Dear Paolo,
Thank you for your reply.
I understand now... I did not use uniquify option first then only uniquify=True. I thought the default would be uniquify=False.
Actually my problem is to find 2 distinct units of isoprene (pattern) in the borneol (smiles) as the latter is a monoterpene.
Do you have any idea I can do this ?
Thanks in advance for your time.
Best regards,
QT
Dear Quoc-Tuan,
On 04/05/2020 09:10, Greenpharma S.A.S. wrote:
Dear All,
Please could you help with the following problem (I could not find answers in discussion list) ?
pattern='C~C~C(~C)~C'
smiles='O[C@H]1C[C@H]2C([C@@]1(C)CC2)(C)C'
pat = Chem.MolFromSmiles(pattern)
mol = Chem.MolFromSmiles(smiles)
res = mol.GetSubstructMatches(pat, uniquify=True)
The results are:
((1, 2, 3, 4, 8), (1, 5, 4, 3, 9), (1, 5, 4, 3, 10), (1, 5, 4, 9, 10), (2, 1, 5, 4, 6), (2, 1, 5, 4, 7), (2, 1, 5, 6, 7), (2, 3, 4, 5, 9), (2, 3, 4, 5, 10), (2, 3, 4, 9, 10), (3, 4, 5, 1, 6), (3, 4, 5, 1, 7), (3, 4, 5, 6, 7), (5, 4, 3, 2, 8), (6, 5, 4, 3, 9), (6, 5, 4, 3, 10), (6, 5, 4, 9, 10), (7, 5, 4, 3, 9), (7, 5, 4, 3, 10), (7, 5, 4, 9, 10), (7, 8, 3, 2, 4), (8, 3, 4, 5, 9), (8, 3, 4, 5, 10), (8, 3, 4, 9, 10), (8, 7, 5, 1, 4), (8, 7, 5, 1, 6), (8, 7, 5, 4, 6), (9, 4, 3, 2, 8), (9, 4, 5, 1, 6), (9, 4, 5, 1, 7), (9, 4, 5, 6, 7), (10, 4, 3, 2, 8), (10, 4, 5, 1, 6), (10, 4, 5, 1, 7), (10, 4, 5, 6, 7))
I expect to have only 2 matches with uniquify=True as I only have 2 units of the pattern.
GetSubstructMatches() will report all matches of the pattern against your molecule. In your case, there are 35 matches which are all constituted by different atom indices.
Furthermore, with or without uniquify, I have the same answers.
If you set uniquify=False, you actually get 70 matches, so twice as many answers. This time, matches can be constitued by the same indices, provided they are in a different permutation.
I have uploaded a gist here:
https://gist.github.com/ptosco/6d70cec235361fbaddc7cbc2cf9c3b5d
that hopefully will make this clearer.
Cheers,
p.
I also expected that there should be 2 "independent" lists but here, there is always at least one common atom between each list.
Is there something misunderstood or misused?
Thanks in advance for your help and explanations.
Best regards,
Quoc-Tuan
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