AlignMolToTemplate2D(mol,
template,
match=None,
clearConfs=False,
templateConfId=-1)
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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]
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