boltz-vsynthes 1.0.40__py3-none-any.whl → 1.0.42__py3-none-any.whl

boltz/data/parse/schema.py

@@ -2,8 +2,6 @@ from collections.abc import Mapping
 from dataclasses import dataclass
 from pathlib import Path
 from typing import Optional
-import json
-import yaml
 
 import click
 import numpy as np
@@ -937,7 +935,6 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
     ccd: Mapping[str, Mol],
     mol_dir: Optional[Path] = None,
     boltz_2: bool = False,
-    output_dir: Optional[Path] = None,
 ) -> Target:
     """Parse a Boltz input yaml / json.
 
@@ -989,8 +986,6 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
         Path to the directory containing the molecules.
     boltz2: bool
         Whether to parse the input for Boltz2.
-    output_dir: Path, optional
-        Path to the output directory. If provided, results will be saved in a subfolder named after the input file.
 
     Returns
     -------
@@ -998,14 +993,6 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
         The parsed target.
 
     """
-    # Create output directory if specified
-    if output_dir is not None:
-        output_dir = Path(output_dir)
-        output_dir.mkdir(parents=True, exist_ok=True)
-        # Create subfolder based on input name
-        subfolder = output_dir / name
-        subfolder.mkdir(parents=True, exist_ok=True)
-
     # Assert version 1
     version = schema.get("version", 1)
     if version != 1:
@@ -1072,7 +1059,6 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
 
     # Check if any affinity ligand is present
     affinity_ligands = set()
-    affinity_proteins = set()
     properties = schema.get("properties", [])
     if properties and not boltz_2:
         msg = "Affinity prediction is only supported for Boltz2!"
@@ -1083,6 +1069,7 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
         if prop_type == "affinity":
             binder = prop["affinity"]["binder"]
             if not isinstance(binder, str):
+                # TODO: support multi residue ligands and ccd's
                 msg = "Binder must be a single chain."
                 raise ValueError(msg)
 
@@ -1090,21 +1077,18 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
                 msg = f"Could not find binder with name {binder} in the input!"
                 raise ValueError(msg)
 
-            # Allow both protein and ligand as binders
-            if chain_name_to_entity_type[binder] == "protein":
-                affinity_proteins.add(binder)
-            elif chain_name_to_entity_type[binder] == "ligand":
-                affinity_ligands.add(binder)
-            else:
+            if chain_name_to_entity_type[binder] != "ligand":
                 msg = (
-                    f"Chain {binder} is not a protein or ligand! "
-                    "Affinity is currently only supported for proteins and ligands."
+                    f"Chain {binder} is not a ligand! "
+                    "Affinity is currently only supported for ligands."
                 )
                 raise ValueError(msg)
 
-    # Check if any affinity binder is present
-    if len(affinity_proteins) + len(affinity_ligands) > 1:
-        msg = "Only one affinity binder is currently supported!"
+            affinity_ligands.add(binder)
+
+    # Check only one affinity ligand is present
+    if len(affinity_ligands) > 1:
+        msg = "Only one affinity ligand is currently supported!"
         raise ValueError(msg)
 
     # Go through entities and parse them
@@ -1127,15 +1111,12 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
             elif isinstance(item[entity_type]["id"], list):
                 ids.extend(item[entity_type]["id"])
 
-        # Check if any affinity binder is present
+        # Check if any affinity ligand is present
         if len(ids) == 1:
-            affinity = ids[0] in affinity_ligands or ids[0] in affinity_proteins
+            affinity = ids[0] in affinity_ligands
         elif (len(ids) > 1) and any(x in affinity_ligands for x in ids):
             msg = "Cannot compute affinity for a ligand that has multiple copies!"
             raise ValueError(msg)
-        elif (len(ids) > 1) and any(x in affinity_proteins for x in ids):
-            # If binder is a protein, allow multiple ligands
-            affinity = True
         else:
             affinity = False
 
