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Projects in Awesome Lists tagged with rdkit

A curated list of projects in awesome lists tagged with rdkit .

https://github.com/rdkit/rdkit

The official sources for the RDKit library

c-plus-plus cheminformatics python rdkit

Last synced: 30 Jan 2026

https://github.com/chemosim-lab/ProLIF

Interaction Fingerprints for protein-ligand complexes and more

cheminformatics docking drug-design drug-discovery mdanalysis molecular-dynamics rdkit

Last synced: 20 Nov 2025

https://github.com/AngelRuizMoreno/Jupyter_Dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

autodock autodock-vina cheminformatics computational-biology drug-design drug-discovery drug-repurposing jupyter-notebook ledock mdanalysis molecular-docking openbabel protein protein-structure py3dmol rdkit

Last synced: 22 Jul 2025

https://github.com/cbouy/mols2grid

Interactive molecule viewer for 2D structures

cheminformatics jupyter molecule-viewer python rdkit visualization

Last synced: 05 Apr 2025

https://github.com/rdkit/rdkit-js

A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit .

cheminformatics drug-discovery javascript molecule molecule-viewer molecule-visualization node-js npm rdkit react wasm

Last synced: 15 May 2025

https://github.com/mcs07/molvs

Molecule Validation and Standardization

cheminformatics chemistry python rdkit standardization validation

Last synced: 06 Apr 2025

https://github.com/kuelumbus/rdkit-pypi

⚛️ RDKit Python Wheels on PyPI. 💻 pip install rdkit

cheminformatics pypi pypi-package python python-library rdkit

Last synced: 02 Mar 2026

https://github.com/glambard/molecules_dataset_collection

Collection of data sets of molecules for a validation of properties inference

classification dataset inference machine-learning molecule moleculenet properties rdkit smiles

Last synced: 23 Oct 2025

https://github.com/grillazz/fastapi-redis

Showcase of Redis integration with Python FastAPI framework supported by Pydantic as API backend for RDKit: Open-Source Cheminformatics Software

api asyncio docker fastapi fastapi-redis pydantic python python3 rdkit redis

Last synced: 07 Apr 2025

https://github.com/rvianello/chemicalite

An SQLite extension for chemoinformatics applications.

rdkit sqlite

Last synced: 21 Feb 2026

https://github.com/liutairan/emolfrag

eMolFrag is a molecular fragmentation tool based on BRICS algorithm written in Python.

brics-algorithm fragments python rdkit

Last synced: 26 Jun 2025

https://github.com/informaticsmatters/pipelines

Containerised components for cheminformatics and computational chemistry

docker dockerfile python rdkit squonk squonk-pipelines

Last synced: 01 Mar 2026

https://github.com/informaticsmatters/docker-rdkit

Lightweight RDKit images for production deployment

docker-image dockerfile lightweight-images rdkit

Last synced: 23 Aug 2025

https://github.com/apahl/mol_frame

Chemical Structure Handling for Pandas DataFrames

pandas rdkit

Last synced: 13 May 2025

https://github.com/ecrl/graphchem

Graph-based machine learning for chemical property prediction

computational-chemistry graph-neural-networks message-passing pytorch pytorch-geometric rdkit

Last synced: 13 Apr 2025

https://github.com/yunjaechoi/vaemols

Variational Autoencoder for Molecules

molecule rdkit tensorflow variational-autoencoder

Last synced: 30 Oct 2025

https://github.com/paccmann/paccmann_datasets

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

bioinformatics chemoinformatics deep-learning python pytorch rdkit smiles

Last synced: 09 Apr 2025

https://github.com/xiaoruidong/rdmc

Reaction Data and Molecular Conformers (RDMC) is a package dealing with reactions, molecules, conformers, majorly in 3D.

