[Rdkit-discuss] Non-redundant database of molecules

2017-09-13 Thread Wandré
Hi, My name is Wandré and I'm from Brazil. I'm trying to do a big database of molecules, but, I want to eliminate all the redundant molecules before insert them in database. I want to know what is the best method to identify one molecule in RDKit. Is SMILES ("Chem.MolToSmiles(mol,isomericS

Re: [Rdkit-discuss] Non-redundant database of molecules

2017-09-14 Thread Wandré
File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line 18, in 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

Re: [Rdkit-discuss] Non-redundant database of molecules

2017-09-13 Thread Wandré
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

Re: [Rdkit-discuss] Non-redundant database of molecules

2017-09-13 Thread Wandré
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

Re: [Rdkit-discuss] Non-redundant database of molecules

2017-09-13 Thread Wandré
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

Re: [Rdkit-discuss] Non-redundant database of molecules (Wandr?)

2017-09-13 Thread Wandré
Why don't use the InChI function on RDKit? Canonical SMILES cannot be generated by RDKit, correct? -- 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

Re: [Rdkit-discuss] Non-redundant database of molecules

2017-09-13 Thread Wandré
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-rdkit-on-ubuntu-12-04/ -- Wandré Nunes de Pinho Veloso Professor Assistente - Unifei - Campus Avançado de Itabira-MG Doutorando em

Re: [Rdkit-discuss] Non-redundant database of molecules

2017-09-14 Thread Wandré
k (most recent call last): File "", line 1, in File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line 18, in from rdkit import rdBase ImportError: cannot import name rdBase -- Wandré Nunes de Pinho Veloso Professor Assistente - Unifei - Campus Avançado

Re: [Rdkit-discuss] Non-redundant database of molecules

2017-09-14 Thread Wandré
- 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

Re: [Rdkit-discuss] Non-redundant database of molecules

2017-09-14 Thread Wandré
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

Re: [Rdkit-discuss] Non-redundant database of molecules

2017-09-14 Thread Wandré
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