@@ -1234,7 +1215,7 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
             )
 
         # Parse a non-polymer
-        elif (entity_type == "ligand") and "ccd" in (items[0][entity_type]):
+        elif (entity_type == "ligand") and ("ccd" in items[0][entity_type]):
             seq = items[0][entity_type]["ccd"]
 
             if isinstance(seq, str):
@@ -1909,64 +1890,3 @@ def standardize(smiles: str) -> Optional[str]:
         raise ValueError("Molecule is broken")
 
     return smiles
-
-
-def parse_boltz_directory(
-    input_dir: Path,
-    output_dir: Path,
-    ccd: Mapping[str, Mol],
-    mol_dir: Optional[Path] = None,
-    boltz_2: bool = False,
-) -> list[Target]:
-    """Parse all YAML files in a directory.
-
-    Parameters
-    ----------
-    input_dir : Path
-        Path to the directory containing YAML files.
-    output_dir : Path
-        Path to the output directory where results will be saved.
-    ccd : Mapping[str, Mol]
-        Dictionary of CCD components.
-    mol_dir : Path, optional
-        Path to the directory containing the molecules.
-    boltz_2 : bool, optional
-        Whether to parse the input for Boltz2.
-
-    Returns
-    -------
-    list[Target]
-        List of parsed targets.
-
-    """
-    input_dir = Path(input_dir)
-    output_dir = Path(output_dir)
-    output_dir.mkdir(parents=True, exist_ok=True)
-
-    targets = []
-    for yaml_file in input_dir.glob("*.yaml"):
-        # Skip hidden files and directories
-        if yaml_file.name.startswith('.') or any(part.startswith('.') for part in yaml_file.parts):
-            continue
-            
-        try:
-            # Load YAML file
-            with open(yaml_file, "r") as f:
-                schema = yaml.safe_load(f)
-
-            # Parse schema
-            target = parse_boltz_schema(
-                name=yaml_file.stem,
-                schema=schema,
-                ccd=ccd,
-                mol_dir=mol_dir,
-                boltz_2=boltz_2,
-                output_dir=output_dir,
-            )
-            targets.append(target)
-
-        except Exception as e:
-            print(f"Error processing {yaml_file}: {str(e)}")
-            continue
-
-    return targets

boltz/data/parse/yaml.py

@@ -1,10 +1,9 @@
 from pathlib import Path
-from typing import Union, List, Optional
 
 import yaml
 from rdkit.Chem.rdchem import Mol
 
-from boltz.data.parse.schema import parse_boltz_schema, parse_boltz_directory
+from boltz.data.parse.schema import parse_boltz_schema
 from boltz.data.types import Target
 
 
@@ -13,9 +12,8 @@ def parse_yaml(
     ccd: dict[str, Mol],
     mol_dir: Path,
     boltz2: bool = False,
-    output_dir: Optional[Path] = None,
-) -> Union[Target, List[Target]]:
-    """Parse a Boltz input yaml / json file or directory.
+) -> Target:
+    """Parse a Boltz input yaml / json.
 
     The input file should be a yaml file with the following format:
 
@@ -51,28 +49,20 @@ def parse_yaml(
     Parameters
     ----------
     path : Path
-        Path to the YAML input file or directory containing YAML files.
-    ccd : Dict
+        Path to the YAML input format.
+    components : Dict
         Dictionary of CCD components.
-    mol_dir : Path
-        Path to the directory containing molecules.
-    boltz2 : bool, optional
+    boltz2 : bool
         Whether to parse the input for Boltz2.
-    output_dir : Path, optional
-        Path to the output directory where results will be saved.
 
     Returns
     -------
-    Union[Target, List[Target]]
-        The parsed target(s).
+    Target
+        The parsed target.
 
