rdkit | Topic | Ecosyste.ms: Repos

Topic: "rdkit"

rdkit/rdkit

The official sources for the RDKit library

Language: HTML - Size: 201 MB - Last synced at: 1 day ago - Pushed at: 3 days ago - Stars: 2,881 - Forks: 912

datamol-io/datamol

Molecular Processing Made Easy.

Language: Python - Size: 114 MB - Last synced at: 6 months ago - Pushed at: 11 months ago - Stars: 463 - Forks: 48

oddt/oddt

Open Drug Discovery Toolkit

Language: Python - Size: 45.8 MB - Last synced at: 18 days ago - Pushed at: over 2 years ago - Stars: 434 - Forks: 122

chemosim-lab/ProLIF

Interaction Fingerprints for protein-ligand complexes and more

Language: Python - Size: 11.2 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 403 - Forks: 80

maabuu/posebusters

Plausibility checks for generated molecule poses.

Language: Python - Size: 3.82 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 274 - Forks: 15

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 at: 5 months ago - Pushed at: over 1 year ago - Stars: 260 - Forks: 67

wjm41/molplotly

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

Language: Python - Size: 17 MB - Last synced at: 13 days ago - Pushed at: about 1 year ago - Stars: 252 - Forks: 27

Mishima-syk/py4chemoinformatics

Python for chemoinformatics

Language: Jupyter Notebook - Size: 33.8 MB - Last synced at: 28 days ago - Pushed at: almost 4 years ago - Stars: 226 - Forks: 91

cbouy/mols2grid

Interactive molecule viewer for 2D structures

Language: Python - Size: 13.6 MB - Last synced at: 12 days ago - Pushed at: over 1 year ago - Stars: 218 - Forks: 30

rdkit/rdkit-js

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

Language: Dockerfile - Size: 15.3 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 183 - Forks: 37

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 at: 13 days ago - Pushed at: about 3 years ago - Stars: 179 - Forks: 40

RadonPy/RadonPy

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

Language: Python - Size: 4.89 MB - Last synced at: 13 days ago - Pushed at: 3 months ago - Stars: 173 - Forks: 25

mcs07/MolVS

Molecule Validation and Standardization

Language: Python - Size: 266 KB - Last synced at: 19 days ago - Pushed at: about 5 years ago - Stars: 170 - Forks: 55

kuelumbus/rdkit-pypi

⚛️ RDKit Python Wheels on PyPI. 💻 pip install rdkit

Language: Python - Size: 300 KB - Last synced at: 15 days ago - Pushed at: 24 days ago - Stars: 132 - Forks: 20

GLambard/Molecules_Dataset_Collection

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

Size: 63.1 MB - Last synced at: 18 days ago - Pushed at: almost 7 years ago - Stars: 102 - Forks: 30

Mishima-syk/psikit

psi4+RDKit

Language: Python - Size: 799 KB - Last synced at: 4 days ago - Pushed at: over 2 years ago - Stars: 100 - Forks: 22

joofio/py4chemoinformatics Fork of Mishima-syk/py4chemoinformatics

Python for chemoinformatics

Language: Jupyter Notebook - Size: 24.3 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 88 - Forks: 26

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: 696 KB - Last synced at: about 8 hours ago - Pushed at: 2 months ago - Stars: 83 - Forks: 10

rvianello/chemicalite

An SQLite extension for chemoinformatics applications.

Language: C++ - Size: 453 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 56 - Forks: 8

liutairan/eMolFrag

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

Language: Python - Size: 8.88 MB - Last synced at: 24 days ago - Pushed at: over 4 years ago - Stars: 49 - 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 at: about 1 month ago - Pushed at: about 2 years ago - Stars: 45 - Forks: 13

chembience/chembience

A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.

Language: Python - Size: 4.17 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 44 - Forks: 3

dylanwal/chemistry_drawer

Draw molecules with plotly!

Language: Python - Size: 1.61 MB - Last synced at: 18 days ago - Pushed at: 21 days ago - Stars: 43 - Forks: 4

lhm30/PIDGINv3

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

Language: Python - Size: 5.27 MB - Last synced at: 19 days ago - Pushed at: almost 5 years ago - Stars: 40 - Forks: 14

Steinbeck-Lab/cheminformatics-microservice

This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.

Language: JavaScript - Size: 18.2 MB - Last synced at: 12 days ago - Pushed at: 13 days ago - Stars: 37 - Forks: 5

Ramprasad-Group/polygnn

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

Language: Python - Size: 22 MB - Last synced at: 18 days ago - Pushed at: 3 months ago - Stars: 37 - Forks: 8

InformaticsMatters/pipelines

Containerised components for cheminformatics and computational chemistry

Language: Python - Size: 60.6 MB - Last synced at: 12 days ago - Pushed at: almost 2 years ago - Stars: 36 - Forks: 19

