How to install RDKit with InChI?
When I run Chem.inchi.INCHI_AVAILABLE, the result is False

--
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 16:30 GMT-03:00 Wandré <wandrevel...@gmail.com>:

> Thanks Malitha.
> I choose this descriptors because I will store this on my database, so,
> will be fast compare one molecule before insert them in database.
> My worry now is if the RDKit will generate different SMILES or InChI in
> same SDF molecule or equals in different molecules (molecules from RCSB
> PDB, PubChem, ChemBL, for example).
>
> --
> 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 16:22 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
>
>> Hi Wandré,
>>
>> It seems you already did intense research on it. Kindly accept my
>> comments as an addition to your idea (not the answer you trying to find
>> out). In my idea, categorizing molecules using it's descriptor should
>> reduce computation time. RDKit currently offer calculation of about 200
>> descriptors! So, a careful look up at those makes a lot of sense to me.
>> Conceptually, descriptor matching should follow a sequence (I don't know
>> what sequence would be ideal) - for example MolWt should match first (H
>> contribution and ions should be taken into consideration here) and then
>> subsequent matching of other descriptors (might be different while writing
>> programs). There are a few reading materials on molecular fingerprint and
>> database schema. You may have a look at those.
>>
>> The links are from Daylight. I am neither involved with the company nor
>> their product.
>> http://www.daylight.com/dayhtml/doc/theory/theory.finger.html
>> http://www.daylight.com/dayhtml/doc/theory/theory.thor.html
>>
>> Best regards,
>> - malitha
>>
>>
>> On Thu, Sep 14, 2017 at 12:43 AM, Wandré <wandrevel...@gmail.com> wrote:
>>
>>> 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, Ri
>>> ngCount, 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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>>>
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>>
>
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