     """
-    path = Path(path)
-    
-    if path.is_dir():
-        return parse_boltz_directory(path, output_dir or path, ccd, mol_dir, boltz2)
-    else:
-        with path.open("r") as file:
-            data = yaml.safe_load(file)
-        name = path.stem
-        return parse_boltz_schema(name, data, ccd, mol_dir, boltz2, output_dir)
+    with path.open("r") as file:
+        data = yaml.safe_load(file)
+
+    name = path.stem
+    return parse_boltz_schema(name, data, ccd, mol_dir, boltz2)

boltz/main.py

@@ -272,7 +272,7 @@ def get_cache_path() -> str:
 
 
 def check_inputs(data: Path) -> list[Path]:
-    """Check the input data.
+    """Check the input data and output directory.
 
     Parameters
     ----------
@@ -282,21 +282,18 @@ def check_inputs(data: Path) -> list[Path]:
     Returns
     -------
     list[Path]
-        The list of input files.
+        The list of input data.
 
     """
+    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)
@@ -306,8 +303,6 @@ 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]
 
@@ -498,25 +493,13 @@ def process_input(  # noqa: C901, PLR0912, PLR0915, D103
 ) -> None:
     try:
         # Parse data
-        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"):
+        if path.suffix in (".fa", ".fas", ".fasta"):
             target = parse_fasta(path, ccd, mol_dir, boltz2)
-            targets = [target]
         elif path.suffix in (".yml", ".yaml"):
-            targets = parse_yaml(path, ccd, mol_dir, boltz2)
-            if not isinstance(targets, list):
-                targets = [targets]
+            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
         else:
             msg = (
                 f"Unable to parse filetype {path.suffix}, "
@@ -524,98 +507,96 @@ def process_input(  # noqa: C901, PLR0912, PLR0915, D103
             )
             raise RuntimeError(msg)  # noqa: TRY301
 
-        # 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,
-                )
+        # 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/utils/sdf_splitter.py

@@ -0,0 +1,63 @@
+from pathlib import Path
+from typing import Optional
+from rdkit import Chem
+
+def split_sdf_to_individuals(
+    input_sdf: Path,
+    output_dir: Path,
+    prefix: str = "ligand_",
+    start_index: int = 1,
+) -> None:
+    """Split a large SDF file into individual SDF files, one molecule per file.
+    
+    Parameters
+    ----------
+    input_sdf : Path
+        Path to the input SDF file.
+    output_dir : Path
+        Path to the output directory where individual files will be saved.
+    prefix : str, optional
+        Prefix for output filenames, by default "ligand_".
+    start_index : int, optional
+        Starting index for output filenames, by default 1.
+    """
+    # Create output directory if it doesn't exist
+    output_dir.mkdir(parents=True, exist_ok=True)
+    
+    # Read all molecules from input SDF
+    supplier = Chem.SDMolSupplier(str(input_sdf))
+    molecules = [mol for mol in supplier if mol is not None]
+    total_molecules = len(molecules)
+    
+    # Write each molecule to a separate file
+    for i, mol in enumerate(molecules):
+        # Create output filename
+        output_file = output_dir / f"{prefix}{start_index + i}.sdf"
+        
+        # Write molecule to file
+        writer = Chem.SDWriter(str(output_file))
+        writer.write(mol)
+        writer.close()
+        
+        print(f"Created {output_file}")
+
+def main():
+    import argparse
+    
+    parser = argparse.ArgumentParser(description="Split a large SDF file into individual files")
+    parser.add_argument("input_sdf", type=str, help="Path to input SDF file")
+    parser.add_argument("output_dir", type=str, help="Path to output directory")
+    parser.add_argument("--prefix", type=str, default="ligand_", help="Prefix for output filenames")
+    parser.add_argument("--start-index", type=int, default=1, help="Starting index for output filenames")
+    
+    args = parser.parse_args()
+    
+    split_sdf_to_individuals(
+        input_sdf=Path(args.input_sdf),
+        output_dir=Path(args.output_dir),
+        prefix=args.prefix,
+        start_index=args.start_index,
+    )
+
+if __name__ == "__main__":
+    main() 

