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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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How do I get molecular structural information from SMILES

My question is: is there any algorithm that can convert a SMILES structure into a topological fingerprint? For example if glycerol is the input the answer would be 3 x -OH , 2x -CH2 and 1x -CH. I'm trying to build a python script that can predict…
Berkay
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rdkit: how to draw high resolution chemical structure

I am using jupyter lab to draw chemical structures. But the output image resolution is too low. How can I improve it? from rdkit import Chem from rdkit.Chem import Draw smiles = 'C1=CC(=C(C=C1C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O)O)O' m =…
Wang
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How to use RDKit to calculte molecular fingerprint and similarity of a list of SMILE structures?

I'm using RDKit to calculate molecular similarity based on Tanimoto coefficient between two lists of molecules with SMILE structures. Now I'm able to extract the SMILE structures from two separate csv files. I'm wondering how to put these structures…
Anna Zhou
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RDKit - Export pandas data frame with mol image

I would like to know whether is it possible to export pandas dataframe with molecular image directly in excel file format? Thanks in advance,
B.Gees
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Chemical representation - SNL to SMILES

I would like to know whether is it possible to convert SYBYL Line Notation (SNL) into Smiles with Python? Example for N-methyl-pyrrolidone: SNL = 'N[1](CH2CH2CH2C@1=O)CH3' SMI = 'CN1CCCC1=O' I haven't found any solution with RDKit :(
B.Gees
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Insert matplotlib images into a pandas dataframe

PURPOSE: I am currently working with rdkit to colour the structures of my molecules according to rdkit.Chem.Draw.SimilarityMaps. Now, I would like to use the matplotlib images SimilarityMaps function to introduce them in a pandas dataframe and…
B.Gees
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Installing RDKit

I have installed Spyder3.2.1 in the current version of Miniconda3 on my Debian v-9.1.0 64 bit Linux platform. Spyder is performing well, but I am having difficulty installing the RDKit. I followed the directions in the RDKit_Docs_current.pdf: How…
Steve
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Finding the relative position of molecular substructures with RDKit

I have a collection of fatty acid molecules (in SMILES format) in which I would like to find the positions of the C=C double bonds. Position meaning: count how many carbons away the double bond is from the first carbon, which is the carbon of the…
jonas87
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Rdkit - ImportError: DLL load failed

I have used pip install rdkit-pypi to install rdkit library. But when I type import rdkit as rd, it shows the error ImportError: DLL load failed while importing rdBase: The specified module was not found. I am using Anaconda as a base. What should…
Urvesh
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How to save RDKit conformer object into a sdf file?

I generated a bunch of conformers for a molecule. For each conformed, I want to save the coordinates in a SDF file. I tried the following, but the coordinates in the sdf file is different from that of the conformer. from rdkit import Chem from…
Zhen Liu
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How to import rdkit in google colab these days?

!wget -c https://repo.continuum.io/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh !chmod +x Miniconda3-py37_4.8.3-Linux-x86_64.sh !time bash ./Miniconda3-py37_4.8.3-Linux-x86_64.sh -b -f -p /usr/local !time conda install -q -y -c conda-forge…
Seungwoo Ryu
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RDKit's function MolFromInchi is not working

I am currently working on a Django project that necessitates the functionality of taking an InChI string and converting it into a molecule, but the package that I'm using seems to have an issue with its function MolFromInchi. Whenever I try to use…
King Burst
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Threading/Multiprocessing - Match searching a 60gb file with 600k terms

I have a python script that would take ~93 days to complete on 1 CPU, or 1.5 days on 64. I have a large file (FOO.sdf) and would like to extract the "entries" from FOO.sdf that match a pattern. An "entry" is a block of ~150 lines delimited by…
Jacob Anderson
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Find chiral centers rdkit

Working with some molecules and reactions, it seems that chiral centers in smiles may not be found after applying reactions. What I get after applying some reactions on a molecule is this smile: C[C](C)[C]1[CH+]/C=C(\\C)CC/C=C(\\C)CC1 which…
Fence
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How can I fix an `OSError: file error: bad input file` in RDkit with .sdf file?

I'm using a third party code in python from an arxiv which use RDkit as a library. It takes a .sdf file with data about chemicals molecules as an argument, but then RDkit throw an error: OSError: File error: Bad input file file.sdf I followed the…
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