How did you install rdkit so far? And where? Is it the conda/anaconda
version?
On Wed, Sep 13, 2017 at 9:39 PM, Wandré <wandrevel...@gmail.com> wrote:
> 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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