boltz/utils/yaml_generator.py

@@ -0,0 +1,120 @@
+from pathlib import Path
+import yaml
+from typing import Optional, Dict, Any
+import string
+
+def get_next_ligand_id(config: Dict[str, Any]) -> str:
+    """Get the next available ligand ID based on existing IDs in the config.
+    
+    Parameters
+    ----------
+    config : Dict[str, Any]
+        The configuration dictionary.
+        
+    Returns
+    -------
+    str
+        The next available ligand ID.
+    """
+    # Get all existing IDs
+    existing_ids = set()
+    for item in config["sequences"]:
+        for key in item:
+            if "id" in item[key]:
+                existing_ids.add(item[key]["id"])
+    
+    # Find the first available letter
+    for letter in string.ascii_uppercase:
+        if letter not in existing_ids:
+            return letter
+    
+    # If we run out of single letters, use AA, AB, etc.
+    for first in string.ascii_uppercase:
+        for second in string.ascii_uppercase:
+            new_id = first + second
+            if new_id not in existing_ids:
+                return new_id
+    
+    raise ValueError("Ran out of available ligand IDs!")
+
+def generate_yamls_from_sdfs(
+    template_yaml: Path,
+    sdf_dir: Path,
+    output_dir: Path,
+    yaml_prefix: str = "config_",
+    start_index: int = 1,
+) -> None:
+    """Generate YAML files from a template and a folder of SDF files.
+    
+    Parameters
+    ----------
+    template_yaml : Path
+        Path to the template YAML file.
+    sdf_dir : Path
+        Path to the directory containing SDF files.
+    output_dir : Path
+        Path to the output directory where YAML files will be saved.
+    yaml_prefix : str, optional
+        Prefix for output YAML filenames, by default "config_".
+    start_index : int, optional
+        Starting index for output filenames, by default 1.
+    """
+    # Create output directory if it doesn't exist
+    output_dir.mkdir(parents=True, exist_ok=True)
+    
+    # Load template YAML
+    with open(template_yaml) as f:
+        template = yaml.safe_load(f)
+    
+    # Get all SDF files
+    sdf_files = sorted(sdf_dir.glob("*.sdf"))
+    
+    # Generate YAML for each SDF
+    for i, sdf_file in enumerate(sdf_files):
+        # Create a copy of the template
+        config = template.copy()
+        
+        # Get next available ligand ID
+        ligand_id = get_next_ligand_id(config)
+        
+        # Update ligand information
+        for item in config["sequences"]:
+            if "ligand" in item:
+                item["ligand"]["id"] = ligand_id
+                item["ligand"]["sdf"] = str(sdf_file)
+        
+        # Update affinity information if present
+        if "properties" in config:
+            for prop in config["properties"]:
+                if "affinity" in prop:
+                    prop["affinity"]["binder"] = ligand_id
+        
+        # Write YAML file
+        output_file = output_dir / f"{yaml_prefix}{start_index + i}.yaml"
+        with open(output_file, "w") as f:
+            yaml.dump(config, f, default_flow_style=False)
+        
+        print(f"Created {output_file} with ligand ID {ligand_id}")
+
+def main():
+    import argparse
+    
+    parser = argparse.ArgumentParser(description="Generate YAML files from a template and SDF files")
+    parser.add_argument("template_yaml", type=str, help="Path to template YAML file")
+    parser.add_argument("sdf_dir", type=str, help="Path to directory containing SDF files")
+    parser.add_argument("output_dir", type=str, help="Path to output directory")
+    parser.add_argument("--yaml-prefix", type=str, default="config_", help="Prefix for output YAML filenames")
+    parser.add_argument("--start-index", type=int, default=1, help="Starting index for output filenames")
+    
+    args = parser.parse_args()
+    
+    generate_yamls_from_sdfs(
+        template_yaml=Path(args.template_yaml),
+        sdf_dir=Path(args.sdf_dir),
+        output_dir=Path(args.output_dir),
+        yaml_prefix=args.yaml_prefix,
+        start_index=args.start_index,
+    )
+
+if __name__ == "__main__":
+    main() 

