rdkit.Chem.TemplateAlign module¶
- rdkit.Chem.TemplateAlign.AlignMolToTemplate2D(mol, template, match=None, clearConfs=False, templateConfId=-1)¶
Arguments:
mol: the molecule to be aligned
template: the template to align to
- match: If provided, this should be a sequence of integers
containing the indices of the atoms in mol that match those in template. This is the result of calling:
mol.GetSubstructMatch(template)
clearConfs: toggles removing any existing conformers on mol
Returns the confId of the conformer containing the depiction
>>> patt = Chem.MolFromSmiles('C1CC1') >>> rdDepictor.Compute2DCoords(patt) 0 >>> mol = Chem.MolFromSmiles('OC1CC1CC1CCC1') >>> rdDepictor.Compute2DCoords(mol) 0 >>> pc = patt.GetConformer(0) >>> mc = mol.GetConformer(0)
We start out with the molecules not aligned:
>>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())] >>> [x<1e-4 for x in vs] [False, False, False]
But then we can replace the conformer of mol:
>>> AlignMolToTemplate2D(mol,patt,clearConfs=True) 0 >>> mol.GetNumConformers() 1 >>> pc = patt.GetConformer(0) >>> mc = mol.GetConformer(0) >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())] >>> [x<1e-4 for x in vs] [True, True, True]
If we like, we can specify the atom map explicitly in order to align to the second matching ring in the probe molecule:
>>> match = (5,6,7) >>> AlignMolToTemplate2D(mol,patt,clearConfs=True,match=match) 0 >>> mol.GetNumConformers() 1 >>> pc = patt.GetConformer(0) >>> mc = mol.GetConformer(0) >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())] >>> [x<1e-4 for x in vs] [False, False, False] >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+5).x) for i in range(pc.GetNumAtoms())] >>> [x<1e-4 for x in vs] [True, True, True]