xiaoruiDong/RDMC

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

Language: Jupyter Notebook - Size: 47.6 MB - Last synced: about 6 hours ago - Pushed: about 9 hours ago - Stars: 20 - Forks: 0

RadonPy/RadonPy

RadonPy is a Python library to automate physical property calculations for polymer informatics.

Language: Python - Size: 4.86 MB - Last synced: about 5 hours ago - Pushed: 5 months ago - Stars: 122 - Forks: 19

DrReetuSharma/Drug-Target-Discovery-Using-LLMs-and-Knowledge-Graphs

Drug target discovery using LLM and Knowledge graphs

Language: Python - Size: 61.5 KB - Last synced: about 10 hours ago - Pushed: about 24 hours ago - Stars: 5 - Forks: 1

rdkit/rdkit

The official sources for the RDKit library

Language: HTML - Size: 195 MB - Last synced: about 23 hours ago - Pushed: 2 days ago - Stars: 2,471 - Forks: 845

alexandreklr/PGdet

A uni project developped to take an organic molecule written in SMILES and give back the point group

Language: Python - Size: 69.3 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 2 - Forks: 2

ale94mleon/MolDrug

MolDrug is a python package for drug-oriented optimization on the chemical space ​

Language: Python - Size: 98.8 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 10 - Forks: 2

maabuu/posebusters

Plausibility checks for generated molecule poses.

Language: Python - Size: 3.68 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 172 - Forks: 12

sustainable-processes/tljh-rxns

Plugin for TLJH for computational chemistry

Language: Python - Size: 2.93 KB - Last synced: 9 days ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

akuroiwa/chem-ant

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

Language: Python - Size: 81.1 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 2 - Forks: 1

DocMinus/psi4_rdkit

Quant Chem python scripts using PSI4 and RdKit

Language: Jupyter Notebook - Size: 308 KB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

UnixJunkie/molenc

MolEnc: a molecular encoder using rdkit and OCaml.

Language: OCaml - Size: 5.53 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 18 - Forks: 2

moltinginstar/discovering-telomerase-inhibitors

Discovering telomerase inhibitors with machine learning.

Language: Jupyter Notebook - Size: 4.91 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

Bobidan97/Cheminformatics

Cheminformatics based project that aims to assess the diversity of the known inhibitors of SarsCov-2 proteases taken from COVID Moonshot project.

Language: Python - Size: 2.86 MB - Last synced: 13 days ago - Pushed: about 2 years ago - Stars: 1 - Forks: 1

PaccMann/paccmann_datasets

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

Language: Python - Size: 5.81 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 25 - Forks: 7

tagirshin/altmol

Plugin to show molecule images on mouseover using RDKit and Altair

Language: Jupyter Notebook - Size: 4.49 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 4 - Forks: 1

klausweinbauer/FGUtils

Utility library to query functional group properties in molecules.

Language: Python - Size: 116 KB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

ciw-project-2023/coaler

CoAler = Core Aligner (Multi-Alignment of Molecules)

Language: C++ - Size: 23.2 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 8 - Forks: 1

datamol-io/datamol

Molecular Processing Made Easy.

Language: Python - Size: 111 MB - Last synced: 25 days ago - Pushed: 4 months ago - Stars: 426 - Forks: 46

chemosim-lab/ProLIF

Interaction Fingerprints for protein-ligand complexes and more

Language: Python - Size: 6.53 MB - Last synced: 19 days ago - Pushed: 3 months ago - Stars: 323 - Forks: 63

kamilpytlak/MoleculaPy

👨‍🔬 A command-line application that utilizes the RDKit library to compute molecular descriptors and fingerprints, aiding in the analysis and characterization of chemical structures

Language: Python - Size: 263 KB - Last synced: 24 days ago - Pushed: 25 days ago - Stars: 0 - Forks: 1

rvianello/chemicalite

An SQLite extension for chemoinformatics applications.

Language: C++ - Size: 452 KB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 53 - Forks: 6

quantaosun/webdock

Open-Sourced. Easy docking in your browser without any login requirement. Post processing and interaction diagram included.

Language: Jupyter Notebook - Size: 6.62 MB - Last synced: 29 days ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

Ramprasad-Group/polygnn

polyGNN is a Python library to automate ML model training for polymer informatics.