conformer molecule rdkit reaction

Last synced: 23 Oct 2025

https://github.com/unixjunkie/smi2sdf3d

3D diverse conformers generation using rdkit

3d chemoinformatics conformer ligand python-script rdkit sdf smi smiles

Last synced: 14 Apr 2025

https://github.com/rdkit-rs/rdkit-sys

Rust crate for linking against the RDKit C++ API

rdkit rust

Last synced: 08 Apr 2026

https://github.com/mcs07/docker-rdkit

RDKit Docker images

cheminformatics docker-image rdkit

Last synced: 08 Jul 2025

https://github.com/mcs07/docker-postgres-rdkit

PostgreSQL Docker image with RDKit cartridge

cheminformatics docker-image postgresql rdkit

Last synced: 28 Oct 2025

https://github.com/andrewtarzia/mol-ellipsize

Molecular size calculation based on ellipsoid fitting over N conformers

chemistry high-throughput molecular-size molecules rdkit

Last synced: 03 Mar 2026

https://github.com/zincware/rdkit2ase

Create atomistic structures with ASE, rdkit and packmol

ase packmol rdkit

Last synced: 22 Jul 2025

https://github.com/rvianello/docker-postgres-rdkit

The PostgreSQL image, just extended with the RDKit cartridge

docker postgresql rdkit

Last synced: 06 Feb 2026

https://github.com/membrizard/ml_conformer_generator

Shape-constrained molecule generation via Equivariant Diffusion and GCN

chemistry conformers diffusion-models graph-convolutional-networks molecule-generation rdkit

Last synced: 11 Apr 2026

https://github.com/michelml/chempp

[paused development] Large scale concurrent chemical search using RDKit cartridge, Oat++ and native Postgres & C++ features.

cheminformatics cpp oatpp postgresql rdkit

Last synced: 07 May 2025

https://github.com/cbouy/bokehmol

Bokeh extensions to plot molecules easily

bokeh cheminformatics interactive-visualizations jupyter rdkit

Last synced: 28 Oct 2025

https://github.com/informaticsmatters/squonk

Squonk platform and computational notebook

chemaxon docker gradle java openshift rdkit squonk

Last synced: 06 Oct 2025

https://github.com/unixjunkie/mol2ecfp4

convert molecules to their ECFP4 fingerprint using rdkit

ecfp4 mol2 python-script rdkit sdf

Last synced: 17 Jun 2025

https://github.com/ciw-project-2023/coaler

CoAler = Core Aligner (Multi-Alignment of Molecules)

alignment bioinformatics conan cpp rdkit

Last synced: 12 Apr 2025

https://github.com/iktos/molecule-representation

Interactif molecule representations / drawing as react components

cheminformatics chemistry molecule-viewer rdkit react typescript

Last synced: 23 Oct 2025

https://github.com/unixjunkie/chemoinfo_recipes

Command line recipes for the working chemoinformatician

chemaxon chemoinformatics howto ligand openbabel rdkit rmsd

Last synced: 05 Jan 2026

https://github.com/cbouy/molhighlighter

Multicolored substructure highlights made easy

cheminformatics chemistry chemoinformatics rdkit

Last synced: 28 Oct 2025

https://github.com/akuroiwa/chem-ant

Select materials to output molecules similar to the target molecule with MCTS Solver and Genetic Programming.

cheminformatics chemoinformatics deap genetic-programming mcts-solver rdkit

Last synced: 17 Jan 2026

https://github.com/apahl/rdkit_nim

Nim bindings for the C++ cheminformatics toolkit RDKit.

nim nim-lang rdkit

Last synced: 22 Jun 2025

https://github.com/thomasjewson/molecular3dlengthdescriptors

A 3D conformational based molecular descriptor set for use in QSPR and Machine Learning.

