Other fixes

README.md

@@ -294,6 +294,7 @@ If modelling multiple copies of the same sequence in Boltz, the input JSON must
   "dialect": "alphafold3",
   "version": 1
 }
+```
 
 If the identical sequences are given as seperate entities (as shown below) you will encounter an error.
 

abcfold/boltz/af3_to_boltz.py

@@ -224,10 +224,17 @@ def add_modifications(self, list_of_modifications: list):
         yaml_string = ""
         yaml_string += f"{DELIM}{DELIM}modifications:\n"
         for modification in list_of_modifications:
-            yaml_string += (
-                f"{DELIM}{DELIM}{DELIM}- position: {modification['ptmPosition']}\n"
-            )
-            yaml_string += f"{DELIM}{DELIM}{DELIM}  ccd: {modification['ptmType']}\n"
+            if "ptmType" in modification and "ptmPosition" in modification:
+                yaml_string += (
+                    f"{DELIM}{DELIM}{DELIM}- position: {modification['ptmPosition']}\n"
+                    f"{DELIM}{DELIM}{DELIM}  ccd: {modification['ptmType']}\n"
+                )
+            elif "modificationType" in modification and "basePosition" in modification:
+                yaml_string += (
+                    f"{DELIM}{DELIM}{DELIM}- position: {modification['basePosition']}\n"
+                    f"{DELIM}{DELIM}{DELIM}  ccd: {modification['modificationType']}\n"
+                )
+
         return yaml_string
 
     def add_key_and_value(self, key: str, value: str):

abcfold/boltz/check_install.py

@@ -4,7 +4,7 @@
 
 logger = logging.getLogger("logger")
 
-BOLTZ_VERSION = "2.1.1"
+BOLTZ_VERSION = "2.2.0"
 
 
 def check_boltz():

abcfold/chai1/af3_to_chai.py

@@ -227,7 +227,6 @@ def add_protein(self, seq: dict, fasta_data: dict):
         return protein_str, fasta_data
 
     def _add_protein(self, seq: dict, prot_id: str, fasta_data: dict):
-        protein_str = f">protein|{prot_id}\n{seq['protein']['sequence']}\n"
         sequence = seq["protein"]["sequence"]
         if "unpairedMsa" in seq["protein"].keys():
             seq_hash = hashlib.sha256(sequence.upper().encode()).hexdigest()
@@ -241,6 +240,11 @@ def _add_protein(self, seq: dict, prot_id: str, fasta_data: dict):
             )
         fasta_data[prot_id] = sequence
 
+        if "modifications" in seq["protein"]:
+            sequence = self.add_modifications(sequence, seq["protein"]["modifications"])
+
+        protein_str = f">protein|{prot_id}\n{sequence}\n"
+
         return protein_str, fasta_data
 
     def add_nucleotide(self, seq: dict, seq_type: str, fasta_data: dict):
@@ -261,8 +265,15 @@ def add_nucleotide(self, seq: dict, seq_type: str, fasta_data: dict):
         return nucleotide_str, fasta_data
 
     def _add_nucleotide(self, seq: dict, seq_type: str, nucl_id: str, fasta_data: dict):
-        nucleotide_str = f">{seq_type}|{nucl_id}\n{seq[seq_type]['sequence']}\n"
-        fasta_data[nucl_id] = seq[seq_type]["sequence"]
+        sequence = seq[seq_type]["sequence"]
+        fasta_data[nucl_id] = sequence
+
+        if "modifications" in seq[seq_type]:
+            sequence = self.add_modifications(
+                sequence, seq[seq_type]["modifications"]
+            )
+
+        nucleotide_str = f">{seq_type}|{nucl_id}\n{sequence}\n"
         return nucleotide_str, fasta_data
 
     def ccd_to_smiles(self, ccd_id: str):
@@ -329,6 +340,31 @@ def add_ligand(self, seq: dict, fasta_data: dict):
 
         return ligand_str
 
+    def add_modifications(self, sequence: str, modifications: list) -> str:
+        """
+        Add modifications to the fasta data
+
+        Args:
+            sequence (str): the sequence to add modifications to be added to
+            modifications (list): list of modifications to be added
+
+        Returns:
+            sequence (str): the sequence with modifications added
+        """
+
+        sequence_list = list(sequence)
+        for mod in modifications:
+            if "ptmType" in mod and "ptmPosition" in mod:
+                ptm_type = mod['ptmType']
+                position = int(mod['ptmPosition']) - 1
+                sequence_list[position] = f"({ptm_type})"
+            elif "modificationType" in mod and "basePosition" in mod:
+                mod_type = mod['modificationType']
+                position = int(mod['basePosition']) - 1
+                sequence_list[position] = f"({mod_type})"
+
+        return ''.join(sequence_list)
+
     def get_atom_name(self, atom: str) -> str:
         for name in ATOMS_NAMES:
             if atom.startswith(name):

