def get_orientation(self, xyz, rtol=0.15):
"""
get orientation, needs to check the tolerance
"""
from rdkit.Geometry import Point3D
from rdkit.Chem import rdMolAlign, RemoveHs, rdmolfiles, rdMolTransforms
mol = self.rdkit_mol(self.smile)
conf0 = mol.GetConformer(0)
conf1 = mol.GetConformer(1)
conf2 = mol.GetConformer(2)
angs = self.get_torsion_angles(xyz)
xyz0 = self.set_torsion_angles(conf0, angs) #conf0 with aligned
xyz1 = self.set_torsion_angles(conf0, angs, True) #conf0 with aligned
for i in range(len(self.mol)):
x0,y0,z0 = xyz0[i]
x1,y1,z1 = xyz1[i]
x,y,z = xyz[i]
conf0.SetAtomPosition(i,Point3D(x0,y0,z0))
conf1.SetAtomPosition(i,Point3D(x,y,z))
conf2.SetAtomPosition(i,Point3D(x1,y1,z1))
mol = RemoveHs(mol)
rmsd1, trans1 = rdMolAlign.GetAlignmentTransform(mol, mol, 1, 0)
rmsd2, trans2 = rdMolAlign.GetAlignmentTransform(mol, mol, 1, 2)
tol = rtol*mol.GetNumAtoms()
#print(rmsd1, rmsd2)
if rmsd1 < tol:
trans = trans1[:3,:3].T
r = Rotation.from_matrix(trans)
return r.as_euler('zxy', degrees=True), rmsd1, False
elif rmsd2 < tol:
trans = trans2[:3,:3].T
r = Rotation.from_matrix(trans)
return r.as_euler('zxy', degrees=True), rmsd2, True
else:
print(rmsd1, rmsd2)
#rdmolfiles.MolToXYZFile(mol, '1.xyz', 0)
#rdmolfiles.MolToXYZFile(mol, '2.xyz', 1)
#rdmolfiles.MolToXYZFile(mol, '3.xyz', 2)
print(self.get_torsion_angles(xyz))
print(self.get_torsion_angles(xyz0))
print(self.get_torsion_angles(xyz1))
raise ValueError("Problem in conformer")
def get_rmsd(mol1, mol2):
mols = [mol1, mol2]
mcs = rdFMCS.FindMCS(mols)
match = rdkit.Chem.MolFromSmarts(mcs.smartsString)
match1 = mol1.GetSubstructMatch(match)
match2 = mol2.GetSubstructMatch(match)
atom_map = zip(match1, match2)
if len(atom_map) == 0:
return np.nan
return rdMolAlign.GetAlignmentTransform(mol1, mol2, atomMap=atom_map)[0]
def test1Basic(self):
file1 = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol',
'MolAlign', 'test_data', '1oir.mol')
file2 = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol',
'MolAlign', 'test_data', '1oir_conf.mol')
mol1 = Chem.MolFromMolFile(file1)
mol2 = Chem.MolFromMolFile(file2)
rmsd = rdMolAlign.AlignMol(mol2, mol1)
self.failUnless(feq(rmsd, 0.6578))
file3 = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol',
'MolAlign', 'test_data', '1oir_trans.mol')
mol3 = Chem.MolFromMolFile(file3)
conf2 = mol2.GetConformer()
conf3 = mol3.GetConformer()
for i in range(mol2.GetNumAtoms()):
self.failUnless(lstFeq(conf2.GetAtomPosition(i), conf3.GetAtomPosition(i)))
rmsd, trans = rdMolAlign.GetAlignmentTransform(mol2, mol1)
self.failUnless(feq(rmsd, 0.6578))
def __get_transformation_matrix(self, model, mapping):
return rdMolAlign.GetAlignmentTransform(self.get_mol(), self.get_mol(model), atomMap=tuple(mapping.items()))[1]
def get_rmsd(mol):
rms, tmat = rdMolAlign.GetAlignmentTransform(mol, mol, prbCid=0, refCid=1)
return rms