I have try this command several times and doesn't fixed. Maybe because all
the others commands, this works now.
Thanks for the help

--
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 19:03 GMT-03:00 Markus Sitzmann <markus.sitzm...@gmail.com>:

> Hmm, your last command "conda install -c rdkit rdkit" should have been
> sufficient for the installation (after installing anaconda)
>
> On Thu, Sep 14, 2017 at 11:57 PM, Malitha Kabir <malitha12...@gmail.com>
> wrote:
>
>> That's great to hear you got things running. That was basically due to
>> the path update. Have a great day! - malitha.
>>
>> On Sep 15, 2017 3:44 AM, "Wandré" <wandrevel...@gmail.com> wrote:
>>
>>> I don't know what I do, but now everything *is working fine.*
>>> My last commands:
>>>
>>> Reinstall Anaconda2
>>>
>>> Trying to compile the RDKit
>>>
>>>    - sudo tar xzvf RDKit_2016_03_1.tgz -C ~/anaconda2/
>>>    - vim ~/.bashrc (update the variables with the new path of rdkit)
>>>    - . ~/.bashrc
>>>    - cd ~/anaconda2/rdkit
>>>    - mkdir build
>>>    - cd build
>>>    - cmake -DRDK_BUILD_INCHI_SUPPORT=ON ..
>>>    - make -j 4 (ERROR on 50%)
>>>    - make install (ERROR on 24%)
>>>
>>>
>>> sudo apt-get install python-rdkit librdkit1 rdkit-data
>>> sudo apt-get update
>>> conda install -c rdkit rdkit
>>>
>>>
>>> --
>>> 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 18:28 GMT-03:00 Wandré <wandrevel...@gmail.com>:
>>>
>>>> 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 <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/blog/2013/02/how-to-install-rdki
>>>>>>>>>>>> t-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/dayhtm
>>>>>>>>>>>>>>>> l/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, py
>>>>>>>>>>>>>>>>> LabuteASA, 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
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>>>>>>>>>>>>>>>>>> engaging tech sites, Slashdot.org!
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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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>>>>>>>>>>>>>>>>> engaging tech sites, Slashdot.org!
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>>>>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>>>> Rdkit-discuss@lists.sourceforge.net
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>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
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>>>>>>>>>>>>>> ------------------
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>>>>>>>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>> Rdkit-discuss@lists.sourceforge.net
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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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