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
>>
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>>
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