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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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
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>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
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>>>>>>
>>>>>
>>>>
>>>
>>
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