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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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IndexError: invalid index to scalar variable when trying to calculate AUC metrics with rdkit

I want to calculate the ROC curve with rdkit implementation: rdkit.ML.Scoring.Scoring.CalcAUC(scores, col) Determines the area under the ROC curve code: import rdkit.ML.Scoring.Scoring rdkit.ML.Scoring.Scoring.CalcAUC(scores, y) and I get the…
rnv86
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graph theory - connect point in 3D space with other three nearest points (distance based)

I want to connect nodes (Atoms) with the three nearest nodes(atoms). I am doing ad1 = np.zeros((31,31)) for i in range(31): dist_i = dist_mat[i] cut_off = sorted(dist_i)[3] ad1[i, np.where((dist_i<=cut_off) & (dist_i!=0.0))] =…
WhySoSerious
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RDKit ERG Node attribute names python

I am using RDKit to extract an ERG [1] (Extended Reduced Graph) Graph for a particular molecule. After the extraction of the ERG graph form the original molecule I am creating a graph to be used for further processing. However, I am noticing that…
D. Agius
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How do I install a module (RDKIT) permanently in Colab

How do I install a library permanently in Colab? I followed the accepted answer from this thread How do I install a library permanently in Colab? # first install gcsfuse %%capture !echo "deb http://packages.cloud.google.com/apt gcsfuse-bionic main"…
Protima Rani Paul
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RDKit in Jupyter Notebook

I want to use RDKit in a Jupyter Notebook. I created a conda environment with rdkit, jupyter, and other packages installed. I can open the Jupyter Notebook and import and use packages like pandas, but I can't import rdkit. It says "no module named…
mir
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Control which python version `sudo apt-get install` installs a package in

I have Python2.7, Python3.6 and Python3.7 on my Ubuntu 18.04 system. I want to install rdkit in Python3.6 using apt-get install. The command to do that is: sudo apt-get install python-rdkit librdkit1 rdkit-data How do I know which python version…
Mahathi Vempati
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Failing to install RDKit on Ubuntu 16.04.6 LTS

I am trying to install RDKit on an Ubuntu 16.04.6 LTS Virtual Machine. Reading the installation guide, I used the following commands: sudo apt-get -y install python-rdkit librdkit1 rdkit-data sudo wget…
user2182857
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Using RDKIT: generate fingerprint in integrer/count form

I'm new to Rdkit. I need to generate fingerprint in integer/count form. I have tried many alternatives but always I get the message: DataStructs.ConvertToNumpyArray(fps2[i], arr[i]) ArgumentError: Python argument types…
Ammar
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Speeding up the implementation of the similarity of compounds' canonical smiles using rdkit

This wannabe bioinformatician needs your help. The code below finds the similarity of compounds' canonical smiles, using rdkit. After some research I understand it must be O(n)! (or not?) because for a small file of 944 entries it took 20 minutes…
Paschalis
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Instance attributes in a subclass of Chem.Atom in rdkit cannot be accessed

I defined a subclass of Atom in rdkit.Chem. I also defined an instance attribute in it but I could not get that instance from RWMol object in rdkit. Below there is a sample code for my problem: from rdkit import Chem class MyAtom(Chem.Atom): …
Halil İbrahim Oymacı
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Can i use RDkit with pure python3 in Windows OS

I want to use RDkit with python3 in windows OS But here are something I got confused Besides the author said the most recommend way is anaconda(I don't want this),the other way is to install RDkit with release binary package. But as I follow the…
chen suyin
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Pre-aligning molecules in Rdkit before computing shape similarity with ShapeTanimotoDist() possible?

I am building a script to compare shapes of Rdkit generated conformers for a query ligand to a reference ligand extracted from a template protein-ligand complex. For this I want to use the shape similarity Tanimoto metric ShapeTanimotoDist()…
et97
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Problem using AddMoleculeColumnToFrame on Google Colab

I’d been using AddMoleculeColumnToFrame on Google Colab with no problem. After not using it for about 1 month I just discovered that it stopped working, i.e. the images are not showing up in the data frame (see below). Any ideas? The most likely…
Jan Jensen
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I need to find a list of all the possible Bonds, angles between atoms in a molecule from a smiles string (or .xyz file)

I am trying to develop force fields and in order to do so I need a list of all the possible bonds , angles and dihedral in a molecule from smiles string oe .xyz file. Is it possible that to do it with RDkit? if so, how?
Juhi Bar
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Validating an SVG file from RDKit

I am attempting to produce an SVG image from the package RDKit. A minimum reproducable example: from rdkit import Chem from rdkit.Chem import Draw img = Draw.MolsToGridImage([Chem.MolFromSmiles(x) for x in ['C', 'CO', 'CN']], useSVG =…
cddt
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