3d cheminformatics chemistry conformer crystallography descriptor learning machine molecule rdkit

Last synced: 07 Mar 2026

https://github.com/wesleybeckner/gains

project that enables molecular design and computational screening of small molecules

machine-learning molecular-evolution rdkit

Last synced: 27 Apr 2025

https://github.com/iktos/rdkit-provider

instantiate an RDKit web worker in a React context

cheminformatics rdkit rdkit-chem react typescript webworker webworkers

Last synced: 19 Jan 2026

https://github.com/deepmatterltd/rdfreader

Read the full contents of CTAB .rdf files in python. Captures RXN and MOL record using RDKit and reads additional data fields (including solvents/catalysts/agents).

cheminformatics ctab rdkit

Last synced: 08 Apr 2025

https://github.com/stefan-schroedl/molecule_classification

"Auto-sklearn for chemistry" - train and run machine-learned classifiers for molecular classification tasks.

automatic automl cheminformatics chemistry chemoinformatics hyperparameter-optimization machine-learning molecule python rdkit scikit-learn

Last synced: 25 Sep 2025

https://github.com/thomasgust/molecumixer

Very incomplete right now, pretrained ARGVAET system for generating, classifying, and predicting the properties of molecules. I couldn't upload the dataset or checkpoints due to size constraints.

argvaet bioinformatics foundation-model generative-ai generative-pretraining gnn molecule neural-network pretraining pytorch rdkit

Last synced: 23 Oct 2025

https://github.com/andgineer/spark-aws-rdkit

Docker image with Apache Spark / Hadoop3 (compatible with AWS services like S3) and with RDKit installed in anaconda environment

anaconda aws pyspark rdkit spark

Last synced: 28 Oct 2025

https://github.com/apahl/rdkit_misc

A collection of miscellaneous personal tools for the RDKit

rdkit

Last synced: 01 Apr 2025

https://github.com/apahl/cellpainting

Tools for Processing Results from CellPainting Assay

cellprofiler nim-lang pandas rdkit

Last synced: 13 May 2025

https://github.com/klausweinbauer/fgutils

Utility library to query functional group properties in molecules.

functional-groups molecular-graph rdkit

Last synced: 26 Jan 2026

https://github.com/prospero1988/demiurge

Demiurge is a Python tool for generating ML input data from simulated ¹H/¹³C NMR spectra or ECFP4 fingerprints. It uses local NMRshiftDB2 prediction and RDKit, producing ML-ready CSVs from SMILES in minutes.

cheminformatics chemistry data-preprocessing deep-learning ecfp4 feature-extraction input-generation java logd machine-learning molfile nmr nmr-spectroscopy nmrshift-db open-source prediction python rdkit

Last synced: 18 May 2026

https://github.com/drreetusharma/molecular_innovations-for-kpgt-knowledge-guided-pre-training-of-graph-transformer-

Knowledge-guided-Pre-training-of-Graph-Transformer: The primary aim of this project is to leverage knowledge-guided pre-training techniques for enhancing the performance of graph transformers in molecular property prediction and drug discovery.

machine machine-learning neural-network pytorch rdkit scikit-learn

Last synced: 04 Mar 2026

https://github.com/insilichem/tangram_subalign

Align two, potentially different, molecules based on partial matches of substructures in UCSF Chimera

rdkit ucsf-chimera

Last synced: 14 Jun 2026

https://github.com/gmattedi/chemicalspace

Object-oriented Representation for Chemical Spaces

chemical-space cheminformatics chemistry computational-chemistry machine-learning rdkit

Last synced: 08 Apr 2026

https://github.com/evitanrelta/reaction-geognn

Re-implementation of GeoGNN in PyTorch + DGL, and further adapted to predict reaction properties.

dgl gnn python pytorch pytorch-lightning rdkit

Last synced: 05 May 2026

https://github.com/adam-maz/cns_mpo_calculator

Here I provide some code that enables users to calculate CNS MPO score for their molecules, based on the SMILES and known pKa values.

chemoinformatics cnsmpo computer-aided-drug-design descriptors filter medicinal-chemistry object-oriented-programming python rdkit virtual-screening

Last synced: 01 Mar 2026

https://github.com/prheenan/mol_from_text

Turn text into molecular images!

chemistry fun molecule python rdkit

Last synced: 16 Oct 2025

https://github.com/rishigurnani/polygnn_kit

A package for performing operations on infinite polymers.

polymer-informatics rdkit

Last synced: 19 Aug 2025

https://github.com/mjmolina/europython_2019

Europython 2019 Talk - When a Biologist met Python.