abcfold/html/html_utils.py

@@ -28,7 +28,7 @@ def get_plddt_regions(plddts: Union[np.ndarray, list]) -> dict:
 
     regions = {}
     # replace none values with -1
-    plddts = np.where(plddts is None, -1, plddts)
+    plddts = np.where(plddts == None, -1, plddts) # noqa F401
 
     v_low = np.where((0 <= plddts) & (plddts <= 50))[0]
     regions["v_low"] = get_regions_helper(v_low)

abcfold/output/boltz.py

@@ -77,9 +77,12 @@ def __init__(
             boltz_yaml = list(parent_dir.glob("*.yaml"))[0]
             if boltz_yaml.exists():
                 boltz_yaml.rename(new_parent / "boltz_input.yaml")
-            boltz_msa = list(parent_dir.glob("*.a3m"))[0]
-            if boltz_msa.exists():
-                boltz_msa.rename(new_parent / boltz_msa.name)
+
+            boltz_msas = list(parent_dir.glob("*.a3m"))
+            if boltz_msas:
+                for boltz_msa in boltz_msas:
+                    if boltz_msa.exists():
+                        boltz_msa.rename(new_parent / boltz_msa.name)
 
         new_output_dirs = []
         for output_dir in self.output_dirs:

abcfold/output/chai.py

@@ -71,9 +71,11 @@ def __init__(
             chai_fasta = parent_dir / "chai1.fasta"
             if chai_fasta.exists():
                 chai_fasta.rename(new_parent / "chai1.fasta")
-            chai_msa = list(parent_dir.glob("*.aligned.pqt"))[0]
-            if chai_msa.exists():
-                chai_msa.rename(new_parent / chai_msa.name)
+            chai_msas = list(parent_dir.glob("*.aligned.pqt"))
+            if chai_msas:
+                for chai_msa in chai_msas:
+                    if chai_msa.exists():
+                        chai_msa.rename(new_parent / chai_msa.name)
 
         new_output_dirs = []
         for output_dir in self.output_dirs:

pyproject.toml

@@ -3,8 +3,8 @@ requires = ["setuptools>=42", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "ABCFold"
-version = "1.0.7"
+name = "abcfold"
+version = "1.0.8"
 description = "Input processing tools for AlphaFold3, Boltz and Chai-1"
 readme = "README.md"
 license = { text = "BSD License" }

tests/test_af3_to_boltz.py

@@ -35,7 +35,6 @@ def test_af3_to_boltz(test_data):
         yaml_string_bonds = boltz_yaml.json_to_yaml(test_data.test_inputA_json)
         yaml_string_bonds = yaml_string_bonds.split("\n")
 
-        print(yaml_string_bonds)
         assert yaml_string_bonds[0] == "version: 1"
         assert yaml_string_bonds[1] == "sequences:"
         assert yaml_string_bonds[2] == f"{DELIM}- protein:"

tests/test_af3_to_chai.py

@@ -124,6 +124,30 @@ def test_af3_to_chai_ligand(test_data):
         assert data == reference
 
 
+@pytest.mark.skipif(not run_chai1, reason="chai_lab not installed")
+def test_af3_to_chai_ptm(test_data):
+    with tempfile.TemporaryDirectory() as temp_dir:
+        chai_fasta = ChaiFasta(temp_dir)
+
+        chai_fasta.json_to_fasta(test_data.test_inputPTM_json)
+
+        reference = (
+            ">protein|A\n"
+            "(HY3)VLS(P1L)GEWQL\n"
+            ">rna|B\n"
+            "(2MG)GC(5MC)\n"
+        )
+
+        filename = Path(temp_dir) / "chai1.fasta"
+
+        assert filename.exists()
+        with open(filename, "r") as f:
+            data = f.read()
+            print(data)
+
+        assert data == reference
+
+
 @pytest.mark.skipif(not run_chai1, reason="chai_lab not installed")
 def test_chai_output_constraints(test_data):
     with tempfile.TemporaryDirectory() as temp_dir:

tests/test_data/inputPTM.json

@@ -0,0 +1,29 @@
+{
+    "name": "PTM example",
+    "modelSeeds": [1],
+    "sequences": [
+        {
+            "protein": {
+                "id": "A",
+                "sequence": "PVLSCGEWQL",
+                "modifications": [
+                    {"ptmType": "HY3", "ptmPosition": 1},
+                    {"ptmType": "P1L", "ptmPosition": 5}
+                ]
+            }
+        },
+        {
+        "rna": {
+                "id": "B",
+                "sequence": "AGCU",
+                "modifications": [
+                    {"modificationType": "2MG", "basePosition": 1},
+                    {"modificationType": "5MC", "basePosition": 4}
+                ]
+            }
+        }
+    ],
+
+    "dialect": "alphafold3",
+    "version": 1
+}