Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5

Great! -- 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

Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5

Just run sudo apt-get install libxrender1 and it works Chris Earnshaw has send me a email with this tip. Thanks!!! -- Wandré Nunes de Pinho Veloso Professor Assistente - Unifei - Campus Avançado de Itabira-MG Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG Pesquisador

[Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5

ome/wandre/anaconda3/envs/flaskapp/lib/python3.6/site-packages/rdkit/Chem/__init__.py", line 25, in from rdkit.Chem.rdmolops import * ImportError: libXrender.so.1: cannot open shared object file: No such file or directory How can I fix this? Where is my error? Thanks! -- Wandré N

Re: [Rdkit-discuss] Errors with RDKit

Hi Carlos, Simmilar to Axel, in my code I use if mol is None: return False (if you are using a function to read each SDF file) if mol is None: continue (to force the next loop) -- Wandré Nunes de Pinho Veloso Professor Assistente - Unifei - Campus Avançado de Itabira-MG Doutorando em

Re: [Rdkit-discuss] Use fingerprint do Clustering a large dataset of molecules

them again? -- 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

Re: [Rdkit-discuss] Use fingerprint do Clustering a large dataset of molecules

Hi Andrew, Thanks for the link. It is very interesting. I will read very carefully. So, as input on ChemFP, I have to put a file with all molecules in 1 SDF? -- Wandré Nunes de Pinho Veloso Professor Assistente - Unifei - Campus Avançado de Itabira-MG Doutorando em Bioinformática - Universidade

[Rdkit-discuss] Use fingerprint do Clustering a large dataset of molecules

I want to store in database (just run once)* sims = DataStructs.BulkTanimotoSimilarity(fps[i], fps[:i]) dists.extend([1 - x for x in sims]) # now cluster the data: cluster_data = Butina.ClusterData(dists, nfps, cutoff, isDistData=True) return cluster_data # End def clusterfps Thanks! -- Wandré Nunes de Pinho Veloso

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

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

- 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

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

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

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

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

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

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

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 (Wandr?)

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

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

[Rdkit-discuss] Non-redundant database of molecules

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