Loading molecules from RDKit

[Tonylac77]

Hi,

I am trying to figure out how to load molecules from RDKit. I would like to first load an SDF file using RDkit then run the RMSD calculations on that. Any tips or example code would be great.

Thanks

[RMeli]

Hi @Tonylac77, thank you for your interest in spyrmsd.

The spyrmsd.molecules.Molecule class has a special constructor to build a spyrmsd molecule directly from and RDKit molecule:

from spyrmsd.molecule import Molecule
m = Molecule().from_rdkit(YOUR_RDKIT_MOLECULE)

You can then use spyrmsd.rmsd.rmsdwrapper which works directly with spyrmsd molecules.

Alternatively, you can use the attributes of the spyrmsd.molecule.Molecule directly in the call to the more bare-bone spyrmsd.rmsd.symmrmsd, as shown in the tutorial.

Finally, you can bypass the spyrmsd.molecule.Molecule class entirely by extracting the relevant information needed by spyrmsd.rmsd.symmrmsd directly from an RDKit molecule as follows (there might be better ways...):

spyrmsd/spyrmsd/optional/rdkit.py

Lines 149 to 165 in 952e356

	atoms = mol.GetAtoms()
	n = len(atoms)
	atomicnums = np.zeros(n, dtype=int)
	coordinates = np.zeros((n, 3))
	conformer = mol.GetConformer()
	for i, atom in enumerate(atoms):
	atomicnums[i] = atom.GetAtomicNum()
	pos = conformer.GetAtomPosition(i)
	coordinates[i] = np.array([pos.x, pos.y, pos.z])
	A: Optional[np.ndarray] = adjacency_matrix(mol) if adjacency else None

---

from rdkit import Chem
from rdkit.Chem import AllChem

# Instead of the following 4 lines of code, load your RDKit molecules from SDF files
rdmol1 = Chem.MolFromSmiles("c1ccccc1")
rdmol2 = Chem.MolFromSmiles("c1ccccc1")
AllChem.EmbedMolecule(rdmol1)
AllChem.EmbedMolecule(rdmol2)

from spyrmsd.molecule import Molecule
from spyrmsd.rmsd import rmsdwrapper

mol1 = Molecule.from_rdkit(rdmol1)
mol2 = Molecule.from_rdkit(rdmol2)

rmsdwrapper(mol1, mol2)

---

I hope this helps. I will try to improve the tutorial/documentation in this regard.