Hi Wandré,

Good day! It's malitha.

Considering your first question I would say, the path variable NOT set
correctly. To avoid having gymnastic with linux system you may consider the
following steps:

   1. Install miniconda or andcona from https://conda.io/miniconda.html and
   command yes (y) when it says to add path variable to python shipped with
   conda. I mean python within conda would be your default python. After
   installing it, when you run the command <<<<<python>>>>>> from shell you
   will see something like <<<Continuum Analytics>>> at the screen
   2. Install rdkit from https://anaconda.org/rdkit/rdkit on top of conda


For question regarding energy minimization, you may find the following link
helpful.
https://sourceforge.net/p/rdkit/mailman/message/28298074/

I hope, it helps!

- malitha

On Thu, Sep 14, 2017 at 4:22 PM, Wandré <wandrevel...@gmail.com> wrote:

> So,
> 1) I run all the commands in tutorial of installation of RDKit in Conda (
> https://github.com/rdkit/conda-rdkit), but, when I run python and try to
> import Chem ("from rdkit import Chem") appears an error message:
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line 18, in
> <module>
>     from rdkit import rdBase
> ImportError: cannot import name rdBase
>
> 2) Thanks for all the references
>
> 3) Which function generate this "energy minimized molecule"?
>
> --
> 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 17:32 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
>
>> Hi Wandré,
>>
>> 1) apt-get installs rdkit 2013 (link below). So, please install it
>> through conda (as Markus suggested)
>> https://packages.ubuntu.com/trusty/python/python-rdkit
>>
>> 2) I am not familiar with the case of wrong SMILE generation. But the
>> link below says something more that I think you need to know.
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495655/
>>
>> 3) As you are trying to store data, it would be great to consider whether
>> you are storing energy minimized molecule or not. (my opinion). Surface
>> area related descriptors will yield different result and bond connectivity
>> related descriptor will yield same result in both cases.
>>
>> 4) Sharing my personal experience, during my undergraduate school part of
>> my final year project was stressed up with conceptual questions. I failed
>> to utilize the  blessing of advanced development due to the lack of time.
>> The later experience was not so good.
>>
>> Please keep in mind that we can generate a non redundant database with
>> few molecules but for millions of molecules it should be quite though task.
>> Have a great day!
>>
>> - malitha
>>
>>
>>
>>
>> On Thu, Sep 14, 2017 at 2:05 AM, Markus Sitzmann <
>> markus.sitzm...@gmail.com> wrote:
>>
>>> 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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>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Rdkit-discuss mailing list
>>>>>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>> ------------------
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>>>>>>>>>> _______________________________________________
>>>>>>>>>> Rdkit-discuss mailing list
>>>>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------
>>>>>>> ------------------
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>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
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>>
>
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