from openpharmacophore import Ligand
from openpharmacophore.io import mol_files, exceptions
[docs]class InMemoryMolDB:
""" A repository of molecules that are stored in memory. Such as
a list of smiles or rdkit molecules.
"""
def __init__(self):
self._read_fn = None
self._molecules = None
[docs] def from_smiles(self, smiles):
""" Adds molecules from a list of SMILES.
Parameters
----------
smiles : list[str]
List with the SMILES.
"""
self._read_fn = lambda m: Ligand.from_string(m, form="smi")
self._molecules = smiles
[docs] def from_rdkit(self, mols):
""" Adds molecules from a list of rdkit Mol.
Parameters
----------
mols : list[rdkit.Mol]
List with the molecules.
"""
self._read_fn = lambda m: Ligand(m)
self._molecules = mols
def __iter__(self):
self._ii = 0
return self
def __next__(self):
""" Iterate the molecules of the database converting
them to the Ligand class.
"""
if self._ii >= len(self._molecules):
del self._ii
raise StopIteration
mol = self._read_fn(self._molecules[self._ii])
self._ii += 1
return mol
class LigandGenerator:
def __init__(self, generator):
self._gen = generator
def __iter__(self):
return self
def __next__(self):
return Ligand(next(self._gen))
[docs]class MolDB:
""" A repository of molecules that are stored in files or file
like objects.
"""
_mol_file_iterators = {
"smi": mol_files._iter_smi,
"sdf": mol_files._iter_sdf,
"mol2": mol_files._iter_mol2,
}
def __init__(self):
self._files = []
self._extensions = []
self._kwargs = {}
[docs] def from_file(self, file_name, **kwargs):
""" Adds molecules from a file.
Parameters
----------
file_name: str
Name or path of the file.
"""
file_extension = file_name.split(".")[-1]
if file_extension not in MolDB._mol_file_iterators:
raise exceptions.InvalidFileFormatError(
f"{file_extension} is not a supported file format"
)
self._from_file(open(file_name), file_extension)
self._kwargs = kwargs
[docs] def from_file_list(self, files, **kwargs):
""" Adds molecules from a list of files.
Parameters
----------
files: list[str]
Name or path of the file.
"""
for filename in files:
self.from_file(filename, **kwargs)
def _from_file(self, file_, extension):
self._files.append(file_)
self._extensions.append(extension)
def __iter__(self):
for ii in range(len(self._files)):
file_ = self._files[ii]
extension = self._extensions[ii]
yield from LigandGenerator(
MolDB._mol_file_iterators[extension](file_, **self._kwargs)
)
file_.close()