Language: Python - Size: 16.6 MB - Last synced: 30 days ago - Pushed: 30 days ago - Stars: 27 - Forks: 4

dylanwal/chemistry_drawer

Draw molecules with plotly!

Language: Python - Size: 1.59 MB - Last synced: 9 days ago - Pushed: almost 2 years ago - Stars: 33 - Forks: 2

wjm41/molplotly

add-on to plotly which show molecule images on mouseover!

Language: Python - Size: 17 MB - Last synced: 20 days ago - Pushed: about 2 months ago - Stars: 230 - Forks: 24

ecrl/graphchem

Graph-based machine learning for chemical property prediction

Language: Python - Size: 2.1 MB - Last synced: 26 days ago - Pushed: 10 months ago - Stars: 27 - Forks: 7

Mishima-syk/psikit

psi4+RDKit

Language: Python - Size: 799 KB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 92 - Forks: 18

rdkit/rdkit-js

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

Language: Dockerfile - Size: 16.4 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 121 - Forks: 36

caiyingchun/pychem

Various python script about cheminformatics.

Language: Jupyter Notebook - Size: 50.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 1

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.

Language: Python - Size: 13.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0

UCLCheminformatics/ScaffoldGraph

ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.

Language: Python - Size: 781 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 158 - Forks: 38

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).

Language: Python - Size: 341 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 1

mcs07/MolVS

Molecule Validation and Standardization

Language: Python - Size: 266 KB - Last synced: 16 days ago - Pushed: about 4 years ago - Stars: 146 - Forks: 51

Mishima-syk/py4chemoinformatics

Python for chemoinformatics

Language: Jupyter Notebook - Size: 33.8 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 217 - Forks: 85

InformaticsMatters/squonk

Squonk platform and computational notebook

Language: Java - Size: 123 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 7 - Forks: 3

Aaryesh-AD/GU-Drug-Pro-Toolkit

A Comprehensive Tool for Drug Property and Likeness Prediction.

Language: Python - Size: 190 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

greglandrum/rdkit-blog

RDKit blog

Language: Jupyter Notebook - Size: 66.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 5 - Forks: 1

vandan-revanur/pychemovality

Estimate ovality of molecules 🌐

Language: Fortran - Size: 19.7 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

vandan-revanur/pychemprojections

Visualize various molecule projections using Python 🎨

Language: Python - Size: 24.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 0

kuelumbus/rdkit-pypi

⚛️ RDKit Python Wheels on PyPI. 💻 pip install rdkit

Language: Python - Size: 306 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 116 - Forks: 12

icanswim/qchem

An exploration of the state of the art in the application of data science to quantum chemistry.

Language: Jupyter Notebook - Size: 3.73 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 10 - Forks: 3

bio-grids/autodocking-utils

Docker implementation of autodocking, openbabel, rdkit and lots of molecular dynamics utilities.

Language: Dockerfile - Size: 6.66 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

cbouy/mols2grid

Interactive molecule viewer for 2D structures

Language: Python - Size: 13.6 MB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 204 - Forks: 24

kotori-y/Scopy

An integrated negative design python library for desirable HTS/VS database design

Language: Python - Size: 8.77 MB - Last synced: 20 days ago - Pushed: over 1 year ago - Stars: 42 - Forks: 13

InformaticsMatters/docker-rdkit

Lightweight RDKit images for production deployment

Language: Shell - Size: 152 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 33 - Forks: 9

mcs07/docker-postgres-rdkit

PostgreSQL Docker image with RDKit cartridge

Language: Dockerfile - Size: 5.86 KB - Last synced: about 1 month ago - Pushed: about 4 years ago - Stars: 16 - Forks: 18

ChidhvilasTanay/drug_discovery_coronavirus_CHEMBL

A Drug Discovery method using CHEMBL database, Lipinski Parameters, molecular fingerprint (padel) for SARS coronavirus 3C-like proteinase.

Language: Jupyter Notebook - Size: 510 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

cheminfolab/flask

An electronic lab notebook based on react and django.

Language: TypeScript - Size: 1.16 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0

AmyQ20/Tutorials

Random tutorials (RDKit, GPR)

Language: HTML - Size: 206 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

InformaticsMatters/pipelines

Containerised components for cheminformatics and computational chemistry

Language: Python - Size: 60.6 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 32 - Forks: 19

oddt/oddt

Open Drug Discovery Toolkit

Language: Python - Size: 45.8 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 392 - Forks: 115

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.

