Hi Jameed,
thanks for your quick answer. It was indeed a problem with my input SMILES. I
prepared the input using RDKit and forgot to turn on writing out the stereo
signs. For the list, here is some sample code from Markus Hartenfeller who
pointed this out to me. Thanks Markus!
------------
from rdkit import Chem
s = 'C[C@H](O)N'
#MolFromSmiles by default uses stereo info, but for MolToSmiles only if turned
on by true as second argument
print Chem.MolToSmiles(Chem.MolFromSmiles(s)) #its read, but not written
print Chem.MolToSmiles(Chem.MolFromSmiles(s),True) #switch on writing stereo
------------
Bests,
Christian
Am 11.11.2013 um 18:23 schrieb Jameed Hussain <[email protected]>:
> Hi Christian,
>
> As long as your input SMILES contains stereochemistry, the fragmentation and
> indexing should keep it (so hopefully, it should just be the case of checking
> your input SMILES).
>
> The output I get from the SMILES below (default settings):
>
> CC[C@H](Cl)Br a
> CCC[C@H](Cl)Br b
>
> is:
>
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C[C@H](Cl)Br>>[*:1]CC[C@H](Cl)Br,[*:1]C
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C[*:2]>>[*:1]CC[*:2],[*:1]C.[*:2][C@H](Cl)Br
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C([*:2])Cl>>[*:1]C[C@@H]([*:2])Cl,[*:2]Br.[*:1]CC
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]CC>>[*:1]CCC,[*:1][C@H](Cl)Br
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C[C@@H]([*:2])Cl>>[*:1]CC[C@@H]([*:2])Cl,[*:1]C.[*:2]Br
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C([*:2])CC>>[*:1]C([*:2])CCC,[*:1]Cl.[*:2]Br
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C>>[*:1]CC,[*:1]C[C@H](Cl)Br
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1][C@@H](Cl)CC>>[*:1][C@@H](Cl)CCC,[*:1]Br
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C([*:2])Br>>[*:1]C[C@@H]([*:2])Br,[*:2]Cl.[*:1]CC
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1][C@H](Cl)Br>>[*:1]C[C@H](Cl)Br,[*:1]CC
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C([*:2])[*:3]>>[*:1]CC([*:2])[*:3],[*:3]Cl.[*:2]Br.[*:1]CC
> CCC[C@H](Cl)Br,CC[C@H](Cl)Br,b,a,[*:1]C>>[*:1][H],[*:1]CC[C@H](Cl)Br
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1][C@@H](Br)CC>>[*:1][C@@H](Br)CCC,[*:1]Cl
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C[C@@H]([*:2])Br>>[*:1]CC[C@@H]([*:2])Br,[*:1]C.[*:2]Cl
> CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]CC([*:2])[*:3]>>[*:1]CCC([*:2])[*:3],[*:1]C.[*:3]Cl.[*:2]Br
>
>
> Thanks
> Jameed
>
> -----Original Message-----
> From: Christian Kramer [mailto:[email protected]]
> Sent: 11 November 2013 13:31
> To: [email protected]
> Subject: [Rdkit-discuss] MMP and Stereo Perception
>
> Hi RD-Kitters,
>
> I have a question to all of you using the great MMP implementation from
> Jameed:
>
> How do you treat stereochemistry?
>
> When I run the programs, the output of the fragmentation and the matching
> does not contain any stereo information any more. Is there a way to keep this
> during the fragmentation? Do you add the stereo information after the
> matching and check whether the major parts or scaffolds of the two molecules
> have the same stereochemistry?
>
> Thanks for your ideas,
> Christian
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