from rdkit import Chem
# MOL2 files
def _mol2(file_):
molecules = []
doc = [line for line in file_.readlines()]
start = [index for (index, p) in enumerate(doc) if '@<TRIPOS>MOLECULE' in p]
finish = [index - 1 for (index, p) in enumerate(doc) if '@<TRIPOS>MOLECULE' in p]
finish.append(len(doc))
interval = list(zip(start, finish[1:]))
for ii in interval:
block = ",".join(doc[ii[0]: ii[1]]).replace(',', '')
mol = Chem.MolFromMol2Block(block)
molecules.append(mol)
return molecules
[docs]def read_mol2(file_name):
""" Load molecules from a mol2 file.
Parameters
----------
file_name : str
Name of the file containing the ligands
Returns
---------
molecules : list[rdkit.Mol]
"""
with open(file_name, 'r') as fp:
molecules = _mol2(fp)
return molecules
def _iter_mol2(file_):
line = file_.readline()
while line:
if not line:
break
if not line.strip():
continue
# Skip comments
if line.startswith("#"):
continue
if '@<TRIPOS>MOLECULE' not in line:
mol2_block = "@<TRIPOS>MOLECULE\n"
mol2_block += line
else:
mol2_block = line
while True:
line = file_.readline()
if '@<TRIPOS>MOLECULE' in line or len(line) == 0:
break
mol2_block += line
yield Chem.MolFromMol2Block(mol2_block)
line = file_.readline()
[docs]def mol2_supplier(file_name):
""" A molecule generator for mol2 files.
Parameters
----------
file_name : str
A file object
Yields
------
mol : rdkit.Mol
A molecule.
"""
with open(file_name) as fp:
return _iter_mol2(fp)
# SDF files
def _sdf(file_, supplier, remove_hs=False):
supp = supplier(file_, removeHs=remove_hs)
molecules = {}
for mol in supp:
name = mol.GetProp("_Name")
try:
molecules[name].AddConformer(mol.GetConformer(), assignId=True)
except KeyError:
molecules[name] = mol
return list(molecules.values())
[docs]def read_sdf(file_path, remove_hs=False):
""" Load an sdf file with molecules that may contain multiple conformers.
Parameters
----------
file_path : str
remove_hs : bool, default=False
Whether to remove the hydrogens from the molecules.
Returns
-------
list : [rdkit.Chem.Mol]
"""
return _sdf(file_path, Chem.SDMolSupplier, remove_hs)
def _iter_sdf(file_, supplier, remove_hs=False):
""" Iterate an sdf file
Parameters
----------
file_ : str or FileIO
A path to a file or an stream io such as a BytesIO
supplier : Callable
remove_hs : bool
Returns
-------
Iterable
An iterable of molecules.
"""
return supplier(file_, removeHs=remove_hs)
# SMI files
def _parse_smi(line, sep):
fragments = line.split(sep)
mol = Chem.MolFromSmiles(fragments[0])
if len(fragments) > 1:
mol.SetProp("_Name", fragments[1])
return mol
def _smi(file_, sep=None, header=False):
start = 1 if header else 0
lines = file_.readlines()
molecules = []
for ii in range(start, len(lines)):
molecules.append(_parse_smi(lines[ii], sep))
return molecules
def read_smi(file_name, sep=None, header=False):
""" Read molecules from a smi file.
Parameters
----------
file_name : str
Name or path to the file
sep : str
Separator between text in a line of the file. Default
behavior is to split between whitespace.
header : bool, default=False
Whether the file contains a header
"""
with open(file_name) as fp:
molecules = _smi(fp, sep, header)
return molecules
def _iter_smi(file_, sep=None, header=False):
""" Iterate a smi file.
Parameters
----------
file_ : FileIO
A file like object.
sep : str
header : bool
Yields
------
rdkit.Mol
"""
if header:
file_.readline()
line = file_.readline()
while line:
yield _parse_smi(line, sep)
line = file_.readline()
