boltz-vsynthes 1.0.37__py3-none-any.whl → 1.0.39__py3-none-any.whl

boltz/main.py

@@ -272,7 +272,7 @@ def get_cache_path() -> str:
 
 
 def check_inputs(data: Path) -> list[Path]:
-    """Check the input data and output directory.
+    """Check the input data.
 
     Parameters
     ----------
@@ -282,18 +282,21 @@ def check_inputs(data: Path) -> list[Path]:
     Returns
     -------
     list[Path]
-        The list of input data.
+        The list of input files.
 
     """
-    click.echo("Checking input data.")
-
     # Check if data is a directory
     if data.is_dir():
         data: list[Path] = list(data.glob("*"))
 
         # Filter out non .fasta or .yaml files, raise
         # an error on directory and other file types
+        filtered_data = []
         for d in data:
+            # Skip hidden files and directories
+            if d.name.startswith('.') or any(part.startswith('.') for part in d.parts):
+                continue
+                
             if d.is_dir():
                 msg = f"Found directory {d} instead of .fasta or .yaml."
                 raise RuntimeError(msg)
@@ -303,6 +306,8 @@ def check_inputs(data: Path) -> list[Path]:
                     "please provide a .fasta or .yaml file."
                 )
                 raise RuntimeError(msg)
+            filtered_data.append(d)
+        data = filtered_data
     else:
         data = [data]
 
@@ -493,13 +498,25 @@ def process_input(  # noqa: C901, PLR0912, PLR0915, D103
 ) -> None:
     try:
         # Parse data
-        if path.suffix in (".fa", ".fas", ".fasta"):
+        if path.is_dir():
+            # Process all YAML and FASTA files in the directory
+            targets = []
+            for file_path in path.glob("*"):
+                if file_path.suffix in (".fa", ".fas", ".fasta"):
+                    target = parse_fasta(file_path, ccd, mol_dir, boltz2)
+                    targets.append(target)
+                elif file_path.suffix in (".yml", ".yaml"):
+                    target = parse_yaml(file_path, ccd, mol_dir, boltz2)
+                    if not isinstance(target, list):
+                        target = [target]
+                    targets.extend(target)
+        elif path.suffix in (".fa", ".fas", ".fasta"):
             target = parse_fasta(path, ccd, mol_dir, boltz2)
+            targets = [target]
         elif path.suffix in (".yml", ".yaml"):
-            target = parse_yaml(path, ccd, mol_dir, boltz2)
-        elif path.is_dir():
-            msg = f"Found directory {path} instead of .fasta or .yaml, skipping."
-            raise RuntimeError(msg)  # noqa: TRY301
+            targets = parse_yaml(path, ccd, mol_dir, boltz2)
+            if not isinstance(targets, list):
+                targets = [targets]
         else:
             msg = (
                 f"Unable to parse filetype {path.suffix}, "
@@ -507,96 +524,98 @@ def process_input(  # noqa: C901, PLR0912, PLR0915, D103
             )
             raise RuntimeError(msg)  # noqa: TRY301
 