InformaticsMatters/docker-rdkit

Lightweight RDKit images for production deployment

Language: Shell - Size: 139 KB - Last synced at: 12 days ago - Pushed at: 5 months ago - Stars: 34 - Forks: 10

apahl/mol_frame

Chemical Structure Handling for Pandas DataFrames

Language: Jupyter Notebook - Size: 8.16 MB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 33 - Forks: 11

ale94mleon/moldrug

moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space

Language: Python - Size: 105 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 32 - Forks: 4

ecrl/graphchem

Graph-based machine learning for chemical property prediction

Language: Python - Size: 2.7 MB - Last synced at: 12 days ago - Pushed at: 2 months ago - Stars: 32 - Forks: 7

YunjaeChoi/vaemols

Variational Autoencoder for Molecules

Language: Jupyter Notebook - Size: 27.2 MB - Last synced at: 16 days ago - Pushed at: over 6 years ago - Stars: 30 - Forks: 11

PaccMann/paccmann_datasets

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

Language: Python - Size: 6.01 MB - Last synced at: 8 days ago - Pushed at: 7 months ago - Stars: 28 - Forks: 7

xiaoruiDong/RDMC

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

Language: Jupyter Notebook - Size: 47.1 MB - Last synced at: 18 days ago - Pushed at: 9 months ago - Stars: 26 - Forks: 1

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 at: 5 months ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 14

UnixJunkie/smi2sdf3d

3D diverse conformers generation using rdkit

Language: Python - Size: 34.2 KB - Last synced at: 11 days ago - Pushed at: about 3 years ago - Stars: 23 - Forks: 12

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 at: over 1 year ago - Pushed at: about 2 years ago - Stars: 22 - Forks: 5

idslme/IDSL_MINT

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

Language: Python - Size: 972 KB - Last synced at: 2 days ago - Pushed at: over 1 year ago - Stars: 20 - Forks: 1

UnixJunkie/molenc

MolEnc: a molecular encoder using rdkit and OCaml.

Language: OCaml - Size: 9.04 MB - Last synced at: 11 days ago - Pushed at: 22 days ago - Stars: 19 - Forks: 2

rdkit-rs/rdkit-sys

Rust crate for linking against the RDKit C++ API

Size: 76.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 19 - Forks: 6

greglandrum/rdkit-blog-fastpages

Language: Jupyter Notebook - Size: 31.5 MB - Last synced at: 11 days ago - Pushed at: about 2 years ago - Stars: 19 - Forks: 7

mcs07/docker-rdkit

RDKit Docker images

Language: Dockerfile - Size: 7.81 KB - Last synced at: 12 days ago - Pushed at: almost 3 years ago - Stars: 19 - Forks: 11

ritabratamaiti/Chem-Faiss

This projects utilises vector similarity search from Faiss, in conjunction with chemical fingerprinting to build a scalabale similarity search architecture for compounds/molecules.

Language: Jupyter Notebook - Size: 3.21 MB - Last synced at: 6 days ago - Pushed at: about 4 years ago - Stars: 19 - Forks: 3

mcs07/docker-postgres-rdkit

PostgreSQL Docker image with RDKit cartridge

Language: Dockerfile - Size: 5.86 KB - Last synced at: 12 days ago - Pushed at: almost 5 years ago - Stars: 18 - Forks: 19

kotori-y/pySmash

Smash molecule and obtain significant fragments

Language: Jupyter Notebook - Size: 12.5 MB - Last synced at: 12 days ago - Pushed at: almost 4 years ago - Stars: 17 - Forks: 3

andrewtarzia/mol-ellipsize

Molecular size calculation based on ellipsoid fitting over N conformers

Language: TeX - Size: 8.19 MB - Last synced at: 27 days ago - Pushed at: over 3 years ago - Stars: 16 - Forks: 0

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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 15 - Forks: 13

rvianello/docker-postgres-rdkit

The PostgreSQL image, just extended with the RDKit cartridge

Language: Dockerfile - Size: 16.6 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 12 - Forks: 6

jeffrichardchemistry/molbokeh

A new python package to visualize molecules in dots hover

Language: Jupyter Notebook - Size: 979 KB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 12 - Forks: 1

tagirshin/altmol

Plugin to show molecule images on mouseover using RDKit and Altair

Language: Jupyter Notebook - Size: 4.49 MB - Last synced at: 10 days ago - Pushed at: 11 months ago - Stars: 11 - Forks: 2

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 at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 11 - Forks: 4

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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 3

AI4PFAS/AI4PFAS

Dataset and code for "Uncertainty-Informed Deep Transfer Learning of PFAS Toxicity"

Language: Jupyter Notebook - Size: 1.24 GB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 10 - Forks: 0

c-feldmann/lassohighlight

Tool to add substructure highlighting to molecules drawn with RDKit

Language: Python - Size: 706 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 1

cbouy/bokehmol

Bokeh extensions to plot molecules easily

Language: HTML - Size: 153 KB - Last synced at: 17 days ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 1

MichelML/chempp

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

Language: C++ - Size: 99.6 KB - Last synced at: 25 days ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 1

cbouy/molhighlighter

Multicolored substructure highlights made easy

Language: Jupyter Notebook - Size: 187 KB - Last synced at: 17 days ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 2

iktos/molecule-representation

Interactif molecule representations / drawing as react components

Language: TypeScript - Size: 3.1 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 8 - Forks: 1

greglandrum/rdkit-blog

RDKit blog

Language: Jupyter Notebook - Size: 93.8 MB - Last synced at: 11 days ago - Pushed at: 12 days ago - Stars: 8 - Forks: 2

ciw-project-2023/coaler

CoAler = Core Aligner (Multi-Alignment of Molecules)

Language: C++ - Size: 23.2 MB - Last synced at: 13 days ago - Pushed at: 11 months ago - Stars: 8 - Forks: 1

caiyingchun/pychem

Various python script about cheminformatics.

