Dear Paolo,
this answers my question as well, but in an unexpected way.
Best,
Jean-Marc
Le 05/05/2020 à 14:52, Paolo Tosco a écrit :
Dear Quoc-Tuan,
this should do what you need:
https://gist.github.com/ptosco/dc4d27153e6e8e45aed654761e4d7409
Cheers,
p.
On 05/05/2020 11:52, Quoc-Tuan DO wrote:
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
Le 04/05/2020 à 19:53, Paolo Tosco a écrit :
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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