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
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>>> ------------------
>>>>>>>>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> ------------------
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> 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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