Language: Jupyter Notebook - Size: 30.8 MB - Last synced: 2 months ago - Pushed: 7 months ago - Stars: 240 - Forks: 58

ThomasJewson/Molecular3DLengthDescriptors

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

Language: Python - Size: 136 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 5 - Forks: 0

grillazz/fastapi-redis

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

Language: Python - Size: 739 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 76 - Forks: 11

gulabpatel/Graph_Neural_Network

Language: Jupyter Notebook - Size: 14.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 8 - Forks: 0

DocMinus/RxnTransformDescriptors

Python code for reaction transform descriptors (TDs)

Language: Python - Size: 33.2 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0

jeffrichardchemistry/molbokeh

A new python package to visualize molecules in dots hover

Language: Jupyter Notebook - Size: 979 KB - Last synced: 15 days ago - Pushed: 3 months ago - Stars: 4 - Forks: 1

phatdatnguyen/JadeChem

A Windows GUI software for performing machine learning (ML) tasks in chemistry.

Language: C# - Size: 1.34 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

idslme/IDSL_MINT

A Deep Learning Framework to Interpret Raw Mass Spectrometry (m/z) Data

Language: Python - Size: 972 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 1

TanushGoel/PharmaceuticAI

An iterative process that uses two machine learning models to generate the best inhibitors for a target protein to help reduce the time and cost of the drug discovery process

Language: Jupyter Notebook - Size: 8.94 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 6 - Forks: 2

adelenelai/onglai-classify-homologues

OngLai: A cheminformatics algorithm to classify homologous chemical series

Language: Python - Size: 72.5 MB - Last synced: 27 days ago - Pushed: over 1 year ago - Stars: 7 - Forks: 5

andrewtarzia/mol-ellipsize

Molecular size calculation based on ellipsoid fitting over N conformers

Language: TeX - Size: 8.19 MB - Last synced: 2 days ago - Pushed: over 2 years ago - Stars: 12 - Forks: 0

UAMCAntwerpen/2040FBDBIC

This repository contains all the course materials that are used in the "Chemo-informatics and computational drug design" course teaches at the University of Antwerp (Belgium)

Language: Jupyter Notebook - Size: 152 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 4 - Forks: 2

kotori-y/pySmash

Smash molecule and obtain significant fragments

Language: Jupyter Notebook - Size: 12.5 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 16 - Forks: 3

Franky1/Streamlit-RDKit

Streamlit example project with RDKit

Language: Makefile - Size: 37.1 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

bmrb-io/smolscripts

small molecule processing scripts

Language: Python - Size: 552 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

rdkit-rs/rdkit-sys

Rust crate for linking against the RDKit C++ API

Size: 76.2 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 19 - Forks: 6

ricardoamferreira/Predicting-Adverse-Drug-Reactions-with-Machine-Learning

The objective of this work is to develop machine learning (ML) methods that can accurately predict adverse drug reactions (ADRs) using the databases SIDER and OFFSIDES.

Language: Jupyter Notebook - Size: 27 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 20 - Forks: 13

suneelbvs/rdkit_tutorials

rdKit basics (provided jupyter notebooks are custom curated and will help the users to start working on rdKit)

Language: Jupyter Notebook - Size: 1.4 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 22 - Forks: 5

UnixJunkie/smi2sdf3d

3D diverse conformers generation using rdkit

Language: Python - Size: 34.2 KB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 19 - Forks: 11

UnixJunkie/mol2ecfp4

convert molecules to their ECFP4 fingerprint using rdkit

Language: Python - Size: 1.95 KB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 8 - Forks: 3

silicos-it/spectrophores-boost

Spectrophore technology with part of it in C++/Boost

Size: 4.91 MB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 1 - Forks: 1

lhm30/PIDGINv3

Protein target prediction using random forests and reliability-density neighbourhood analysis

Language: Python - Size: 5.27 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 38 - Forks: 13

kcncell/Deepchem_toxicityPredictionModel

This is an introductory deep learning model which uses the Deepchem package. Lots of credit has to be given to the authors(Ramsundar B., Eastman P., Walters P., Pande V.) of the book "Deep Learning for the Life Sciences". This book has been a gold mine in terms of my exploration and journey in DeepLearning in the field of biochemistry.

