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