Thank you Wim, this is good to know.
Ling
Wim Dehaen <wimdeh...@gmail.com> 於 2021年11月4日週四 下午3:48寫道：
> Re: your second issue with the 2D depiction, especially for these kinds of
> bicyclic structures, the Schrödinger coordgen that is a part of RDKit gives
> better looking results(at the cost of a somewhat longer running time). You
> can turn it on using:
> from rdkit.Chem import rdDepictor
> rdDepictor.SetPreferCoordGen(True)
> before rendering. It works nicely on the molecules from this question.
> best wishes
> wim
>
> On Thu, Nov 4, 2021 at 11:33 PM Ivan Tubert-Brohman <
> ivan.tubert-broh...@schrodinger.com> wrote:
>
>> That does seem like a bug. You can also see it without involving
>> DeleteSubstructs, by starting from different SMILES representations of the
>> same molecule:
>>
>> >>> m1 = Chem.MolFromSmiles('FC12C3CCCC1C32F')
>>
>>
>> >>> m2 = Chem.MolFromSmiles('C12C3CCCC1C32')
>>
>>
>> >>> m3 = Chem.MolFromSmiles('C1CC2C3C(C1)C23')
>>
>> >>> Chem.MolToSmiles(m2) == Chem.MolToSmiles(m3)
>>
>> True
>>
>> >>> m1.GetSubstructMatch(m2)
>>
>> (1, 2, 3, 4, 5, 6, 7)
>>
>> >>> m1.GetSubstructMatch(m3)
>>
>> ()
>>
>> Note that if you parse the problem SMILES as a SMARTS, you do get a match:
>>
>> >>> m4 = Chem.MolFromSmarts('C1CC2C3C(C1)C23')
>>
>>
>> >>> m1.GetSubstructMatch(m4)
>>
>> (4, 3, 2, 1, 6, 5, 7)
>>
>> Another interesting bit is that while the Inchis of m2 and m3 are also
>> the same, the conversion produces a warning about stereochemistry:
>>
>> >>> Chem.MolToInchi(m2) == Chem.MolToInchi(m3)
>>
>> [18:26:48] WARNING: Omitted undefined stereo
>> [18:26:48] WARNING: Omitted undefined stereo
>> True
>>
>> Ivan
>>
>> On Wed, Nov 3, 2021 at 3:59 PM Ling Chan <lingtrek...@gmail.com> wrote:
>>
>>> Dear colleagues,
>>>
>>> I have a molecule "FC12C3CCCC1C32F". I stripped it of the F's, and tried
>>> to do a GetSubstructMatch. It worked. But if I reconstruct the stripped
>>> molecule from a smiles string, it does not. Please see attached.
>>>
>>> I suppose some info is lost when you reconstruct the stripped core from
>>> a smiles string. But still, I would think it should match anyway.
>>>
>>> Another issue is that the 2D depiction has the left most carbons lying
>>> exactly on top of each other, creating a false impression. A better
>>> depiction would be like the second attached image. (Not sure if this is
>>> easy to fix though.)
>>>
>>> Thank you for you attention.
>>>
>>> Ling
>>>
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>> _______________________________________________
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>>
>
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