def align(self, refmol):
from rdkit.Chem.rdMolAlign import GetO3A
from moleculekit.molecule import Molecule
if isinstance(refmol, SmallMol):
refmol = refmol._mol
if isinstance(refmol, Molecule):
refmol = SmallMol(refmol)._mol
pyO3A = GetO3A(self._mol, refmol)
rmsd = pyO3A.Align()
logger.info('Alignment with a RMSD of {}'.format(rmsd))
def untransformed_rmsd(reference,
probe,
sanitize=True,
uniquify=False,
reflect=True,
method='sub',
**kwargs):
rdk_reference = _chimera_to_rdkit(reference, sanitize=sanitize)
rdk_probe = _chimera_to_rdkit(probe, sanitize=sanitize)
if method in ('sub', 'best'):
matches = rdk_reference.GetSubstructMatches(rdk_probe,
uniquify=uniquify)
elif method == 'o3a':
rdk_reference2 = _chimera_to_rdkit(reference, sanitize=sanitize)
rdk_probe2 = _chimera_to_rdkit(probe, sanitize=sanitize)
FastFindRings(rdk_reference)
FastFindRings(rdk_probe)
reference_params = MMFFGetMoleculeProperties(rdk_reference)
probe_params = MMFFGetMoleculeProperties(rdk_probe)
o3a = GetO3A(rdk_probe2,
rdk_reference2,
probe_params,
reference_params,
maxIters=0,
reflect=reflect)
matches = o3a.Matches()
else:
raise chimera.UserError('`method` must be sub, best or o3a')
if not matches:
raise chimera.UserError('Could not find any matches.')
maps = [list(enumerate(match)) for match in matches]
best_rmsd = 1000.
for atom_map in maps:
rmsd = AlignMol(rdk_probe,
rdk_reference,
-1,
-1,
atomMap=atom_map,
maxIters=0,
reflect=reflect)
if rmsd < best_rmsd:
best_rmsd = rmsd
return best_rmsd
def alignMol(smallmol, refmol):
"""
Return a new SmallMol object aligned to a refmol that can be a htmd.smallmol.smallmol.SmallMol
or rdkit.Chem.rdchem.Mol. It removes all the conformers stored in the original object.
Parameters
----------
smallmol: htmd.smallmol.smallmol.SmallMol
The SmallMol object to align
refmol: htmd.smallmol.smallmol.SmallMol or rdkit.Chem.rdchem.Mol
The molecule to align to
Return
------
newsmallmol: htmd.smallmol.smallmol.SmallMol
a new SmallMol aligned to reference molecule
"""
from htmd.smallmol.smallmol import SmallMol
from rdkit.Chem.rdMolAlign import GetO3A
if isinstance(refmol, SmallMol):
refmol = refmol.toRdkitMol(includeConformer=True)
sm_rdkit = smallmol.toRdkitMol(includeConformer=True)
pyO3A = GetO3A(sm_rdkit, refmol)
rmsd = pyO3A.Align()
print('Alignment with a RMSD of {}'.format(rmsd))
coords_new = sm_rdkit.GetConformer().GetPositions()
sm_new = SmallMol(smallmol, fixHs=False)
sm_new.removeConformers()
sm_new.coords = coords_new[:, :, np.newaxis]
return sm_new
def align_o3a(reference,
probe,
transform=True,
sanitize=True,
maxIters=50,
reflect=False,
**kwargs):
rdk_reference = _chimera_to_rdkit(reference, sanitize=sanitize)
rdk_probe = _chimera_to_rdkit(probe, sanitize=sanitize)
FastFindRings(rdk_reference)
FastFindRings(rdk_probe)
reference_params = MMFFGetMoleculeProperties(rdk_reference)
probe_params = MMFFGetMoleculeProperties(rdk_probe)
o3a = GetO3A(rdk_probe,
rdk_reference,
prbPyMMFFMolProperties=probe_params,
refPyMMFFMolProperties=reference_params,
maxIters=maxIters,
reflect=reflect)
rmsd, xform = o3a.Trans()
if transform:
_transform_molecule(probe, chimera_xform(xform[:3]))
return rmsd