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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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Can't convert molecule to fingerprint with rdkit

I'm trying to convert molecular smiles into fingerprints using rdkit. I have two smiles: Nc1cccc(N)n1 and Nc1cc(CSc2ccc(O)cc2)cc(N)n1. The first one was expanded into the second one. In other words, the second molecule contains the first one in its…
Jozef
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How to draw sub-structures of a polycyclic aromatic which shows bond angles correctly?

thank you for reading my question. Assume that I have a polycyclic aromatic (let's call it "parent molecule") as shown below: smile = "c1ccc2ocnc2c1" mol = Chem.MolFromSmiles(smile) When I draw sub-structures of the parent molecule, I notice…
Mohammad
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How to save "IPython.core.display.SVG" as PNG file?

I am trying to save a variable with data-type of "IPython.core.display.SVG" as a PNG file in Jupyter Notebook environment. First I tried: with open('./file.png','wb+') as outfile: outfile.write(my_svg.data) And I got the error: TypeError: a…
Mohammad
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How can I read the values of a GraphMolWrap.SWIGTYPE_p_double in .NET?

I am trying to use the cheminformatics library RDKit in .NET with F#, using this wrapper. Here is a small sample of code: #r "nuget: RDKit.DotNetWrap" open GraphMolWrap let mol = RWMol.MolFromSmiles "COc1cccc(=O)c2cc(F)c(N3CCNCC3)cc21" let adjMat =…
Shredderroy
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Why is this rdkit script not working in visual studio code?

I've been using VS code via jupyter notebook. So, I have to produce grid image of 15 molecules and save it to my computer, but the script I've been using is not showing any errors, but still doesn't produce any images nor save them to designated…
rosana
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How to export my results from visual studio code to file on my computer

After filtering sdf database I've ended up with results that are only printed on the screen. How can I export results into separate sdf file on my computer? Below is my code for filtering. I think I need to use SDWriter Rdkit module, but can't find…
rosanna
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Problem transforming a SEQUENCE into SMILES with RDKit

I have a data set of enzyme sequences and a target variable to predict. The process I am doing is transforming sequences into smiles and then get numerical inputs for machine learning models. Problem is: rdkit fails to transform some of the…
Triki Sadok
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TypeError: 'NoneType' object is not an iterator Rdkit VS code

I'm trying to filter molecules from database 'part1' via Lipinski,Ghose and RUle of 3 filter but I keep getting error. So, after I ran this script, I get an error 'object is not an iterator' at the line where 'progressbar' is mentioned twice. I'm…
rosanna
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SetOwningMol RDKIT in python3

I have a couple of function definitions in a wider class that I'm writing in python. For one function I embed the molecules with n number of conformers, I then want to make sure that these conformers remain with the parsed molecule after the…
Goffredo Bosco
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Converting pandas columns of chemical formulas to SMILES

I’m wondering if there’s a way to get SMILES strings starting from a pandas data frame that looks like this: Formula. Band_Gap(eV) He 3.1 NaCl 1.2 NO2 3.5 ... ... Basically, I want to perform a regression task…
James Arten
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How would you convert a large sdf file of chemical compounds into individual files containing molecular images?

A new deep-learning algorithm for drug-discovery based on images, requires splitting a file containing ~3000 chemical compounds in png files containing individual 2D 200 x 200 pixel images (.: SN00001400.png, SN00002805.png, SN00002441.png........).…
Julio Coll
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Unable to use RDKit in Jupyter or iPython

I want to use RDKit in a Jupyter environment. However, after I followed the procedure outlined in this document. After following the process, including getting the kernel for jupyter, I tried to access RDKit and play with it. (rdkit-test) [user] ~ $…
megamence
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from PyBioMed.PyMolecule import moe; ModuleNotFoundError: No module named 'rdkit'

I tried to install the pybiomed package by using this link: 1- Download the PyBioMed-1.0.zip 2- Extract the PyBioMed-1.0.zip file 3- cd PyBioMed-1.0 4-python setup.py install Then I found out I need to install the rdkit package too. Based on this…
Amin Khodamoradi
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Is there anyway to load SDF file and fetch details like mols,inchi and reagent so on?

I have been using RDKIT for load and fetch details from SDF file but it is not working. from rdkit import Chem from rdkit.Chem.ChemUtils.SDFToCSV import Convert from rdkit.Chem import PandasTools import pandas as pd import os from rdkit import…
demo brain
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UnboundLocalError: local variable 'ff_cog' referenced before assignment, unsolved

I have got this piece of code that does not really want to work. I already tried to use Global, but it gave me a different mistake error (it tells me that ff_cog is not defined in that way), I tried to change the position of "numat", which was over …
Davide Annese
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