rdkit

How can I build RDKits C# Wrappers — Visual Studio 2019 x64

由 被刻印的时光 ゝ 提交于 2020-04-16 02:47:21
问题 I have followed the steps described here: https://github.com/bp-kelley/rdkit-csharp to try and create RDKits C# Wrappers. git clone https://github.com/bp-kelley/rdkit-csharp.git git clone https://github.com/rdkit/rdkit.git cd rdkit-csharp build.bat While trying running the build.bat I've run into an error to do with creating named generators (among many others) and I'm not sure how to sort it out. The build.bat references Visual Studio 14 and Visual Studio 14 Win64 I have tried to update this

Output of Graph Convolution in deepchem

由 那年仲夏 提交于 2020-01-25 08:14:27
问题 I am using Deepchem to create features for the my GraphConvolution model as follows. import deepchem as dc from rdkit import Chem import numpy as np import pandas as pd from rdkit.Chem import Draw from rdkit.Chem.Draw import IPythonConsole smile = 'O=C(C1=CC=C(C=C1)C(O)=O)O' molecules = [] molecules.append(Chem.MolFromSmiles(smile)) featurizer = dc.feat.graph_features.ConvMolFeaturizer() mol_object = featurizer.featurize(mols=molecules) Now I want to know the output mol_object . I know that

Getting ImportError /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version 'CXXABI_1.3.11' not found

由 梦想与她 提交于 2020-01-06 04:37:09
问题 I'm currently trying to run a Python program that uses RDKit and am facing an error. The get straight to the point, the complete traceback is: Traceback (most recent call last): File "./main.py", line 4, in <module> from train import Trainer File "/home/user1/repo1/train.py", line 12, in <module> from utils import make_batches File "/home/user1/repo1/utils.py", line 9, in <module> from rdkit import Chem, DataStructs File "/home/user1/anaconda3/envs/user1conda/lib/python3.7/site-packages/rdkit

Insert matplotlib images into a pandas dataframe

由 早过忘川 提交于 2019-12-28 16:14:29
问题 PURPOSE: I am currently working with rdkit to colour the structures of my molecules according to rdkit.Chem.Draw.SimilarityMaps . Now, I would like to use the matplotlib images SimilarityMaps function to introduce them in a pandas dataframe and export this table in the form of an html file. CODE: I tried to do that with the following code import pandas as pd from rdkit import Chem from rdkit.Chem import Draw from rdkit.Chem.Draw import SimilarityMaps from rdkit.Chem.Draw import IPythonConsole

Insert matplotlib images into a pandas dataframe

由 冷暖自知 提交于 2019-12-28 16:13:03
问题 PURPOSE: I am currently working with rdkit to colour the structures of my molecules according to rdkit.Chem.Draw.SimilarityMaps . Now, I would like to use the matplotlib images SimilarityMaps function to introduce them in a pandas dataframe and export this table in the form of an html file. CODE: I tried to do that with the following code import pandas as pd from rdkit import Chem from rdkit.Chem import Draw from rdkit.Chem.Draw import SimilarityMaps from rdkit.Chem.Draw import IPythonConsole

SMILES from graph

由 你离开我真会死。 提交于 2019-12-18 04:54:14
问题 Is there a method or package that converts a graph (or adjacency matrix) into a SMILES string? For instance, I know the atoms are [6 6 7 6 6 6 6 8] ([C C N C C C C O]) , and the adjacency matrix is [[ 0., 1., 0., 0., 0., 0., 0., 0.], [ 1., 0., 2., 0., 0., 0., 0., 1.], [ 0., 2., 0., 1., 0., 0., 0., 0.], [ 0., 0., 1., 0., 1., 0., 0., 0.], [ 0., 0., 0., 1., 0., 1., 0., 0.], [ 0., 0., 0., 0., 1., 0., 1., 1.], [ 0., 0., 0., 0., 0., 1., 0., 0.], [ 0., 1., 0., 0., 0., 1., 0., 0.]] I need some

ValueError when doing validation with random forests

由 ☆樱花仙子☆ 提交于 2019-12-13 03:47:31
问题 I'm trying to build a model that would predict the caco-2 coefficient of a molecule given its smiles string representation. My solution is based on this example. Since I need to predict a real value, I use a RandomForestRegressor . With some molecules added to the code manually, everything works (although the predictions themselves are wildly wrong): from rdkit import Chem, DataStructs #all the nice chemical stuff, ConvertToNumpyArray from rdkit.Chem import AllChem from sklearn.ensemble

RDKit Building Error

由 半腔热情 提交于 2019-12-11 15:14:41
问题 Rdkit (version: 2013_09_1) make gives some errors: make[2]: [Code/GraphMol/SLNParse/testSLNParse] [Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/all] Error 2 Previous Steps (Boost 1.54.0, EIGEN3) -------------------------------------------------- BOOST -------------------------------------------------- mkdir ~/boost mkdir ~/boost/boost-home cd ~/boost/ wget "source to boost" tar zxvf boost_1_54_0.tar.bz2 cd boost_1_54_0/ ./bootstrap.sh --with-python-version=2.7 ./b2 --prefix=/lustre/home

How can I compute a Count Morgan fingerprint as numpy.array?

由 蓝咒 提交于 2019-12-11 09:30:00
问题 I would like to use rdkit to generate count Morgan fingerprints and feed them to a scikit Learn model (in Python). However, I don't know how to generate the fingerprint as a numpy array. When I use from rdkit import Chem from rdkit.Chem import AllChem m = Chem.MolFromSmiles('c1cccnc1C') fp = AllChem.GetMorganFingerprint(m, 2, useCounts=True) I get a UIntSparseIntVect that I would need to convert. The only thing I found was cDataStructs (see: http://rdkit.org/docs/source/rdkit.DataStructs

SMILES from graph

由 ε祈祈猫儿з 提交于 2019-11-30 20:48:41
Is there a method or package that converts a graph (or adjacency matrix) into a SMILES string? For instance, I know the atoms are [6 6 7 6 6 6 6 8] ([C C N C C C C O]) , and the adjacency matrix is [[ 0., 1., 0., 0., 0., 0., 0., 0.], [ 1., 0., 2., 0., 0., 0., 0., 1.], [ 0., 2., 0., 1., 0., 0., 0., 0.], [ 0., 0., 1., 0., 1., 0., 0., 0.], [ 0., 0., 0., 1., 0., 1., 0., 0.], [ 0., 0., 0., 0., 1., 0., 1., 1.], [ 0., 0., 0., 0., 0., 1., 0., 0.], [ 0., 1., 0., 0., 0., 1., 0., 0.]] I need some function to output 'CC1=NCCC(C)O1' . It also works if some function can output the corresponding "mol" object
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