Hello,
I'd like to enumerate all possible permutations of symmetric atoms.
Consider the following code:
phenol = Chem.MolFromSmiles("Oc1ccccc1")
equivalencies = list(Chem.CanonicalRankAtoms(mol, breakTies=False))
print(equivalencies)
[0, 6, 4, 2, 1, 2, 4]
Atoms that have the same value in list "equivalencies" are symmetric. For
phenol, the equivalent atoms correspond to a 180 degree rotation of the
aromatic ring over the axis containing the carbon-oxygen bond. The possible
permutations, expressed as atom indices, are:
[0, 1, 2, 3, 4, 5, 6]
[0, 1, 6, 5, 4, 3, 2]
By permutations, I mean that it is possible to replace the coordinates of
the atoms and produce a realistic molecule.
A brute force approach comes to mind, where one would enumerate all
possible combinations, and exclude those that change the molecular graph.
In the example above there are four possible combinations, because there
are two groups of two symmetric atoms. An example of an "invalid"
combination is swapping the third and seventh atoms without swapping the
fourth and sixth atoms:
[0, 1, 6, 3, 4, 5, 2]
This would be excluded as it breaks the bond between the third and fourth
atoms (among other bonds).
Is there a method in the RDKit to enumerate the valid permutations?
Thank you,
Diogo
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