PS. The conda version has InChI support
On Wed, Sep 13, 2017 at 10:04 PM, Markus Sitzmann <markus.sitzm...@gmail.com
> wrote:
> 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 😁
>> I'm trying to solve this with this link: http://www.blopig.com/bl
>> og/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 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 16:55 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 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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>>>
>>
>
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