I just run sudo apt-get install python-rdkit librdkit1 rdkit-data ūüėĀ
I'm trying to solve this with this link:
http://www.blopig.com/blog/2013/02/how-to-install-rdkit-on-ubuntu-12-04/

--
Wandré Nunes de Pinho Veloso
Professor Assistente - Unifei - Campus Avançado de Itabira-MG
Doutorando em Bioinform√°tica - 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 Bioinform√°tica Estrutural da UFMG
Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG

2017-09-13 16:55 GMT-03:00 Markus Sitzmann <markus.sitzm...@gmail.com>:

> 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 Bioinform√°tica - 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 Bioinform√°tica 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 Bioinform√°tica - 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 Bioinform√°tica 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 Bioinform√°tica - 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 Bioinform√°tica 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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