biopython bokeh networkx pytorch rdkit

Last synced: 18 May 2026

https://github.com/amarkar7/autodockvina_batchdocking

A complete step-by-step pipeline to dock multiple ligands using AutoDock Vina. Includes ligand preparation, file format conversion, batch docking, and result extraction.

autodock-vina bioinformatics docking molecular-docking openbabel perl rdkit shell virtual-screening

Last synced: 02 May 2026

https://github.com/drreetusharma/molapp

Molecular property prediction application.

cloud google python rdkit

Last synced: 18 Jun 2025

https://github.com/nbehrnd/regiosqm

A quick prediction of selectivities for the electrophilic substitution of homo- & heteroaromatic systems (Kromann et al., 2018ChemSci660 (http://dx.doi.org/10.1039/C7SC04156J) now ported to Python3.

computational-chemistry openbabel python python27 python38 rdkit synthesis

Last synced: 03 Oct 2025

https://github.com/camannguyen/rdkit_chem

Ruby GEM for RDKit (cheminformatics toolkits)

cheminformatics rdkit rdkit-chem rubygem

Last synced: 04 Feb 2026

https://github.com/apahl/cluster_mst

Compound clustering as MST

networkx panel rdkit

Last synced: 01 Apr 2025

https://github.com/paulzierep/flp

find long path (flp) algorithm

python rdkit

Last synced: 13 Jul 2025

https://github.com/avanishd-3/chemistry-calculator

Command-line tool for various chemical calculations

computational-chemistry python rdkit

Last synced: 24 Mar 2025

https://github.com/adam-maz/virtual_screening

Within this repository I present scripts that can be helpful during virtual screening in drug design & development.

clusterization jupyter-notebook k-means-clustering maestro-schrodinger medicinal-chemistry molecular-fingerprints pandas python rdkit scikit-learn scoring-functions virtual-screening

Last synced: 04 May 2026

https://github.com/gfrogat/qsar-pipeline

Distributed computation of molecular descriptors for QSAR modelling.

distributed python ray rdkit

Last synced: 23 Jul 2025

https://github.com/apahl/cellpainting2

Analyzing Cell Painting results with Dask and Pandas - not yet ready for use by others

cellprofiler dask jupyter-notebook pandas rdkit

Last synced: 09 May 2026

https://github.com/kbhalajiyadav/lipophilicity_model

This project trains a Morgan Fingerprint model to predict lipophilicity.

maccs-fingerprint mlpregressor morgan-fingerprints nn rdkit rdkit-chem rmse-score sklearn smiles

Last synced: 16 Apr 2026

https://github.com/arhs99/rdkit-cpp-utils

rdkit scripts for C++

cheminformatics chemistry rdkit

Last synced: 16 Jul 2025

https://github.com/jhylin/ml2-3_boosted_trees

Machine learning series 2.3 on boosted trees

adaboost-classifier rdkit scikit-learn-python xgboost-classifier

Last synced: 14 Feb 2026

https://github.com/haripasapuleti/web_apps

This web app predicts the solubility (LogS) of molecules based on their SMILES representation. It calculates key molecular descriptors and uses a machine learning model to make accurate solubility predictions.

machine-learning molecular-descriptors python rdkit streamlit webapp-development

Last synced: 16 May 2026

https://github.com/anandsahuofficial/tbxt-hit-id

Multi-signal computational pipeline for TBXT G177D (Brachyury), chordoma's master regulator. TBXT Hackathon 2026.

autodock-vina boltz-2 chordoma computational-chemistry drug-discovery gnina hit-identification mmgbsa muni-bio onepot openmm pillar-vc qsar rdkit rowan tbxt tbxt-hackathon-2026 virtual-screening

Last synced: 15 May 2026

https://github.com/nbehrnd/xyz2mol_b

based on a structure provided as .xyz file, attempt the generation of a .sdf block

computational-chemistry conversion rdkit sdf structure xyz

Last synced: 20 Apr 2026