction network Monte Carlo simulator using the # Gillespie algorithm: https://github.com/BlauGroup/RNMC. Here we run 1000 # trajectories each of 200 steps. - subprocess.run([ - 'GMC', - '--reaction_database=' + folder + '/rn.sqlite', - '--initial_state_database=' + folder + '/initial_state.sqlite', - '--number_of_simulations=1000', - '--base_seed=1000', - '--thread_count=' + number_of_threads, - '--step_cutoff=200' - ]) + subprocess.run( + [ + "GMC", + "--reaction_database=" + folder + "/rn.sqlite", + "--initial_state_database=" + folder + "/initial_state.sqlite", + "--number_of_simulations=1000", + "--base_seed=1000", + "--thread_count=" + number_of_threads, + "--step_cutoff=200", + ] + ) # The network loader builds a python object around a reaction network # and the molecules to make it easier to use them. network_loader = NetworkLoader( - folder + '/rn.sqlite', - folder + '/mol_entries.pickle', - folder + '/initial_state.sqlite' - ) - - network_loader.load_trajectories() - network_loader.load_initial_state() - + folder + "/rn.sqlite", + folder + "/mol_entries.pickle", + folder + "/initial_state.sqlite", + ) + network_loader.load_initial_state_and_trajectories() # HiPRGen has analysis tools to understand what happened in our simulation. # The output files are written into the same folder in which the reaction @@ -244,31 +231,23 @@ def li_test(): # This report is empty, but we use it to generate the molecule pictures. # This is an expensive operation, so we only want do do it once. report_generator = ReportGenerator( - network_loader.mol_entries, - folder + '/dummy.tex', - rebuild_mol_pictures=True) - + network_loader.mol_entries, folder + "/dummy.tex", rebuild_mol_pictures=True + ) # The tally report shows reactions sorted by the number of times fired. - reaction_tally_report( - network_loader, - folder + '/reaction_tally.tex' - ) + reaction_tally_report(network_loader, folder + "/reaction_tally.tex") # Run `pdflatex reaction_tally.tex` in `scratch/li_test` to generate # the tally report PDF. - # The species report shows every specie in the network and their IDs. - species_report(network_loader, folder + '/species_report.tex') + species_report(network_loader, folder + "/species_report.tex") # Run `pdflatex species_report.tex` in `scratch/li_test` to generate # the species report PDF. - # Pathfinding is a central goal of HiPRGen / GMC. See mc_analysis.py for # further documentation of the Pathfinding class. pathfinding = Pathfinding(network_loader) - # The pathway report shows all the ways that a target species was # produced in the simulation trajectories, where each simulation only # contributes the shortest path responsible for the first formation @@ -276,31 +255,25 @@ def li_test(): # pathway frequency, but instead here we sort by pathway cost. Note # that the test network has ~5000 reactions while production networks # have between 50-100 million reactions. - generate_pathway_report( - pathfinding, - LEDC_id, - folder + '/LEDC_pathways.tex', - sort_by_frequency=False + pathway_report( + pathfinding, LEDC_id, folder + "/LEDC_pathways.tex", sort_by_frequency=False ) # Run `pdflatex LEDC_pathways.tex` in `scratch/li_test` to generate # the LEDC pathway report PDF. - # The simulation replayer sweeps through all trajectories in order # to extract additional information that is used for consumption # reports and sink reports. simulation_replayer = SimulationReplayer(network_loader) - # The consumption report shows reactions which consumed a target # species, sorted by the number of times the reaction fired. - consumption_report(simulation_replayer, - LEDC_id, - folder + '/LEDC_consumption_report.tex') + consumption_report( + simulation_replayer, LEDC_id, folder + "/LEDC_consumption_report.tex" + ) # Run `pdflatex LEDC_consumption_report.tex` in `scratch/li_test` # to generate the LEDC consumption report PDF. - # The sink report shows species which have a production to # consumption ratio of greater than 3/2 and which have an expected # value above 0.1. These are two of the three heuristic criteria @@ -312,33 +285,23 @@ def li_test(): # sink report will show that only Li2CO3, C2H4, LiEDC-, and DLEMC # have sufficiently low-cost paths to pass the third criteria and # thus to be considered products of the test network used here. - sink_report(simulation_replayer, folder + '/sink_report.tex') + sink_report(simulation_replayer, folder + "/sink_report.tex") # Run `pdflatex sink_report.tex` in `scratch/li_test` to generate # the sink report PDF. - - tests_passed = True + print("Number of species:", network_loader.number_of_species) if network_loader.number_of_species == 190: - print(bcolors.PASS + - "li_test: correct number of species" + - bcolors.ENDC) + print(bcolors.PASS + "li_test: correct number of species" + bcolors.ENDC) else: - print(bcolors.FAIL + - "li_test: correct number of species" + - bcolors.ENDC) + print(bcolors.FAIL + "li_test: correct number of species" + bcolors.ENDC) tests_passed = False - - + print("Number of reactions:", network_loader.number_of_reactions) if network_loader.number_of_reactions == 4921: - print(bcolors.PASS + - "li_test: correct number of reactions" + - bcolors.ENDC) + print(bcolors.PASS + "li_test: correct number of reactions" + bcolors.ENDC) else: - print(bcolors.FAIL + - "li_test: correct number of reactions" + - bcolors.ENDC) + print(bcolors.FAIL + "li_test: correct number of reactions" + bcolors.ENDC) tests_passed = False return tests_passed @@ -346,291 +309,730 @@ def li_test(): def mg_test(): + folder = "./scratch/mg_test" + subprocess.run(["mkdir", folder]) - folder = './scratch/mg_test' - subprocess.run(['mkdir', folder ]) - - mol_json = './data/sam_G2.json' + mol_json = "./data/sam_G2.json" species_decision_tree = mg_species_decision_tree database_entries = loadfn(mol_json) - - + params = {"temperature": ROOM_TEMP, "electron_free_energy": -2.06} mol_entries = species_filter( database_entries, - folder + '/mol_entries.pickle', - folder + '/unfiltered_species_report.tex', + folder + "/mol_entries.pickle", + folder + "/unfiltered_species_report.tex", species_decision_tree, - coordimer_weight=lambda mol: (mol.penalty, mol.solvation_free_energy) + coordimer_weight=lambda mol: (mol.penalty, mol.solvation_correction + mol.get_free_energy(params["temperature"])), ) - - - bucket(mol_entries, folder + '/buckets.sqlite') - + bucket(mol_entries, folder + "/buckets.sqlite") dispatcher_payload = DispatcherPayload( - folder + '/buckets.sqlite', - folder + '/rn.sqlite', - folder + '/reaction_report.tex' + folder + "/buckets.sqlite", + folder + "/rn.sqlite", + folder + "/reaction_report.tex", ) worker_payload = WorkerPayload( - folder + '/buckets.sqlite', + folder + "/buckets.sqlite", default_reaction_decision_tree, - { - 'temperature' : ROOM_TEMP, - 'electron_free_energy' : -2.06 - }, - Terminal.DISCARD + params, + Terminal.DISCARD, ) - - dumpfn(dispatcher_payload, folder + '/dispatcher_payload.json') - dumpfn(worker_payload, folder + '/worker_payload.json') + dumpfn(dispatcher_payload, folder + "/dispatcher_payload.json") + dumpfn(worker_payload, folder + "/worker_payload.json") subprocess.run( [ - 'mpiexec', - '--use-hwthread-cpus', - '-n', + "mpiexec", + "--use-hwthread-cpus", + "-n", number_of_threads, - 'python', - 'run_network_generation.py', - folder + '/mol_entries.pickle', - folder + '/dispatcher_payload.json', - folder + '/worker_payload.json' + "python", + "run_network_generation.py", + folder + "/mol_entries.pickle", + folder + "/dispatcher_payload.json", + folder + "/worker_payload.json", ] ) - mg_g2_plus_plus_id = find_mol_entry_from_xyz_and_charge( - mol_entries, - './xyz_files/mgg2.xyz', - 2) + mol_entries, "./xyz_files/mgg2.xyz", 2 + ) - c2h4_id = find_mol_entry_from_xyz_and_charge( - mol_entries, - './xyz_files/c2h4.xyz', - 0) + c2h4_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/c2h4.xyz", 0) - c2h6_id = find_mol_entry_from_xyz_and_charge( - mol_entries, - './xyz_files/c2h6.xyz', - 0) + c2h6_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/c2h6.xyz", 0) - initial_state = { - 33 : 30, - 81 : 30 - } + initial_state = {33: 30, 81: 30} + + insert_initial_state(initial_state, mol_entries, folder + "/initial_state.sqlite") + + subprocess.run( + [ + "GMC", + "--reaction_database=" + folder + "/rn.sqlite", + "--initial_state_database=" + folder + "/initial_state.sqlite", + "--number_of_simulations=1000", + "--base_seed=1000", + "--thread_count=" + number_of_threads, + "--step_cutoff=200", + ] + ) + network_loader = NetworkLoader( + folder + "/rn.sqlite", + folder + "/mol_entries.pickle", + folder + "/initial_state.sqlite", + ) - insert_initial_state(initial_state, mol_entries, folder + '/initial_state.sqlite') + network_loader.load_initial_state_and_trajectories() + report_generator = ReportGenerator( + network_loader.mol_entries, folder + "/dummy.tex", rebuild_mol_pictures=True + ) - subprocess.run([ - 'GMC', - '--reaction_database=' + folder + '/rn.sqlite', - '--initial_state_database=' + folder + '/initial_state.sqlite', - '--number_of_simulations=1000', - '--base_seed=1000', - '--thread_count=' + number_of_threads, - '--step_cutoff=200' - ]) + reaction_tally_report(network_loader, folder + "/reaction_tally.tex") + pathfinding = Pathfinding(network_loader) + pathway_report( + pathfinding, c2h6_id, folder + "/C2H6_pathways.tex", sort_by_frequency=False + ) - network_loader = NetworkLoader( - folder + '/rn.sqlite', - folder + '/mol_entries.pickle', - folder + '/initial_state.sqlite' - ) + pathway_report( + pathfinding, c2h4_id, folder + "/C2H4_pathways.tex", sort_by_frequency=False + ) + + species_report(network_loader, folder + "/species_report.tex") + + tests_passed = True + print("Number of species:", network_loader.number_of_species) + if network_loader.number_of_species == 83: + print(bcolors.PASS + "mg_test: correct number of species" + bcolors.ENDC) + else: + print(bcolors.FAIL + "mg_test: correct number of species" + bcolors.ENDC) + tests_passed = False + + print("Number of reactions:", network_loader.number_of_reactions) + if network_loader.number_of_reactions == 788: + print(bcolors.PASS + "mg_test: correct number of reactions" + bcolors.ENDC) + else: + print(bcolors.FAIL + "mg_test: correct number of reactions" + bcolors.ENDC) + tests_passed = False + + return tests_passed - network_loader.load_trajectories() - network_loader.load_initial_state() +# def flicho_test(): +# folder = "./scratch/flicho_test" +# subprocess.run(["mkdir", folder]) - report_generator = ReportGenerator( - network_loader.mol_entries, - folder + '/dummy.tex', - rebuild_mol_pictures=True) +# mol_json = "./data/flicho_test.json" +# database_entries = loadfn(mol_json) +# species_decision_tree = li_species_decision_tree + +# mol_entries = species_filter( +# database_entries, +# mol_entries_pickle_location=folder + "/mol_entries.pickle", +# species_report=folder + "/unfiltered_species_report.tex", +# species_decision_tree=species_decision_tree, +# coordimer_weight=lambda mol: (mol.penalty, mol.solvation_free_energy), +# ) + +# bucket(mol_entries, folder + "/buckets.sqlite") + +# params = {"temperature": ROOM_TEMP, "electron_free_energy": -1.4} + +# dispatcher_payload = DispatcherPayload( +# folder + "/buckets.sqlite", +# folder + "/rn.sqlite", +# folder + "/reaction_report.tex", +# ) + +# worker_payload = WorkerPayload( +# folder + "/buckets.sqlite", +# default_reaction_decision_tree, +# params, +# Terminal.DISCARD, +# ) + +# dumpfn(dispatcher_payload, folder + "/dispatcher_payload.json") +# dumpfn(worker_payload, folder + "/worker_payload.json") + +# subprocess.run( +# [ +# "mpirun", +# "--use-hwthread-cpus", +# "-n", +# number_of_threads, +# "python", +# "run_network_generation.py", +# folder + "/mol_entries.pickle", +# folder + "/dispatcher_payload.json", +# folder + "/worker_payload.json", +# ] +# ) + +# Li_plus_id = find_mol_entry_from_xyz_and_charge( +# mol_entries, "./xyz_files/Li.xyz", 1 +# ) + +# EC_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/EC.xyz", 0) - reaction_tally_report( - network_loader, - folder + '/reaction_tally.tex' +# initial_state = {Li_plus_id: 30, EC_id: 30} + +# insert_initial_state(initial_state, mol_entries, folder + "/initial_state.sqlite") + +# subprocess.run( +# [ +# "GMC", +# "--reaction_database=" + folder + "/rn.sqlite", +# "--initial_state_database=" + folder + "/initial_state.sqlite", +# "--number_of_simulations=1000", +# "--base_seed=1000", +# "--thread_count=" + number_of_threads, +# "--step_cutoff=200", +# ] +# ) + +# network_loader = NetworkLoader( +# folder + "/rn.sqlite", +# folder + "/mol_entries.pickle", +# folder + "/initial_state.sqlite", +# ) + +# network_loader.load_initial_state_and_trajectories() + +# report_generator = ReportGenerator( +# network_loader.mol_entries, folder + "/dummy.tex", rebuild_mol_pictures=True +# ) + +# coordination_report(network_loader, folder + "/coodination_report.tex", "Li1", 1) + +# decoordination_report( +# network_loader, folder + "/decoodination_report.tex", "Li1", 1 +# ) + +# return tests_passed + + +# def co2_test(): + +# folder = "./scratch/co2_test" +# subprocess.run(["mkdir", folder]) + +# mol_json = "./data/co2_summary_docs.json" +# database_entries = loadfn(mol_json) + +# species_decision_tree = nonmetal_species_decision_tree + +# mol_entries = species_filter( +# database_entries, +# mol_entries_pickle_location=folder + "/mol_entries.pickle", +# species_report=folder + "/unfiltered_species_report.tex", +# species_decision_tree=species_decision_tree, +# coordimer_weight=lambda mol: (mol.free_energy), +# species_logging_decision_tree=species_decision_tree, +# generate_unfiltered_mol_pictures=True, +# ) + +# bucket(mol_entries, folder + "/buckets.sqlite") + +# params = {"temperature": ROOM_TEMP, "electron_free_energy": -4.04} + +# dispatcher_payload = DispatcherPayload( +# folder + "/buckets.sqlite", +# folder + "/rn.sqlite", +# folder + "/reaction_report.tex", +# ) + +# worker_payload = WorkerPayload( +# folder + "/buckets.sqlite", +# co2_reaction_decision_tree, +# params, +# co2_reaction_decision_tree, +# ) + +# dumpfn(dispatcher_payload, folder + "/dispatcher_payload.json") +# dumpfn(worker_payload, folder + "/worker_payload.json") + +# subprocess.run( +# [ +# "mpirun", +# "--use-hwthread-cpus", +# "-n", +# number_of_threads, +# "python", +# "run_network_generation.py", +# folder + "/mol_entries.pickle", +# folder + "/dispatcher_payload.json", +# folder + "/worker_payload.json", +# ] +# ) + + return + + +def euvl_phase1_test(): + + folder = "./scratch/euvl_phase1_test" + subprocess.run(["mkdir", folder]) + + mol_json = "./data/euvl_test_set.json" + database_entries = loadfn(mol_json) + + species_decision_tree = euvl_species_decision_tree + + params = { + "temperature": ROOM_TEMP, + "electron_free_energy": 0.0, + } + + mol_entries = species_filter( + database_entries, + mol_entries_pickle_location=folder + "/mol_entries.pickle", + species_report=folder + "/unfiltered_species_report.tex", + species_decision_tree=species_decision_tree, + coordimer_weight=lambda mol: (mol.get_free_energy(params["temperature"])), + species_logging_decision_tree=species_decision_tree, + generate_unfiltered_mol_pictures=False, ) - pathfinding = Pathfinding(network_loader) + print(len(mol_entries), "initial mol entries") + + bucket(mol_entries, folder + "/buckets.sqlite") + + params["electron_species"] = len(mol_entries) + + mol_entries = add_electron_species( + mol_entries, + mol_entries_pickle_location=folder + "/mol_entries.pickle", + electron_free_energy=params["electron_free_energy"], + ) + + print(len(mol_entries), "final mol entries") + + dispatcher_payload = DispatcherPayload( + folder + "/buckets.sqlite", + folder + "/rn.sqlite", + folder + "/reaction_report.tex", + ) + + worker_payload = WorkerPayload( + folder + "/buckets.sqlite", + euvl_phase1_reaction_decision_tree, + params, + euvl_phase1_reaction_decision_tree + ) + + dumpfn(dispatcher_payload, folder + "/dispatcher_payload.json") + dumpfn(worker_payload, folder + "/worker_payload.json") + + subprocess.run( + [ + "mpirun", + "--use-hwthread-cpus", + "-n", + number_of_threads, + "python", + "run_network_generation.py", + folder + "/mol_entries.pickle", + folder + "/dispatcher_payload.json", + folder + "/worker_payload.json", + ] + ) + + tps_plus1_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/tps.xyz", 1) + phs_0_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/phs.xyz", 0) + tba_0_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/tba.xyz", 0) + nf_minus1_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/nf.xyz", -1) + + initial_state = {tps_plus1_id: 20, phs_0_id: 24, tba_0_id: 36, nf_minus1_id: 20} - generate_pathway_report( - pathfinding, - c2h6_id, - folder + '/C2H6_pathways.tex', - sort_by_frequency=False + insert_initial_state(initial_state, mol_entries, folder + "/initial_state.sqlite") + + subprocess.run( + [ + "GMC", + "--reaction_database=" + folder + "/rn.sqlite", + "--initial_state_database=" + folder + "/initial_state.sqlite", + "--number_of_simulations=1000", + "--base_seed=1000", + "--thread_count=" + number_of_threads, + "--step_cutoff=200", + "--energy_budget=92", + ] ) - generate_pathway_report( - pathfinding, - c2h4_id, - folder + '/C2H4_pathways.tex', - sort_by_frequency=False + network_loader = NetworkLoader( + folder + "/rn.sqlite", + folder + "/mol_entries.pickle", + folder + "/initial_state.sqlite", ) + network_loader.load_initial_state_and_trajectories() + report_generator = ReportGenerator( + network_loader.mol_entries, folder + "/dummy.tex", rebuild_mol_pictures=True + ) - species_report(network_loader, folder + '/species_report.tex') + reaction_tally_report(network_loader, folder + "/reaction_tally.tex", cutoff=10) + species_report(network_loader, folder + "/species_report.tex") + simulation_replayer = SimulationReplayer(network_loader) + final_state_report(simulation_replayer, folder + "/final_state_report.tex") tests_passed = True - if network_loader.number_of_species == 83: - print(bcolors.PASS + - "mg_test: correct number of species" + - bcolors.ENDC) + print("Number of species:", network_loader.number_of_species) + if network_loader.number_of_species == 104: + print(bcolors.PASS + "euvl_phase_1_test: correct number of species" + bcolors.ENDC) else: - print(bcolors.FAIL + - "mg_test: correct number of species" + - bcolors.ENDC) + print(bcolors.FAIL + "euvl_phase_1_test: correct number of species" + bcolors.ENDC) tests_passed = False - - - if network_loader.number_of_reactions == 788: - print(bcolors.PASS + - "mg_test: correct number of reactions" + - bcolors.ENDC) + print("Number of reactions:", network_loader.number_of_reactions) + if network_loader.number_of_reactions == 563: + print(bcolors.PASS + "euvl_phase_1_test: correct number of reactions" + bcolors.ENDC) else: - print(bcolors.FAIL + - "mg_test: correct number of reactions" + - bcolors.ENDC) + print(bcolors.FAIL + "euvl_phase_1_test: correct number of reactions" + bcolors.ENDC) tests_passed = False return tests_passed -def flicho_test(): - +def euvl_phase2_test(): - folder = './scratch/flicho_test' - subprocess.run(['mkdir', folder ]) + phase1_folder = "./euvl_phase1_test" + folder = "./scratch/euvl_phase2_test" + subprocess.run(["mkdir", folder]) - mol_json = './data/flicho_test.json' + mol_json = "./data/euvl_test_set.json" database_entries = loadfn(mol_json) - species_decision_tree = li_species_decision_tree + species_decision_tree = euvl_species_decision_tree + + params = { + "temperature": ROOM_TEMP+200.0, + "electron_free_energy": 0.0, + } mol_entries = species_filter( database_entries, - mol_entries_pickle_location=folder + '/mol_entries.pickle', - species_report=folder + '/unfiltered_species_report.tex', + mol_entries_pickle_location=folder + "/mol_entries.pickle", + species_report=folder + "/unfiltered_species_report.tex", species_decision_tree=species_decision_tree, - coordimer_weight=lambda mol: (mol.penalty, mol.solvation_free_energy), + coordimer_weight=lambda mol: (mol.get_free_energy(params["temperature"])), + species_logging_decision_tree=species_decision_tree, + generate_unfiltered_mol_pictures=False, ) + print(len(mol_entries), "initial mol entries") - bucket(mol_entries, folder + '/buckets.sqlite') + bucket(mol_entries, folder + "/buckets.sqlite") - params = { - 'temperature' : ROOM_TEMP, - 'electron_free_energy' : -1.4 - } + print(len(mol_entries), "final mol entries") dispatcher_payload = DispatcherPayload( - folder + '/buckets.sqlite', - folder + '/rn.sqlite', - folder + '/reaction_report.tex' + folder + "/buckets.sqlite", + folder + "/rn.sqlite", + folder + "/reaction_report.tex", ) worker_payload = WorkerPayload( - folder + '/buckets.sqlite', - default_reaction_decision_tree, + folder + "/buckets.sqlite", + euvl_phase2_reaction_decision_tree, params, - Terminal.DISCARD + euvl_phase2_logging_tree, ) - - dumpfn(dispatcher_payload, folder + '/dispatcher_payload.json') - dumpfn(worker_payload, folder + '/worker_payload.json') + dumpfn(dispatcher_payload, folder + "/dispatcher_payload.json") + dumpfn(worker_payload, folder + "/worker_payload.json") subprocess.run( [ - 'mpirun', - '--use-hwthread-cpus', - '-n', + "mpirun", + "--use-hwthread-cpus", + "-n", number_of_threads, - 'python', - 'run_network_generation.py', - folder + '/mol_entries.pickle', - folder + '/dispatcher_payload.json', - folder + '/worker_payload.json' + "python", + "run_network_generation.py", + folder + "/mol_entries.pickle", + folder + "/dispatcher_payload.json", + folder + "/worker_payload.json", ] ) - Li_plus_id = find_mol_entry_from_xyz_and_charge( - mol_entries, - './xyz_files/Li.xyz', - 1) - - EC_id = find_mol_entry_from_xyz_and_charge( - mol_entries, - './xyz_files/EC.xyz', - 0) + phase1_network_loader = NetworkLoader( + phase1_folder + "/rn.sqlite", + phase1_folder + "/mol_entries.pickle", + phase1_folder + f"/initial_state.sqlite", + ) + phase1_network_loader.load_initial_state_and_trajectories() + phase1_simulation_replayer = SimulationReplayer(phase1_network_loader) + phase1_simulation_replayer.compute_trajectory_final_states() - initial_state = { - Li_plus_id : 30, - EC_id : 30 - } + for seed in range(1000, 2000): - insert_initial_state(initial_state, mol_entries, folder + '/initial_state.sqlite') + initial_state = {} + for ii, val in enumerate(phase1_simulation_replayer.final_states[seed]): + if int(val) > 0: + initial_state[ii] = int(val) + insert_initial_state( + initial_state, + mol_entries, + folder + "/initial_state_" + str(seed) + ".sqlite", + ) - subprocess.run([ - 'GMC', - '--reaction_database=' + folder + '/rn.sqlite', - '--initial_state_database=' + folder + '/initial_state.sqlite', - '--number_of_simulations=1000', - '--base_seed=1000', - '--thread_count=' + number_of_threads, - '--step_cutoff=200' - ]) + subprocess.run( + [ + "GMC", + "--reaction_database=" + folder + "/rn.sqlite", + "--initial_state_database=" + folder + "/initial_state_" + str(seed) + ".sqlite", + "--number_of_simulations=" + number_of_threads, + "--base_seed=" + str(1000+(seed-1000)*int(number_of_threads)), + "--thread_count=" + number_of_threads, + "--step_cutoff=500", + ] + ) network_loader = NetworkLoader( - folder + '/rn.sqlite', - folder + '/mol_entries.pickle', - folder + '/initial_state.sqlite' - ) + folder + "/rn.sqlite", + folder + "/mol_entries.pickle", + ) - network_loader.load_trajectories() - network_loader.load_initial_state() + for seed in range(1000, 2000): + network_loader.set_initial_state_db(folder + "/initial_state_"+str(seed)+".sqlite") + network_loader.load_initial_state_and_trajectories() report_generator = ReportGenerator( - network_loader.mol_entries, - folder + '/dummy.tex', - rebuild_mol_pictures=True) + network_loader.mol_entries, folder + "/dummy.tex", rebuild_mol_pictures=True + ) + reaction_tally_report(network_loader, folder + "/reaction_tally.tex", cutoff=10) + species_report(network_loader, folder + "/species_report.tex") + simulation_replayer = SimulationReplayer(network_loader) + final_state_report(simulation_replayer, folder + "/final_state_report.tex") + + sink_report(simulation_replayer, folder + "/sink_report.tex") - coordination_report( - network_loader, - folder + '/coodination_report.tex', - 'Li1', - 1) + tps_plus1_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/tps.xyz", 1) + phs_0_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/phs.xyz", 0) + tba_0_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/tba.xyz", 0) + nf_minus1_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/nf.xyz", -1) + + phase2_important_species = [tps_plus1_id, phs_0_id, tba_0_id, nf_minus1_id] + + colors = list(mcolors.TABLEAU_COLORS.values()) + phase2_colorstyle_list = [] + for ii, species in enumerate(phase2_important_species): + phase2_colorstyle_list.append([colors[ii], "solid"]) + + ii = 0 + for mol_id in simulation_replayer.sinks: + if mol_id not in phase2_important_species: + phase2_important_species.append(mol_id) + phase2_colorstyle_list.append([colors[ii%len(colors)], "dashed"]) + ii += 1 + + phase1_important_species = copy.deepcopy(phase2_important_species) + phase1_important_species.append(len(mol_entries)) + + phase1_colorstyle_list = copy.deepcopy(phase2_colorstyle_list) + phase1_colorstyle_list.append(["black", "dotted"]) + + phase1_simulation_replayer.time_series_graph( + seeds=[i for i in range(1000,2000)], + species_of_interest=phase1_important_species, + path=os.path.join(folder,"phase1_time_series"), + custom_y_max=36, + custom_colorstyle_list=phase1_colorstyle_list + ) - decoordination_report( - network_loader, - folder + '/decoodination_report.tex', - 'Li1', - 1) + simulation_replayer.time_series_graph( + seeds=[i for i in range(1000,1000+1000*int(number_of_threads))], + species_of_interest=phase2_important_species, + path=os.path.join(folder,"phase2_time_series"), + custom_y_max=36, + custom_colorstyle_list=phase2_colorstyle_list + ) + tests_passed = True + print("Number of species:", network_loader.number_of_species) + if network_loader.number_of_species == 103: + print(bcolors.PASS + "euvl_phase_2_test: correct number of species" + bcolors.ENDC) + else: + print(bcolors.FAIL + "euvl_phase_2_test: correct number of species" + bcolors.ENDC) + tests_passed = False + print("Number of reactions:", network_loader.number_of_reactions) + if network_loader.number_of_reactions == 3912: + print(bcolors.PASS + "euvl_phase_2_test: correct number of reactions" + bcolors.ENDC) + else: + print(bcolors.FAIL + "euvl_phase_2_test: correct number of reactions" + bcolors.ENDC) + tests_passed = False return tests_passed +def bfo_test(): + + # folder is the where we store all our intermediate databases + folder = "./scratch/bfo_test" + subprocess.run(["mkdir", folder]) + + # Generated json from quacc calc + mol_json = "./data/bfo_hiprgen_dataset_test.json" + database_entries = loadfn(mol_json) + # step 1: pass the input molecules through the species decision tree to discard molecules + species_decision_tree = bfo_species_decision_tree + + params = {"temperature": ROOM_TEMP, "electron_free_energy": 0.0} + + # We consider two molecules to be equivalent if they have the same total charge, + # composition, and covalent bonds, even if they have different metal coordination + # ASK: mol.solvation_correction | AttributeError: 'MoleculeEntry' object has no attribute 'solvation_correction' + + mol_entries = species_filter( + database_entries, + mol_entries_pickle_location=folder + "/mol_entries.pickle", + species_report=folder + "/unfiltered_species_report.tex", + species_decision_tree=species_decision_tree, + coordimer_weight=lambda mol: (mol.penalty, mol.get_free_energy(params["temperature"])), + ) + + # continuing from where we stopped + with open(folder + "/mol_entries.pickle", "rb") as f: + mol_entries = pickle.load(f) + print(len(mol_entries)) + + bucket(mol_entries, folder + "/buckets.sqlite") + # 3rd parameter --> log file + dispatcher_payload = DispatcherPayload( + folder + "/buckets.sqlite", + folder + "/rn.sqlite", + folder + "/reaction_report.tex", + ) + # last parameter: make a custom decision tree to pick the filtered reactions, change later + worker_payload = WorkerPayload( + folder + "/buckets.sqlite", + bfo_reaction_decision_tree, + params, + bfo_reaction_decision_tree, + ) + + # The dispatcher and worker payloads are passed through the MPI barrier + # as JSON blobs dispatcher_payload and worker_payload + dumpfn(dispatcher_payload, folder + "/dispatcher_payload.json") + dumpfn(worker_payload, folder + "/worker_payload.json") + + # Running HiPRGen --> rn.sqlite + subprocess.run( + [ + "mpirun", + "--use-hwthread-cpus", + "-n", + number_of_threads, + "python", + "run_network_generation.py", + folder + "/mol_entries.pickle", + folder + "/dispatcher_payload.json", + folder + "/worker_payload.json", + ] + ) + + + # Load crn and generate mol pictures and