def detectChiralCenters(mol, atom_types=None):
"""
Detect chiral centers
Parameters
----------
mol: Molecule
Molecule to detect chiral centers
Return
------
results: List of tuples
List of chircal centers, where the chiral centers are tuples made of an atom index and a label ('S', 'R', '?').
Examples
--------
>>> from parameterize.home import home
>>> from moleculekit.molecule import Molecule
>>> molFile = os.path.join(home('test-param'), 'H2O2.mol2')
>>> mol = Molecule(molFile)
>>> detectChiralCenters(mol)
[]
>>> molFile = os.path.join(home('test-param'), 'fluorchlorcyclopronol.mol2')
>>> mol = Molecule(molFile)
>>> detectChiralCenters(mol)
[(0, 'R'), (2, 'S'), (4, 'R')]
>>> molFile = os.path.join(home('test-param'), 'fluorchlorcyclopronol.mol2')
>>> mol = Molecule(molFile)
>>> detectChiralCenters(mol, atom_types=mol.atomtype)
[(0, 'R'), (2, 'S'), (4, 'R')]
"""
from moleculekit.molecule import Molecule
from moleculekit.smallmol.smallmol import SmallMol
from rdkit.Chem import AssignAtomChiralTagsFromStructure, FindMolChiralCenters
if not isinstance(mol, Molecule):
raise TypeError('"mol" has to be instance of {}'.format(Molecule))
if mol.numFrames != 1:
raise ValueError('"mol" can have just one frame, but it has {}'.format(
mol.numFrames))
# Set atom types, overwise rdkit refuse to read some MOL2 files
htmd_mol = mol.copy()
if atom_types is not None:
htmd_mol.atomtype = atom_types
# Detect chiral centers and assign their labels
sm = SmallMol(htmd_mol,
fixHs=False,
removeHs=False,
verbose=False,
force_reading=True)
AssignAtomChiralTagsFromStructure(sm._mol)
chiral_centers = FindMolChiralCenters(sm._mol, includeUnassigned=True)
return chiral_centers
def detectChiralCenters(mol):
"""
Detect chiral centers
Parameters
----------
mol: Molecule
Molecule to detect chiral centers
Return
------
results: List of tuples
List of chircal centers, where the chiral centers are tuples made of an atom index and a label ('S', 'R', '?').
Examples
--------
>>> from htmd.home import home
>>> from htmd.molecule.molecule import Molecule
>>> molFile = os.path.join(home('test-param'), 'H2O2.mol2')
>>> mol = Molecule(molFile)
>>> detectChiralCenters(mol)
[]
>>> molFile = os.path.join(home('test-param'), 'fluorchlorcyclopronol.mol2')
>>> mol = Molecule(molFile)
>>> detectChiralCenters(mol)
[(0, 'R'), (2, 'S'), (4, 'R')]
"""
from htmd.molecule.molecule import Molecule
from rdkit.Chem import MolFromMol2File, AssignAtomChiralTagsFromStructure, FindMolChiralCenters
if not isinstance(mol, Molecule):
raise TypeError('"mol" has to be instance of {}'.format(Molecule))
if mol.numFrames != 1:
raise ValueError('"mol" can have just one frame, but it has {}'.format(
mol.numFrames))
# Set atom types to elements, overwise rdkit refuse to read a MOL2 file
htmd_mol = mol.copy()
htmd_mol.atomtype = htmd_mol.element
# Convert Molecule to rdkit Mol
with TemporaryDirectory() as tmpDir:
filename = os.path.join(tmpDir, 'mol.mol2')
htmd_mol.write(filename)
rdkit_mol = MolFromMol2File(filename, removeHs=False)
assert mol.numAtoms == rdkit_mol.GetNumAtoms()
# Detect chiral centers and assign their labels
AssignAtomChiralTagsFromStructure(rdkit_mol)
chiral_centers = FindMolChiralCenters(rdkit_mol, includeUnassigned=True)
return chiral_centers
def open_molecule_file(uploadedfile, logfile=os.devnull, filetype=None):
#charset = 'utf-8'
#if "charset" in uploadedfile and uploadedfile.charset is not None:
#charset = uploadedfile.charset
if filetype is None:
if "filetype" not in uploadedfile or uploadedfile.filetype is None:
basename, ext = os.path.splitext(uploadedfile.name)
ext = ext.lower()
ext = ext.strip('.')
if ext in MOLECULE_EXTENSION_TYPES.keys():
filetype = MOLECULE_EXTENSION_TYPES[ext]
uploadedfile.filetype = filetype
else:
raise InvalidMoleculeFileExtension(ext=ext)
else:
filetype = uploadedfile.filetype
with stdout_redirected(to=logfile, stdout=sys.stderr):
with stdout_redirected(to=logfile, stdout=sys.stdout):
print('Loading molecule...')
uploadedfile.seek(0)
if filetype == 'sdf' or filetype == 'mol':
suppl = ForwardSDMolSupplier(uploadedfile, removeHs=False)
mol = next(suppl)
try:
next(suppl)
except StopIteration:
pass
except:
raise
else:
raise MultipleMoleculesinSDF()
finally:
del suppl
if mol is None:
if filetype == 'sdf':
raise ParsingError("Invalid SDFile file.")
else:
raise ParsingError("Invalid MDL Mol file.")
print('Assigning chirality from struture...')
AssignAtomChiralTagsFromStructure(mol, replaceExistingTags=False)
print('Finished loading molecule.')
return mol
def _assignAtomChiralTagsFromStructure(mol):
return AssignAtomChiralTagsFromStructure(mol)