from rdkit import Chem
from openpharmacophore import Ligand, Protein
from openpharmacophore import mol_files
from openpharmacophore.io.exceptions import InvalidFileFormatError
from openpharmacophore.molecular_systems import create_topology
import openpharmacophore.constants as config
def protein_from_file(traj_file, topology_file):
""" Create a protein object from a file
"""
topology, coords = create_topology(traj_file, topology_file)
return Protein(topology, coords)
def load_ligands_from_file(file_path, file_format):
""" Load ligands from a file.
Returns
-------
list[Ligand]
"""
if file_format == "smi":
return [Ligand(mol) for mol in Chem.SmilesMolSupplier(file_path)]
if file_format == "sdf":
return [Ligand(mol) for mol in mol_files.read_sdf(file_path)]
if file_format == "mol2":
return [Ligand(mol) for mol in mol_files.mol2(file_path)]
if file_format == "xyz":
return [Ligand(Chem.MolFromXYZFile(file_path))]
if file_format == "mol":
return [Ligand(Chem.MolFromMolFile(file_path))]
[docs]def load(file_name, topology_file=None):
""" Load ligands, protein, protein-ligand complexes, or MD trajectories
from a file.
Parameters
----------
file_name : str
Name of the file containing the data.
topology_file : str, optional
File with the topology of the system for a MD trajectory.
Returns
-------
LigandSet or Protein
"""
file_format = file_name.split(".")[-1]
if file_format in config.TRAJ_FORMATS:
if topology_file is not None and topology_file not in config.TOP_FORMATS:
file_format = topology_file.split(".")[-1]
raise InvalidFileFormatError(file_format)
return protein_from_file(file_name, topology_file)
elif file_format in config.MOL_FORMATS:
return load_ligands_from_file(file_name, file_format)
else:
raise InvalidFileFormatError(file_format)
class InvalidFormError(ValueError):
pass
[docs]def load_ligands(ligands, form):
""" Load ligands from a list of SMILES, SMARTS, Inchi, Mol2 block
or PDB block.
Parameters
----------
ligands : list[str]
List with the ligands
form : str
The form of the ligands. Can be "smi", "smarts", "inchi",
"mol2", "pdb".
Returns
-------
list[Ligand]
The set with all the ligands.
"""
if form not in config.MOL_STR_FORMATS:
raise InvalidFormError(f"Form {form} is not a supported form")
return [
Ligand.from_string(lig, form=form) for lig in ligands
]
