def test_10_removeGenerateConformer(self):
molsmile = SMILE_SMI
sm = SmallMol(molsmile)
sm.generateConformers(num_confs=10, append=False)
n_confs = sm.numConformers
sm.removeConformers([0])
n_confs_del = sm.numConformers
sm.removeConformers()
n_confs_zero = sm.numConformers
self.assertEqual(n_confs_del, n_confs - 1, "The number of conformations after the deletion was not reduced of "
"exactly one unit")
self.assertEqual(n_confs_zero, 0, "The number of conformations after the deletion was not reduced to 0")
def test_10_removeGenerateConformer(self):
molsmile = SMILE_SMI
sm = SmallMol(molsmile)
sm.generateConformers(num_confs=10, append=False)
n_confs = sm.numConformers
sm.removeConformers([0])
n_confs_del = sm.numConformers
sm.removeConformers()
n_confs_zero = sm.numConformers
self.assertEqual(
n_confs_del, n_confs - 1,
"The number of conformations after the deletion was not reduced of "
"exactly one unit")
self.assertEqual(
n_confs_zero, 0,
"The number of conformations after the deletion was not reduced to 0"
)
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 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