species report + network_loader = NetworkLoader( + folder + "/rn.sqlite", + folder + "/mol_entries.pickle", + ) + + # Skip this if continue with RNMC, do it after + # generate mol pictures and make pdf + #report_generator = ReportGenerator( + # network_loader.mol_entries, folder + "/dummy.tex", rebuild_mol_pictures=True + #) + #species_report(network_loader, folder + "/species_report.tex") + + #### RNMC + + # find the indices of species to be used in the initial condition for propagating trajectories + bino3_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/bino3.xyz", 0) # init + moe_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/moe.xyz", 0) # init + #bimoe_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/bino31moe.xyz", 0) # step 1 target + bimoe_id = find_mol_entry_from_xyz_and_charge(mol_entries, "./xyz_files/bimoe.xyz", 0) # target + + # After generating a reaction network, it is stored in rn.sqlite. + # define an initial condition for Monte Carlo simulation | how much + initial_state = {bino3_id: 1, moe_id: 100} + + # The initial state and the trajectories (after simulation) are stored in + # a seperate database from the network, here called initial_state.sqlite. + insert_initial_state(initial_state, mol_entries, folder + "/initial_state.sqlite") + + # GMC is a high performance reaction network Monte Carlo simulator using the Gillespie algorithm: https://github.com/BlauGroup/RNMC + # we run 100 trajectories (small set of species) each of 10000 steps (dG>0, we allow loops) + subprocess.run( + [ + "GMC", + "--reaction_database=" + folder + "/rn.sqlite", + "--initial_state_database=" + folder + "/initial_state.sqlite", + "--number_of_simulations=100", + "--base_seed=1000", + "--thread_count=" + number_of_threads, + "--step_cutoff=10000", + ] + ) + + network_loader = NetworkLoader( + folder + "/rn.sqlite", + folder + "/mol_entries.pickle", + folder + "/initial_state.sqlite", + ) + + network_loader.load_initial_state_and_trajectories() + + # generate mol pictures and make pdf + report_generator = ReportGenerator( + network_loader.mol_entries, folder + "/dummy.tex", rebuild_mol_pictures=True + ) + + # The tally report shows reactions sorted by the number of times fired. + reaction_tally_report(network_loader, folder + "/reaction_tally.tex") + + # The species report shows every specie in the network and their IDs. + species_report(network_loader, folder + "/species_report.tex") + + # Pathfinding is a central goal of HiPRGen / GMC. + pathfinding = Pathfinding(network_loader) + # The pathway report shows all the ways that a target species was produced. + # We sort by pathway cost + pathway_report( + pathfinding, bimoe_id, folder + "/bimoe_pathways.tex", sort_by_frequency=False + ) + simulation_replayer = SimulationReplayer(network_loader) + # The consumption report shows reactions which consumed a target + # species, sorted by the number of times the reaction fired. + consumption_report( + simulation_replayer, bimoe_id, folder + "/bimoe_consumption_report.tex" + ) + + tests_passed = True + + return tests_passed tests = [ - mg_test, - li_test, - # flicho_test + # mg_test, + # li_test, + # flicho_test, + # co2_test, + # euvl_phase1_test, + #euvl_phase2_test, + bfo_test ] for test in tests: diff --git a/xyz_files/bimoe.xyz b/xyz_files/bimoe.xyz new file mode 100644 index 0000000..0c3018d --- /dev/null +++ b/xyz_files/bimoe.xyz @@ -0,0 +1,39 @@ +37 +Properties=species:S:1:pos:R:3:initial_magmoms:R:1:initial_charges:R:1 pbc="F F F" +Bi -0.23814277 0.68158269 -0.45260953 0.00000000 0.00000000 +C 1.10188602 -2.47369534 -0.93234296 0.00000000 0.00000000 +O 0.01386499 -1.89642546 -0.22015028 0.00000000 0.00000000 +C -0.02811321 -2.24369594 1.16103724 0.00000000 0.00000000 +C 0.67089665 -1.15215764 1.95276773 0.00000000 0.00000000 +O 0.12012405 0.08501838 1.62775057 0.00000000 0.00000000 +H 0.95111966 -3.56037540 -1.00605438 0.00000000 0.00000000 +H 2.05754419 -2.26309790 -0.43315164 0.00000000 0.00000000 +H 1.10154770 -2.01901352 -1.92503266 0.00000000 0.00000000 +H 0.42743592 -3.23247218 1.31789151 0.00000000 0.00000000 +H -1.08943392 -2.28551527 1.43995341 0.00000000 0.00000000 +H 1.75766881 -1.18607210 1.73650176 0.00000000 0.00000000 +H 0.55121437 -1.36286204 3.03030469 0.00000000 0.00000000 +C -3.65519857 0.15734373 -0.36760789 0.00000000 0.00000000 +O -2.55129181 -0.71809531 -0.53918891 0.00000000 0.00000000 +C -2.51586983 -1.36508933 -1.81619297 0.00000000 0.00000000 +C -1.78131894 -0.50333947 -2.83405613 0.00000000 0.00000000 +O -0.46846595 -0.23200809 -2.44139801 0.00000000 0.00000000 +H -4.59660033 -0.41034211 -0.38170574 0.00000000 0.00000000 +H -3.69051609 0.92829158 -1.15233479 0.00000000 0.00000000 +H -3.54010978 0.64507966 0.60670772 0.00000000 0.00000000 +H -3.54236657 -1.58692282 -2.14749012 0.00000000 0.00000000 +H -1.97229439 -2.30362288 -1.66386073 0.00000000 0.00000000 +H -2.36461970 0.42522990 -3.00446573 0.00000000 0.00000000 +H -1.78877696 -1.04629830 -3.79657401 0.00000000 0.00000000 +C 1.08939465 3.15149677 1.76195955 0.00000000 0.00000000 +O 1.22469078 2.93938144 0.36412325 0.00000000 0.00000000 +C 2.55183655 2.60512998 -0.04010527 0.00000000 0.00000000 +C 2.73652391 1.09818683 -0.03632118 0.00000000 0.00000000 +O 1.82605255 0.47968862 -0.90814191 0.00000000 0.00000000 +H 1.67189183 4.03291478 2.06793983 0.00000000 0.00000000 +H 1.41429471 2.27097269 2.33304766 0.00000000 0.00000000 +H 0.02787609 3.32899106 1.96476841 0.00000000 0.00000000 +H 3.28507120 3.10204973 0.61453483 0.00000000 0.00000000 +H 2.67439304 2.98888122 -1.06144199 0.00000000 0.00000000 +H 2.63018587 0.72062285 0.99688403 0.00000000 0.00000000 +H 3.76395526 0.86714917 -0.36367540 0.00000000 0.00000000 diff --git a/xyz_files/bino3.xyz b/xyz_files/bino3.xyz new file mode 100644 index 0000000..3c00717 --- /dev/null +++ b/xyz_files/bino3.xyz @@ -0,0 +1,15 @@ +13 +Properties=species:S:1:pos:R:3:initial_magmoms:R:1:initial_charges:R:1 pbc="F F F" +Bi 0.08008060 -0.24912774 -0.75224895 0.00000000 0.00000000 +N 0.51560178 -1.58391457 1.65468524 0.00000000 0.00000000 +O 0.11584878 -0.36114881 1.50841032 0.00000000 0.00000000 +O 0.71798765 -2.20026190 0.57331108 0.00000000 0.00000000 +O 0.67035714 -2.05880104 2.73718030 0.00000000 0.00000000 +N -2.59322863 -0.03778581 0.11958899 0.00000000 0.00000000 +O -1.81378214 0.95769049 -0.11210149 0.00000000 0.00000000 +O -2.08184851 -1.17765869 -0.08605410 0.00000000 0.00000000 +O -3.71477327 0.11975097 0.50243581 0.00000000 0.00000000 +N 2.11991444 1.49243438 0.11959782 0.00000000 0.00000000 +O 0.90558514 1.84109770 -0.11768391 0.00000000 0.00000000 +O 2.37461536 0.26872801 -0.08166978 0.00000000 0.00000000 +O 2.93454576 2.27884712 0.50324025 0.00000000 0.00000000 diff --git a/xyz_files/bino31moe.xyz b/xyz_files/bino31moe.xyz new file mode 100644 index 0000000..f1bc5a9 --- /dev/null +++ b/xyz_files/bino31moe.xyz @@ -0,0 +1,23 @@ +21 +Properties=species:S:1:pos:R:3:initial_magmoms:R:1:initial_charges:R:1 pbc="F F F" +Bi 0.08346671 0.03025861 -0.13750061 0.00000000 0.00000000 +N 1.43685677 1.36125935 2.10724027 0.00000000 0.00000000 +O 1.12446352 1.77651934 0.91671812 0.00000000 0.00000000 +O 1.17593043 0.17742449 2.36463486 0.00000000 0.00000000 +O 1.95326276 2.12988872 2.87993608 0.00000000 0.00000000 +N -2.60990983 0.33121432 0.80831629 0.00000000 0.00000000 +O -1.55613992 0.86025059 1.31825900 0.00000000 0.00000000 +O -2.42062307 -0.41974177 -0.17921790 0.00000000 0.00000000 +O -3.69826507 0.55822174 1.26919429 0.00000000 0.00000000 +C 3.25784392 1.00142798 -1.11660121 0.00000000 0.00000000 +O 1.97939568 0.61476247 -1.63219524 0.00000000 0.00000000 +C 1.45919507 1.46985778 -2.66840732 0.00000000 0.00000000 +C 0.34889405 2.31472598 -2.07841706 0.00000000 0.00000000 +O -0.61397604 1.48542143 -1.45568195 0.00000000 0.00000000 +H 3.51550931 0.30162725 -0.31622562 0.00000000 0.00000000 +H 3.22197611 2.02314586 -0.71859569 0.00000000 0.00000000 +H 4.00481528 0.92993482 -1.91599649 0.00000000 0.00000000 +H 1.06606587 0.81311328 -3.45423269 0.00000000 0.00000000 +H 2.26835082 2.08505595 -3.08118998 0.00000000 0.00000000 +H -0.14393942 2.87925912 -2.88214046 0.00000000 0.00000000 +H 0.76443703 3.03846266 -1.35783664 0.00000000 0.00000000 diff --git a/xyz_files/cnbz.xyz b/xyz_files/cnbz.xyz new file mode 100644 index 0000000..7fcb2a5 --- /dev/null +++ b/xyz_files/cnbz.xyz @@ -0,0 +1,17 @@ +15 + +O -0.8313 -3.3009 0.4452 +O -2.4412 -2.3700 -0.4446 +N 2.0420 3.5366 0.0000 +C -0.6121 -1.0598 -0.0001 +C 0.8044 -1.0287 0.0132 +C -1.2934 0.1828 -0.0134 +C 0.8162 1.4137 0.0000 +C 1.5131 0.1871 0.0086 +C -0.5946 1.4042 -0.0086 +C -1.3069 -2.2633 -0.0002 +C 1.4678 2.5421 0.0000 +H 1.3486 -1.8962 0.0163 +H -2.3167 0.2204 -0.0164 +H 2.5378 0.1558 0.0101 +H -1.1339 2.2761 -0.0101 diff --git a/xyz_files/f5bs.xyz b/xyz_files/f5bs.xyz new file mode 100644 index 0000000..7ac69f3 --- /dev/null +++ b/xyz_files/f5bs.xyz @@ -0,0 +1,17 @@ +15 + +S 2.3986 -0.1017 -0.0481 +F 0.5366 -2.4172 -0.0281 +F 0.6921 2.3306 -0.0224 +F -2.0303 2.4125 0.0134 +F -2.1853 -2.3209 0.0073 +F -3.4741 0.0904 0.0279 +O 2.8804 1.1574 0.8764 +O 2.8165 -1.3161 0.6366 +O 2.8132 0.1584 -1.4177 +C 0.6527 -0.0445 -0.0259 +C -0.0839 -1.2290 -0.0180 +C -0.0047 1.1857 -0.0153 +C -1.3987 1.2313 0.0031 +C -1.4778 -1.1835 0.0002 +C -2.1354 0.0467 0.0107 diff --git a/xyz_files/moe.xyz b/xyz_files/moe.xyz new file mode 100644 index 0000000..ca2ff43 --- /dev/null +++ b/xyz_files/moe.xyz @@ -0,0 +1,15 @@ +13 +Properties=species:S:1:pos:R:3:initial_magmoms:R:1:initial_charges:R:1 pbc="F F F" +C 0.36259352 -0.82996662 -1.81481857 0.00000000 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