-        # Get target id
-        target_id = target.record.id
-
-        # Get all MSA ids and decide whether to generate MSA
-        to_generate = {}
-        prot_id = const.chain_type_ids["PROTEIN"]
-        for chain in target.record.chains:
-            # Add to generate list, assigning entity id
-            if (chain.mol_type == prot_id) and (chain.msa_id == 0):
-                entity_id = chain.entity_id
-                msa_id = f"{target_id}_{entity_id}"
-                to_generate[msa_id] = target.sequences[entity_id]
-                chain.msa_id = msa_dir / f"{msa_id}.csv"
-
-            # We do not support msa generation for non-protein chains
-            elif chain.msa_id == 0:
-                chain.msa_id = -1
-
-        # Generate MSA
-        if to_generate and not use_msa_server:
-            msg = "Missing MSA's in input and --use_msa_server flag not set."
-            raise RuntimeError(msg)  # noqa: TRY301
-
-        if to_generate:
-            msg = f"Generating MSA for {path} with {len(to_generate)} protein entities."
-            click.echo(msg)
-            compute_msa(
-                data=to_generate,
-                target_id=target_id,
-                msa_dir=msa_dir,
-                msa_server_url=msa_server_url,
-                msa_pairing_strategy=msa_pairing_strategy,
-            )
+        # Process each target
+        for target in targets:
+            # Get target id
+            target_id = target.record.id
+
+            # Get all MSA ids and decide whether to generate MSA
+            to_generate = {}
+            prot_id = const.chain_type_ids["PROTEIN"]
+            for chain in target.record.chains:
+                # Add to generate list, assigning entity id
+                if (chain.mol_type == prot_id) and (chain.msa_id == 0):
+                    entity_id = chain.entity_id
+                    msa_id = f"{target_id}_{entity_id}"
+                    to_generate[msa_id] = target.sequences[entity_id]
+                    chain.msa_id = msa_dir / f"{msa_id}.csv"
+
+                # We do not support msa generation for non-protein chains
+                elif chain.msa_id == 0:
+                    chain.msa_id = -1
+
+            # Generate MSA
+            if to_generate and not use_msa_server:
+                msg = "Missing MSA's in input and --use_msa_server flag not set."
+                raise RuntimeError(msg)  # noqa: TRY301
+
+            if to_generate:
+                msg = f"Generating MSA for {path} with {len(to_generate)} protein entities."
+                click.echo(msg)
+                compute_msa(
+                    data=to_generate,
+                    target_id=target_id,
+                    msa_dir=msa_dir,
+                    msa_server_url=msa_server_url,
+                    msa_pairing_strategy=msa_pairing_strategy,
+                )
 
-        # Parse MSA data
-        msas = sorted({c.msa_id for c in target.record.chains if c.msa_id != -1})
-        msa_id_map = {}
-        for msa_idx, msa_id in enumerate(msas):
-            # Check that raw MSA exists
-            msa_path = Path(msa_id)
-            if not msa_path.exists():
-                msg = f"MSA file {msa_path} not found."
-                raise FileNotFoundError(msg)  # noqa: TRY301
-
-            # Dump processed MSA
-            processed = processed_msa_dir / f"{target_id}_{msa_idx}.npz"
-            msa_id_map[msa_id] = f"{target_id}_{msa_idx}"
-            if not processed.exists():
-                # Parse A3M
-                if msa_path.suffix == ".a3m":
-                    msa: MSA = parse_a3m(
-                        msa_path,
-                        taxonomy=None,
-                        max_seqs=max_msa_seqs,
-                    )
-                elif msa_path.suffix == ".csv":
-                    msa: MSA = parse_csv(msa_path, max_seqs=max_msa_seqs)
-                else:
-                    msg = f"MSA file {msa_path} not supported, only a3m or csv."
-                    raise RuntimeError(msg)  # noqa: TRY301
-
-                msa.dump(processed)
-
-        # Modify records to point to processed MSA
-        for c in target.record.chains:
-            if (c.msa_id != -1) and (c.msa_id in msa_id_map):
-                c.msa_id = msa_id_map[c.msa_id]
-
-        # Dump templates
-        for template_id, template in target.templates.items():
-            name = f"{target.record.id}_{template_id}.npz"
-            template_path = processed_templates_dir / name
-            template.dump(template_path)
-
-        # Dump constraints
-        constraints_path = processed_constraints_dir / f"{target.record.id}.npz"
-        target.residue_constraints.dump(constraints_path)
-
-        # Dump extra molecules
-        Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.AllProps)
-        with (processed_mols_dir / f"{target.record.id}.pkl").open("wb") as f:
-            pickle.dump(target.extra_mols, f)
-
-        # Dump structure
-        struct_path = structure_dir / f"{target.record.id}.npz"
-        target.structure.dump(struct_path)
-
-        # Dump record
-        record_path = records_dir / f"{target.record.id}.json"
-        target.record.dump(record_path)
+            # Parse MSA data
+            msas = sorted({c.msa_id for c in target.record.chains if c.msa_id != -1})
+            msa_id_map = {}
+            for msa_idx, msa_id in enumerate(msas):
+                # Check that raw MSA exists
+                msa_path = Path(msa_id)
+                if not msa_path.exists():
+                    msg = f"MSA file {msa_path} not found."
+                    raise FileNotFoundError(msg)  # noqa: TRY301
+
+                # Dump processed MSA
+                processed = processed_msa_dir / f"{target_id}_{msa_idx}.npz"
+                msa_id_map[msa_id] = f"{target_id}_{msa_idx}"
+                if not processed.exists():
+                    # Parse A3M
+                    if msa_path.suffix == ".a3m":
+                        msa: MSA = parse_a3m(
+                            msa_path,
+                            taxonomy=None,
+                            max_seqs=max_msa_seqs,
+                        )
+                    elif msa_path.suffix == ".csv":
+                        msa: MSA = parse_csv(msa_path, max_seqs=max_msa_seqs)
+                    else:
+                        msg = f"MSA file {msa_path} not supported, only a3m or csv."
+                        raise RuntimeError(msg)  # noqa: TRY301
+
+                    msa.dump(processed)
+
+            # Modify records to point to processed MSA
+            for c in target.record.chains:
+                if (c.msa_id != -1) and (c.msa_id in msa_id_map):
+                    c.msa_id = msa_id_map[c.msa_id]
+
+            # Dump templates
+            for template_id, template in target.templates.items():
+                name = f"{target.record.id}_{template_id}.npz"
+                template_path = processed_templates_dir / name
+                template.dump(template_path)
+
+            # Dump constraints
+            constraints_path = processed_constraints_dir / f"{target.record.id}.npz"
+            target.residue_constraints.dump(constraints_path)
+
+            # Dump extra molecules
+            Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.AllProps)
+            with (processed_mols_dir / f"{target.record.id}.pkl").open("wb") as f:
+                pickle.dump(target.extra_mols, f)
+
+            # Dump structure
+            struct_path = structure_dir / f"{target.record.id}.npz"
+            target.structure.dump(struct_path)
+
+            # Dump record
+            record_path = records_dir / f"{target.record.id}.json"
+            target.record.dump(record_path)
 