Language: Jupyter Notebook - Size: 50.2 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 8 - Forks: 1

gulabpatel/Graph_Neural_Network

Language: Jupyter Notebook - Size: 14.4 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 0

silicos-it/qed

The QED (Quantitative Estimation of Drug-likeness) molecular descriptor to use in combination with RDKit

Language: Python - Size: 135 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 6

c-feldmann/rdkit_heatmaps

A package to draw custom heatmaps on molecular depictions of RDKit

Language: Python - Size: 3.7 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 8 - Forks: 0

k-ujihara/build-rdkit

RDKit .NET wrapper for Windows/Linux.

Language: Python - Size: 280 KB - Last synced at: 17 days ago - Pushed at: about 3 years ago - Stars: 8 - Forks: 7

InformaticsMatters/squonk

Squonk platform and computational notebook

Language: Java - Size: 123 MB - Last synced at: 12 days ago - Pushed at: about 4 years ago - Stars: 8 - Forks: 3

yamasakih/docker-compose-razi

docker-compose + JupyterNotebook + RDKit database cartridge + PostgreSQL

Language: Jupyter Notebook - Size: 537 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 8 - Forks: 6

UnixJunkie/mol2ecfp4

convert molecules to their ECFP4 fingerprint using rdkit

Language: Python - Size: 1.95 KB - Last synced at: 11 days ago - Pushed at: about 8 years ago - Stars: 8 - Forks: 3

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: 362 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 7 - Forks: 3

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

Drug target discovery using LLM and Knowledge graphs

Language: Python - Size: 126 KB - Last synced at: 16 days ago - Pushed at: 7 months ago - Stars: 7 - Forks: 1

adelenelai/onglai-classify-homologues

OngLai: A cheminformatics algorithm to classify homologous chemical series

Language: Python - Size: 72.5 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 7 - Forks: 5

UnixJunkie/chemoinfo_recipes

Command line recipes for the working chemoinformatician

Size: 33.2 KB - Last synced at: 30 days ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 0

KCF-Convoy/kcfconvoy

Python package to convert KCF chemical substructure fingerprints

Language: Jupyter Notebook - Size: 6.79 MB - Last synced at: 22 days ago - Pushed at: almost 4 years ago - Stars: 7 - Forks: 4

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 at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 7 - Forks: 4

chemkg/c3p

LLM-generated CHEBI classifiers

Language: Python - Size: 106 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 6 - Forks: 1

iktos/rdkit-provider

instantiate an RDKit web worker in a React context

Language: TypeScript - Size: 920 KB - Last synced at: 16 days ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 0

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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 2

wesleybeckner/gains

project that enables molecular design and computational screening of small molecules

Language: Python - Size: 68.8 MB - Last synced at: 20 days ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 2

apahl/rdkit_nim

Nim bindings for the C++ cheminformatics toolkit RDKit.

Language: Nim - Size: 85 KB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0

ThomasJewson/Molecular3DLengthDescriptors

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

Language: Python - Size: 136 KB - Last synced at: 6 months ago - Pushed at: almost 4 years ago - Stars: 6 - Forks: 0

DECL-Gen is a toolkit for DNA encoded library to provide the ability to create combinatorial libraries *in situ* and to easily evaluate next generation sequencing results comming from library enrichments.

Language: Python - Size: 207 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 3

yamasakih/docker-compose-django-rdkit

docker-compose + Django + RDKit database cartridge + PostgreSQL

Language: Python - Size: 36.1 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 6 - Forks: 3

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 at: 17 days ago - Pushed at: 24 days ago - Stars: 5 - Forks: 1

jcorreia11/SMILESAugmentation

SMILES, SELFIES and Reaction SMILES augmentation using RDKit

Language: Python - Size: 50.8 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 5 - Forks: 1

akuroiwa/chem-ant

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

Language: Python - Size: 120 KB - Last synced at: 18 days ago - Pushed at: 6 months ago - Stars: 5 - 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 at: 18 days ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 1

farhad-abdi/InSilicoQ

Quantum Computing and Machine Learning for Drug Design and Proteins Engineering

Language: Python - Size: 487 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 1

suneelbvs/Streamlit-app

Streamlit multipage app on rdKit Cheatsheet

Language: Python - Size: 8.79 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 0

Henrique-rt/QSAR_applicability_domain_convex_hull

Allows to visualize and analyze if the molecules of the test set and of an external set are contained in the convex hull defined by the molecules of the training set.

Language: Python - Size: 56.6 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 2