Language: Jupyter Notebook - Size: 5.86 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

apahl/cellpainting

Tools for Processing Results from CellPainting Assay

Language: Python - Size: 181 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 2 - Forks: 4

apahl/rdkit_nim

Nim bindings for the C++ cheminformatics toolkit RDKit.

Language: Nim - Size: 85 KB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0

GLambard/Molecules_Dataset_Collection

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

Size: 63.1 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 86 - Forks: 31

liutairan/eMolFrag

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

Language: Python - Size: 8.88 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 37 - Forks: 22

albags/ProjectTargetPredictionApp

Target Prediction and Similarity 2D&3D using Python scientific libraries

Language: HTML - Size: 8.11 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 2 - Forks: 1

cbouy/molhighlighter

Multicolored substructure highlights made easy

Language: Jupyter Notebook - Size: 187 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 7 - Forks: 1

mcsorkun/Conformer-Search

A simple workflow for minimum energy conformer search based on force field optimization methods (UFF and MMFF94) available from RDKit.

Language: Python - Size: 195 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 7 - Forks: 4

ThWIC-AutoQSPR/iterstruc

Language: Python - Size: 319 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

TraceLD/rdkit-csharp-wrapper

C# Wrapper for the RDKit C++ cheminformatics library with support for Windows, Linux and macOS.

Language: C++ - Size: 587 KB - Last synced: 2 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

kazuyaujihara/build-rdkit

RDKit .NET wrapper for Windows/Linux.

Language: Python - Size: 280 KB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 5

c-feldmann/lassohighlight

Tool to add substructure highlighting to molecules drawn with RDKit

Language: Python - Size: 706 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 10 - Forks: 1

nbehrnd/RegioSQM Fork of jensengroup/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.

Language: Python - Size: 9.78 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

c-feldmann/rdkit_heatmaps

A package to draw custom heatmaps on molecular depictions of RDKit

Language: Python - Size: 3.7 MB - Last synced: 9 months ago - Pushed: about 2 years ago - Stars: 8 - Forks: 0

mcs07/docker-rdkit

RDKit Docker images

Language: Dockerfile - Size: 7.81 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 18 - Forks: 11

santuchal/molecule_descriptors_and_fingerprint

SMILE to Descriptors and Fingerprint Generators

Language: Python - Size: 16.6 KB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

kareemjeiroudi/molecules_and_ml

An online repository to access my bachelor project files wherever I go. However, this might be of interest to some bioinformaticians. For full description please refer to the README file.

Language: Jupyter Notebook - Size: 490 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 4 - Forks: 1

SylwiaNowakowska/Graph_Neural_Network_Drug_Discovery

Classification of molecules' ability to inhibit HIV with Graph Neural Networks (PyTorch Geometric) - work in progress.

Language: Jupyter Notebook - Size: 552 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

lhm30/scikitlearn_clustermap_rdkit_bicluster_molecules

hacked code to bicluster molecules using rdkit and scikitlearn

Language: Python - Size: 1.95 KB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

liskovaf/COCONUT

Feature interrelation profiling using COCONUT and ZINC database

Language: Jupyter Notebook - Size: 200 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 0

nbehrnd/xyz2mol_b

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

Language: Python - Size: 14.6 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

greglandrum/rdkit-blog-fastpages

Language: Jupyter Notebook - Size: 31.5 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 19 - Forks: 7

the-metabolic-disassembler/metadisassembler

Language: Jupyter Notebook - Size: 3.08 MB - Last synced: 2 days ago - Pushed: over 4 years ago - Stars: 3 - Forks: 1

KCF-Convoy/kcfconvoy

Python package to convert KCF chemical substructure fingerprints

Language: Jupyter Notebook - Size: 6.79 MB - Last synced: 14 days ago - Pushed: almost 3 years ago - Stars: 5 - Forks: 4

jeffrichardchemistry/pySiRC

Simple web application for prediction of reaction rate constant through machine learning models using molecular fingerprints.

Language: Python - Size: 233 MB - Last synced: 12 months ago - Pushed: over 2 years ago - Stars: 11 - Forks: 4

rinikerlab/PyGromosTools

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

Language: Python - Size: 218 MB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 15 - Forks: 13

iktos/rdkit-provider

instantiate an RDKit web worker in a React context

Language: TypeScript - Size: 1.4 MB - Last synced: 19 days ago - Pushed: about 2 months ago - Stars: 5 - Forks: 0