     except Exception as e:  # noqa: BLE001
         import traceback

{boltz_vsynthes-1.0.37.dist-info → boltz_vsynthes-1.0.39.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.37
+Version: 1.0.39
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.37.dist-info → boltz_vsynthes-1.0.39.dist-info}/RECORD

@@ -1,5 +1,5 @@
 boltz/__init__.py,sha256=F_-so3S40iZrSZ89Ge4TS6aZqwWyZXq_H4AXGDlbA_g,187
-boltz/main.py,sha256=AMYdcqTLOL5Mbo8P2ix1KeNwTijH5fWNzKUnLHBNtn0,39735
+boltz/main.py,sha256=SHM-t-9wjwjTJmWR4N5SrAHxk2vgz7fTruz5shiixVc,40882
 boltz/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 boltz/data/const.py,sha256=1M-88Z6HkfKY6MkNtqcj3b9P-oX9xEXluh3qM_u8dNU,26779
 boltz/data/mol.py,sha256=maOpPHEGX1VVXCIFY6pQNGF7gUBZPAfgSvuPf2QO1yc,34268
@@ -107,9 +107,9 @@ boltz/model/optim/scheduler.py,sha256=nB4jz0CZ4pR4n08LQngExL_pNycIdYI8AXVoHPnZWQ
 boltz/model/potentials/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 boltz/model/potentials/potentials.py,sha256=vev8Vjfs-ML1hyrdv_R8DynG4wSFahJ6nzPWp7CYQqw,17507
 boltz/model/potentials/schedules.py,sha256=m7XJjfuF9uTX3bR9VisXv1rvzJjxiD8PobXRpcBBu1c,968
-boltz_vsynthes-1.0.37.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.37.dist-info/METADATA,sha256=WhICTabdnBWjYVatPqvnCo9EutL801DxXi4tT5LcP2A,7171
-boltz_vsynthes-1.0.37.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.37.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.37.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.37.dist-info/RECORD,,
+boltz_vsynthes-1.0.39.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.39.dist-info/METADATA,sha256=s4YTm6DLYVooEmxNB0gz1_0aFspJeAqR5KWVZDyTEv4,7171
+boltz_vsynthes-1.0.39.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.39.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.39.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.39.dist-info/RECORD,,