GitPlanet

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

Created with love in Canada, visit hostnodejs.com today

Feel like to post an Ad? Learn Details
All Projects → mojaie → MolecularGraph.jl

mojaie / MolecularGraph.jl

Licence: MIT license
Graph-based molecule modeling toolkit for cheminformatics

Programming Languages

julia
2034 projects

Labels

chemistrygraphcheminformaticstoolkitmoleculejulia-languagemcsmolecular-modeling

Projects that are alternatives of or similar to MolecularGraph.jl

Thermo
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
Stars: ✭ 279 (+93.75%)
Mutual labels:  chemistry, cheminformatics, molecule
Version3-1
Version 2020 (3.1) of Chem4Word - A Chemistry Add-In for Microsoft Word
Stars: ✭ 14 (-90.28%)
Mutual labels:  chemistry, cheminformatics, molecule
Kekule.js
A Javascript cheminformatics toolkit.
Stars: ✭ 156 (+8.33%)
Mutual labels:  chemistry, cheminformatics, molecule
Version3
Version 3 of Chem4Word - A Chemistry Add-In for Microsoft Word
Stars: ✭ 53 (-63.19%)
Mutual labels:  chemistry, cheminformatics, molecule
Pubchempy
Python wrapper for the PubChem PUG REST API.
Stars: ✭ 171 (+18.75%)
Mutual labels:  chemistry, cheminformatics
Chembl webresource client
Official Python client for accessing ChEMBL API.
Stars: ✭ 165 (+14.58%)
Mutual labels:  chemistry, cheminformatics
GLaDOS
Web Interface for ChEMBL @ EMBL-EBI
Stars: ✭ 28 (-80.56%)
Mutual labels:  chemistry, cheminformatics
senpai
Molecular dynamics simulation software
Stars: ✭ 124 (-13.89%)
Mutual labels:  chemistry, cheminformatics
Chemozart
Web-based 3D molecule editor and visualizer with molecular mechanics calculators.
Stars: ✭ 142 (-1.39%)
Mutual labels:  chemistry, molecule
Awesome Cheminformatics
A curated list of Cheminformatics libraries and software.
Stars: ✭ 244 (+69.44%)
Mutual labels:  chemistry, cheminformatics
chembience
A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
Stars: ✭ 41 (-71.53%)
Mutual labels:  chemistry, cheminformatics
Fermi.jl
Fermi quantum chemistry program
Stars: ✭ 107 (-25.69%)
Mutual labels:  chemistry, molecular-modeling
Indigo
Universal cheminformatics libraries, utilities and database search tools
Stars: ✭ 146 (+1.39%)
Mutual labels:  chemistry, cheminformatics
xyz2graph
Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
Stars: ✭ 36 (-75%)
Mutual labels:  chemistry, molecule
Ase ani
ANI-1 neural net potential with python interface (ASE)
Stars: ✭ 145 (+0.69%)
Mutual labels:  chemistry, cheminformatics
MolDQN-pytorch
A PyTorch Implementation of "Optimization of Molecules via Deep Reinforcement Learning".
Stars: ✭ 58 (-59.72%)
Mutual labels:  chemistry, molecule
chemprop
Fast and scalable uncertainty quantification for neural molecular property prediction, accelerated optimization, and guided virtual screening.
Stars: ✭ 75 (-47.92%)
Mutual labels:  chemistry, molecule
panel-chemistry
🧪📈 🐍. The purpose of the panel-chemistry project is to make it really easy for you to do DATA ANALYSIS and build powerful DATA AND VIZ APPLICATIONS within the domain of Chemistry using using Python and HoloViz Panel.
Stars: ✭ 94 (-34.72%)
Mutual labels:  chemistry, molecule
Chemfiles
Library for reading and writing chemistry files
Stars: ✭ 95 (-34.03%)
Mutual labels:  chemistry, cheminformatics
Stk
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
Stars: ✭ 99 (-31.25%)
Mutual labels:  chemistry, cheminformatics
View All Similar Projects ➔

MolecularGraph.jl

DOI Build Status TagBot

MolecularGraph.jl is a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia.

Usage

Features

  • Chemical structure file I/O

    • 2D structure image drawing and export to SVG
    • 3D structure drawing
    • SDFile import/export (.sdf, .mol)
    • SMILES/SMARTS parser

  • Database

    • InChI (InChI)
    • Serialization (molecule object <-> JSON)

  • Basic descriptors

    • H-bond donor/acceptor
    • rotatable bonds
    • Aromaticity
    • Wildman-Crippen logP

  • Atomic mass

    • standard atomic/molecular weight
    • relative atomic/molecular mass
    • isotopic composition

  • Molecular graph topology

    • Ring, scaffold, connected components
    • Minimum cycle basis (de Pina algorithm)
      • Smallest set of smallest rings (SSSR)
    • Planarity (left-right planarity test)
    • Maximum matching
      • Kekulization
    • Graph traversal

  • 2D geometry

    • Stereochemistry drawing
    • Coordinates generation (coordgenlibs)

  • Sub(super)structure

    • Library search by using SMARTS query
    • Subgraph isomorphism detection with VF2 algorithm
    • Monomorphism, node-induced and edge-induced
    • Constraints (mandatory/forbidden mapping)

  • SMARTS query-based substructure analysis

    • functional group mining
    • structural alerts (by using ChEMBL dataset)

  • Maximum common substructure (MCS)

    • By clique detection algorithm
    • Node-induced (MCIS) and edge-induced (MCES)
    • Connected and disconnected
    • Topological constraint (known as tdMCS)
    • Diameter restriction (MCS-DR) and graph-based local similarity (GLS)

License

MIT license
See Assets/README.md for details of external data sets and their licenses.

Copyright

(C) 2018-2021 Seiji Matsuoka and contributors

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].