I really can't do this right...
I am thinking in reinstall Ubuntu and try again. Now the RDKit doesn't
works.
--
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
2017-09-14 15:07 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
> Hi Wandré,
>
> Sorry to see you in trouble again.
>
> If you see the massages then
> # All requested packages already installed.
> # packages in environment at /home/wandre/anaconda2:
> #
> rdkit 2017.03.3 np111py27_1 rdkit
>
> so your rdkit should be at
> /home/wandre/anaconda2/<some other folders>
>
> But it is trying to import from
> /opt/rdkit-Release_2016_03_1/rdkit/
>
> So the path variable is still NOT correct. It is good to see that you
> installed conda correctly and rdkit i think installed correctly.
>
> Therefore I suspect that you need to remove the previously path for rdkit
> (you probably set those during installing from source).
>
> I forgot what linux command will do that for you. Have a great day!
>
> *** I will update the answer whenever I get the appropriate linux command.
>
> - malitha
>
>
>
> On Thu, Sep 14, 2017 at 11:38 PM, Wandré <wandrevel...@gmail.com> wrote:
>
>> Thanks Malitha,
>>
>> When I install Anaconda I said yes to all questions.
>> When I trying to reinstall the RDKit, this message appears:
>>
>> wandre@wandreLinux:~/anaconda2$ conda install -c rdkit rdkit
>> Fetching package metadata ...........
>> Solving package specifications: .
>>
>> # All requested packages already installed.
>> # packages in environment at /home/wandre/anaconda2:
>> #
>> rdkit 2017.03.3 np111py27_1 rdkit
>>
>> When I run "python", appears:
>>
>> Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15)
>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>> Anaconda is brought to you by Continuum Analytics.
>> Please check out: http://continuum.io/thanks and https://anaconda.org
>> >>> import rdkit
>> >>> from rdkit import Chem
>> 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
>>
>>
>> --
>> 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
>>
>> 2017-09-14 9:17 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
>>
>>> 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>>>>> ------------------
>>>>>>>>>>>>>> Check out the vibrant tech community on one of the world's
>>>>>>>>>>>>>> most
>>>>>>>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> 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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>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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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>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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