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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.

251 questions
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13 answers

How to solve an error that appears in conda proxy configuration?

I am trying to install Rdkit on ubuntu and I have problem with the conda configuration. I have reinstalled anaconda3 and python3 versions on my desktop and installed it from the beginning. When I run the command: conda create -c rdkit -n…
djordje
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4 answers

How to generate a graph from a SMILES molecule representation?

I have a dataset of molecules represented with SMILES strings. I was trying to represent this as graphs. Is there a way to do so? For instance, let's say I have string CC(C)(C)c1ccc2occ(CC(=O)Nc3ccccc3F)c2c1, is there a general way to convert this…
Blade
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2 answers

RDKit: how to check molecules for exact match?

I'm using RDKit and trying to check molecules for exact match. After using Chem.MolFromSmiles() the expression m == p apparently doesn't lead to the desired result. Of course, I can check whether p is a substructure of m and whether m is a…
theozh
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11
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1 answer

SMILES from graph

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., …
Joe
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9
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3 answers

How to install a package rdkit from Conda with pip?

I am trying to install rdkit using pip3. But it doesn't work. sudo pip3 install rdkit Error: Could not find a version that satisfies the requirement rdkit (from versions: ) No matching distribution found for rdkit There is only apparently one…
Rebecca
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9
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4 answers

rdkit installation issues with Anaconda

I am trying to get rdkit working on my Windows 7 system with Anaconda and Python 2.7. I have been following the instructions from http://www.rdkit.org/docs/Install.html conda create -c https://conda.anaconda.org/rdkit -n my-rdkit-env rdkit activate…
Crath
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8
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2 answers

RDKit installation under Windows and Python3.7.4

RDKit could be a nice package if it wasn't so complicated to install. Here on SO, there are several questions having problems with the installation of RDKit. However, on different operating systems or different environments. My configuration…
theozh
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7
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1 answer

Morgan fingerprint rdkit

Working in an example I realized that there are at least two ways of computing morgan fingerprints for a molecule using rdkit. But using the exact same properties in both ways I get different vectors. Am I missing something? First approach: info =…
Fence
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3 answers

rdkit: How to show molecular's atoms number

Hello1 I was trying to use rdkit pack to finish the work of displaying the molecular's atom numbers in Jupyter Notebook ,"import IPython.core.interactiveshell" and "import InteractiveShell" ,and "from rdkit.Chem.Draw import DrawingOptions"…
jFang
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6
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1 answer

IPython.display: how to change width, height and resolution of a displayed image

I am displaying an image of a molecule using IPython.display in Jupyter. The resolution of the image is quite low. Is there a way to specify the width and height of the displayed image and its resolution? I googled it and could not find anything.…
themennice
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6
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2 answers

Converting SMILES to chemical name or IUPAC name using rdkit or other python module

Is there a way to convert SMILES to either chemical name or IUPAC name using RDKit or other python modules? I couldn't find something very helpful in other posts. Thank you very much!
Alex
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6
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4 answers

Installing RDKit in Google Colab

I cannot figure out how to fix the following issue. Up until today I was using the following code snippet for installing RDKit in Google Colab: !wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh !chmod +x…
Alderson
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6
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1 answer

Trying to build the C# wrappers for RDKit with build.bat from bp-kelley/rdkit-csharp

I'm trying to build the C# wrappers for RDKit, but have been struggling to make progress. I've attempted two routes: n.b. This question is long and unhelpful. Long story short use NuGet (see answer below). Attempt One Docs from RDKit…
OrderAndChaos
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5
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3 answers

Problems installing RDKit in python 3.8 Ubuntu 20.04 LTS

I have had a lot of trouble trying to install RDKit using python3 and Ubuntu 20.04 LTS Tried to install rdkit this way: sudo apt-get install python3-rdkit But then when I try to import it using python3 it doesn't work. It installed indeed, but it…
SEBASTIAN
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5
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2 answers

How to add RDKit to project in PyCharm?

So, I am trying to add RDKit to my project in PyCharm. I have found that if you are using interpreter /usr/bin/python2.7 PyCharm will try to install stuff using the pip. While, RDKit requires conda. I have tried to change the interpreter to conda,…
Anna-Lischen
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