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
2
votes
1 answer
RDKit fingerprint inconsistency
Two molecules have different substructures in bit-1 (see image attached below).
If I have a large number of molecules, how to force them to have the same substructure in the same bit? I want to use them for Machine Learning, so I have to ensure that…
Zihao Wang
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- 4
2
votes
1 answer
How to highlight the substructure of a molecule with thick red lines in RDKit as SVG (high res)
I have the following code:
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG
m =…
littleworth
- 4,781
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2
votes
0 answers
Installing RDKit using Conda
I have Anaconda installed on my Windows 10 machine.
In Spyder, I tried to install RDKit using the instructions found here: How to install RDKit with Conda, but nothing happened when I typed:
$ conda create -c conda-forge -n my-rdkit-env rdkit
It…
SG876
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- 1
2
votes
2 answers
ValueError: BitVects must be same length (rdkit)
I am calculating the structure similarity profile between 2 moles using rdkit. When I am running the program in google colab (rdkit=2020.09.2 python=3.7) the program is working fine.
I am getting an error when I am running on my PC (rdkit=2021.03.2…
Opps_0
- 408
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2
votes
1 answer
ArgumentError: rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect(Mol, int)
I'm working with RDKit and have the following issue. I'm trying to create a function that encode a molecule from a SMILES string into a fingerprint. But an ArgumentError occurs and I can't figure it out.
This is my code:
def get_fp(dfx,…
SEBASTIAN
- 75
- 1
- 8
2
votes
1 answer
Possible to directly feed SMILE structures stored in a pandas dataframe into RDKit to calculate molecular fingerprint and similarity?
ref_Molecule = Chem.MolFromSmiles('CC1=C(C(O)=O)C2=CC(=CC=C2N=C1C3=CC=C(C=C3)C4=CC=CC=C4F)F')
merged_data['Molecule_Tan'] = DataStructs.TanimotoSimilarity(Chem.RDKFingerprint(ref_Brequinar),…
Paul
- 165
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2
votes
1 answer
I am trying to compile a bb recipe file in yocto. I am facing : make: *** No targets specified and no makefile found. Stop. erorr
LICENSE = "CLOSED"
S = "${WORKDIR}/git"
FILESEXTRAPATHS_prepend := "${THISDIR}/${PN}:"
SRCREV = "eb5499c2732fbf500c54fd5f1bded9e45793728e"
SRC_URI = "file://new.tar.gz"
S = "${WORKDIR}/git"
inherit autotoools
#this is the bb file
#after compiling…
Nikhil R
- 21
- 1
- 2
2
votes
0 answers
rdkit produces two different images using MolToFile() and displaying in Jupyter
I am generating an image of a molecule using rdkit in Python.
Using from IPython.display import display and display(mol) produces the output image I need.
However, when I try saving it using Draw.MolToFile(mol, 'mol.png'), I get an image with…
themennice
- 177
- 1
- 9
2
votes
1 answer
Generating conformers of small ligands but preserving correct aromaticity
I'm trying to generate conformers for a number of small-molecule ligands to eventually do docking with. I generated the conformers using RDkit's EmbedMultipleConfs function. However, when subsequently visually inspecting the conformers in PyMol I…
user21398
- 419
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2
votes
1 answer
How can I determine the number of paraffinic CH3, CH2 and CH groups for any molecule with rdkit in Python?
I am trying to determine the number of paraffinic groups in any molecule using the rdkit package in Python. Initially I start to determine paraffinic CH3 groups, which I have to extend to paraffinic CH2, and paraffinic CH groups.
In the MWE, I am…
Tom Kurushingal
- 6,086
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2
votes
0 answers
Accessing Python Modules Installed with Brew
I am trying to access "rdkit" module in python, but my python install doesn't seem to find the module. I installed it using brew as suggested here. I included the commands I use to reproduce the problem.
Is a simple fix just adding the…
Jacob Anderson
- 85
- 6
2
votes
1 answer
Python argument error occurs when running rdkit.Chem.SaltRemover(). (Python argument types did not match C++ signature)
I'm working on some tasks using RDKit and have some problems.
I'm trying to sanitize my dataset with SaltRemover() function but the ArgumentError occurs and I cannot figure out it.
The code used is this:
from rdkit import Chem
from rdkit.Chem…
Myon
- 63
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- 6
2
votes
1 answer
Deepchem disk data to numpy array
I am using Deepchem wrapper for GraphConvolution model as follows. I have my smiles data in .csv which consists of 5 molecules with their smiles representation and their respective activities. The data can be accessed from here directly.
Importing…
Stupid420
- 1,347
- 3
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- 44
2
votes
1 answer
On finding chirality using RDKit
In the paper: "Graph Networks as a Universal Machine Learning
Framework for Molecules and Crystals", authors introduce chirality as an atom feature input to analyze QM9 dataset. I was trying to recreate this atom feature as following
Chirality:…
Blade
- 984
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2
votes
1 answer
Sanitization error applying reaction to molecule RDKit
Sanitization error while applying a reaction to an molecule with wedged bond.
I am getting this error while applying a proton removal reaction to a molecule but I do not see any error in MolBlock information.
This is for a reaction problem in which…
Fence
- 323
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