{boltz_vsynthes-1.0.40.dist-info → boltz_vsynthes-1.0.42.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.40
+Version: 1.0.42
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.40.dist-info → boltz_vsynthes-1.0.42.dist-info}/RECORD

@@ -1,5 +1,5 @@
 boltz/__init__.py,sha256=F_-so3S40iZrSZ89Ge4TS6aZqwWyZXq_H4AXGDlbA_g,187
-boltz/main.py,sha256=SHM-t-9wjwjTJmWR4N5SrAHxk2vgz7fTruz5shiixVc,40882
+boltz/main.py,sha256=AMYdcqTLOL5Mbo8P2ix1KeNwTijH5fWNzKUnLHBNtn0,39735
 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
@@ -40,9 +40,9 @@ boltz/data/parse/mmcif.py,sha256=25kEXCkx-OuaawAs7cdz0fxdRu5_CCO0AV00u84PrjQ,368
 boltz/data/parse/mmcif_with_constraints.py,sha256=WHYZckSqUwu-Nb9vmVmxHmC7uxwVrF7AVUeVKsc5wGQ,51473
 boltz/data/parse/pdb.py,sha256=iybk4p2UgUy_ABGprDq_xxyPSdm1HAZsGTM0lhxVEwM,1654
 boltz/data/parse/pdb_download.py,sha256=wge-scX-lOatX0q83W1wOsaql99rYp-6uGWSHEc995M,2718
-boltz/data/parse/schema.py,sha256=p4KIAVzQAuApcxRLHc6-KKG7ICgLmEWVzE8Qqm6v04w,66402
+boltz/data/parse/schema.py,sha256=kNu28U2_MGiecwWNlcxgaDH3WOcO0P-q2LdoSPSb66w,63826
 boltz/data/parse/sdf.py,sha256=fs3MQVClDcCzxJaeVYiDuoh-fUrYc8Tcd5Bz8ws3FKI,2052
-boltz/data/parse/yaml.py,sha256=M3dRQK2mMDue3bPSO_T2ThaVojSMrOV7rMY-KXQvaGQ,2047
+boltz/data/parse/yaml.py,sha256=GRFRMtDD4PQ4PIpA_S1jj0vRaEu2LlZd_g4rN1zUrNo,1505
 boltz/data/sample/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 boltz/data/sample/cluster.py,sha256=9Sx8qP7zGZOAyEspwYFtCTbGTBZnuN-zfCKFbbA_6oI,8175
 boltz/data/sample/distillation.py,sha256=ABzst2FBr_E54KqZWIHc1bYtKYr79lxRJM7PnS4ifK0,1789
@@ -107,9 +107,11 @@ 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-1.0.40.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.40.dist-info/METADATA,sha256=z2kizv_5w3PrpKHsDV_GXjhzQDRxRCWWT2pOESvbcFU,7171
-boltz_vsynthes-1.0.40.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.40.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.40.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.40.dist-info/RECORD,,
+boltz/utils/sdf_splitter.py,sha256=ZHn_syOcmm-fDnJ3YEGyGv_vYz2IRzUW7vbbMSU2JBY,2108
+boltz/utils/yaml_generator.py,sha256=0Lg7F5dQRX75_xR8jiFVokSprDmFzsNmhaITI4fHjao,3980
+boltz_vsynthes-1.0.42.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.42.dist-info/METADATA,sha256=IKbpa2PuzcHwROQ7sbRRf2GXL7HmlWzHRg3NUHGrZ58,7171
+boltz_vsynthes-1.0.42.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.42.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.42.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.42.dist-info/RECORD,,