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Questions tagged [rdkit]

RDKit is a popular open-source library for chemoinformatics and machine learning applied to chemoinformatics.

RDKit is a popular open-source library for chemoinformatics and machine learning applied to chemoinformatics.

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how do I install a specific version of the rdkit library for Python2?

I need to install a version of the rdkit library released prior to 2019, when support for Python 2 was removed. This is needed to work with this library: https://github.com/brain-research/deep-molecular-massspec I have downloaded the library from…
Ninja Chris
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RDKit SetScale method for drawing

RDKit Chem Python tutorial is not so good. I needed the Set Scale function for drawing, but I have difficulty to understand the arguments. Although my research, I have not seen an example of use on the Internet and no description available. Thanks…
scylla
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How to convert Smiles to Fingerprint with rdkit?

I have to convert a list of Smiles in a list of Fingerprints with rdkit. But I don't know how. I searched for solutions in the internet, but there is actually no Example working... Does anyone has experience with the conversion from a list of…
Mr. Chang
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Find set of unique fragments with DrawMorganBits

I am training a random forest with scikit-learn on Morgan fingerprints and would like to know which structural motifs are most important. For that I would like to draw all fragments that produce an on-bit in the x most important features. I have…
evilolive
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Atoms mapping reaction RDKit

After applying a simple reaction I am getting the following warning message: product 1 has no mapped atoms. I am guessing that has something to do with atoms mapping after reaction, but I am including and index to the smarts formula to avoid this…
Fence
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How to protonate a molecule in rdkit?

I m tring to present the workflow for the positive ion ESI mass spectra, based on the fragmentation of [M+H]+ ions. I want to simulate the ionisation by the addition of one proton to heteroatoms. For example, from rdkit.Chem import AllChem from…
H.Ji
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RDKit Build errors

I'm using Ubuntu 16.04 and tried installing the RDKit from the official documentation. I installed the pre-requisites, downloaded the zip file and extracted it to my folder. Made a build directory, entered it and I entered cmake .. and this was the…
Krishna Swaroop K
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RDKit drawing problem: fingerprint graph didn't show up using Draw.DrawRDKitBit command

I simply copied and pasted these code from rdkit (https://www.rdkit.org/docs/GettingStartedInPython.html#generating-images-of-fingerprint-bits) I was expecting to generate graphs. However, I got a long string. from rdkit import Chem from rdkit.Chem…
Shuan
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Convert list of smiles strings ['x', 'y', 'z'] to mol files or MDL mol blocks using RDKit

I have generated a list of smiles strings and defined them as 'result' I'd like to convert each SMILES string in the list to separate mol files using RDKit. My current code is this: m = Chem.MolFromSmiles('result') print(Chem.MolToMolBlock(m)) This…
Matt Hostetler
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Conda install conflict with remaining packages

For some reason, I can't install any packages with my current setup. I have conda version 3.7 and python 3.4. I've tried the following: conda install -c conda-forge rdkit conda install -c rdkit rdkit conda install -c conda-forge plotnine and in…
chemdatafarmer
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Boost.Python.ArgumentError: Python argument types in ~did not match C++ signature, How can I handle it?

I want to predict Knoell data using ppar_ligand_model. But some SMILES display this error message. How can I handle it? Is this problem of SMILE's structure? And What code should I add to exclude the material's SMILE that causes the error? Here is…
Chang Hun Kim
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Can't import Chem from rdkit in Anaconda Python 3.6.5

I install the Anaconda 4.5.4 with Python 3.6.5 and install rdkit (with command "conda install -c rdkit rdkit") and I'm trying to import the Chem and does not works. from rdkit import Chem Traceback (most recent call last): File "", line…
Wandré Veloso
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How to search faster, RDkit and Pandas, Chemical Database

I am trying to search through a large chemical database (chembl, >1,000,000 entries), and am having problems executing code on my work computer. Our focus is chemicals, so high quality computers are not available. My code is below, and works…
MrJones
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RDKit Building Error

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,…
e7lT2P
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ValueError when doing validation with random forests

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…
Chiffa
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