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.htm
>>>>> l 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
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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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>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
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>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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