Thanks for all the answers.

Reading all answers, I think in something different... If the SMILES
(Chem.MolToSmiles(mol,isomericSmiles=True)) and Inchi
(Chem.MolToInchi(mol)) can generate the same value in different molecules,
I will generate others descriptors
(NumHDonors, NumHAcceptors, RingCount, GetNumAtoms, TPSA, pyLabuteASA,
MolWt, CalcNumRotatableBonds
and MolLogP) to compare all the molecules that SMILES and Inchi are the
same.
If all this data are the same, I will generate the fingerprint (Atompair
for exemple) and use Tanimoto coefficient and, if this value, when I
compare two molecules, is 1, this molecules are the same.

Where is my mistake (I think that is, one or more, mistakes)?

Thanks!

--
Wandré Nunes de Pinho Veloso
Professor Assistente - Unifei - Campus Avançado de Itabira-MG
Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
Inteligência Computacional - UNIFEI
Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG

2017-09-13 14:19 GMT-03:00 Dimitri Maziuk <dmaz...@bmrb.wisc.edu>:

> On 09/13/2017 11:46 AM, Markus Sitzmann wrote:
> > The case that you have 3D information available for a molecule dataset
> is rare, if you want it trustworthy it gets even worse than that. And what
> is the point then to generate the configuration of a molecule first if you
> can not trust that either?
>
> Veering further off topic, do you even care in the first place? E.g. if
> your molecule always exists as a mixture of isomers, except in some
> megabuck-per-microgram painstakingly created reference samples, a
> 3D-based system will represent it as two distinct molecules. Whereas you
> want it represented as one.
>
> Last I looked PDB Ligand Expo had two different benzenes. Their software
> doesn't (didn't?) do the circle version so they don't have the third one.
>
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
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