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.
Questions tagged [rdkit]
251 questions
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2 answers
How to install rdkit with anaconda
I'm trying to install rdkit with
conda create -c rdkit -n my-rdkit-env rdkit
but when it's Downloading and Extracting Packages it's stopping! what should I do? I tried every command I found on the internet and none of them work!
negariiii
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1 answer
Clean way to select from many options in Python
I work in data science and a typical problem I encounter while cleaning up Pandas dataframes is converting columns from one string format to another (in particular, the strings I'm looking at are chemical identifiers and each of them represents a…
mgarort
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Conda dependent packages(rdkit) will not install properly for use in web servers(importError:DLL load failed). Is there an alternative install method?
UPDATE 1: PIL and RDKIT produced import errors because the .dll files were not placed in /venv//Lib/site-packages
I removed both packages from environment and commented out their code from my project.
Next I updated the base base environment:
conda…
dpoiesz
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1 answer
Rdkit: MaeMolSupplier NameError
I would like to able to extract details about a molecule in ".mae" format. I imported the rdkit.Chem.rdmolfiles functions and it seems to work for MolFromSmiles, but not for MaeMolSupplier as suggested in the 2019 documentation. Instead I get a…
Jacob Anderson
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2 answers
Get structure from morgan fingerprint, RDKit
I made a model to predict molecules' solubility from their morgan fingerprint and now I have found the specific bits of fingerprints the model had a hard time predicting.
I would like to see what each bit of a fingerprint correlates to in structure…
KBJ
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- 4
1
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1 answer
Pyspark string comparison with == for RDkit functions throws error
I've a Pyspark UDF defined as below -
from rdkit import Chem
input_smile = 'CCOC(=O)c1cc2cc(ccc2[nH]1)C(=O)O'
converted_smile_in = Chem.MolToSmiles(Chem.MolFromSmiles(input_smile)
def convertSmile(smile):
return…
sopana
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2 answers
Getting ImportError /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version 'CXXABI_1.3.11' not found
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
from train import Trainer
…
Sean
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1
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1 answer
Output of Graph Convolution in deepchem
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…
Stupid420
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1 answer
Using RDKit to calcutate Tanimoto similarity between sdf file and a structure SMILE?
I'm using RDKIt with Python 3.7 to calculate the similarity of a database in sdf (smile of every structure) with a molecule, of which i have the smile. I found a way to calculate Tanimoto index only between two SMILES using this code:
import numpy…
giovanni_polato
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0 answers
What is the difference between the results of atom.GetIdx() and Chem.CanonicalRankAtoms()?
In the RDKit docs it is said that the rdkit.Chem.rdChem.GetIdx(Atom atom) returns the atom's index according to the molecule.
Docs: Chem.rdchem.Atom.GetIdx
Also rdkit.Chem.rdmolfiles.CanonicalRankAtoms (Mol mol) returns the canonical ranking of the…
dia
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1 answer
RDKIT: Combine/Add particles
I have a database of macrocycles and covalent organic cages, where I wish to add a molecule/ion into the cavity. I need to do this through RDKIT. Is there an easy method to accomplish this task?
For example:
from rdkit import AllChem
guest =…
Wychh
- 656
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0 answers
Im trying to convert my SmilesCode to Fingerprints. It does work, but I have problems to use the function for my SmilesCode-List
I'm trying to iterate my function over a column but it doesn't work properly.
I get this error code:
ArgumentError: Python argument types in
rdkit.Chem.rdmolops.RDKFingerprint(NoneType, int, int, int, int, int, float, int)
did not match C++…
Mr. Chang
- 11
- 4
1
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1 answer
Is there a way to show the index of atoms in rdkit.Chem.rdmolops.GetAdjacencyMatrix?
I'm trying to convert a compound from mol to adjacency matrix. However, i encountered a problem that rdkit.Chem.rdmolops.GetAdjacencyMatrix() doesn't provide the index of the atoms for the adjacency matrix. Is there any way to include the index data…
Juhan Hong
- 11
- 3
1
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1 answer
How can I build RDKits C# Wrappers — Visual Studio 2019 x64
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…
OrderAndChaos
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1 answer
RDKIT: Find Substructure Atom Coordinates
I have imported a molecule as a .mol file into rdkit.
The molecule contains a CN=NC substructure.
I wish to find the coordinates of the CN=NC substructure.
I have tried using Chem.MolToBlock(molfile) to list the 3D coordinates; however, this returns…
Wychh
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