Strong recommendation: use the conda version:

http://www.rdkit.org/docs/Install.html

On Wed, Sep 13, 2017 at 9:58 PM, Wandré <wandrevel...@gmail.com> wrote:

> 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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>>
>
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