Difference between revisions of "Related Projects"

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This page is a work in progress, to gather links of related open-source chemistry projects. If you have suggestions/corrections/complaints, please send them to the [mailto:[email protected] openbabel-discuss] mailing list.
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There are many projects which use Open Babel code internally, including several easy-to-use "front end" interfaces, as well as a variety of related open source chemistry projects.
  
* [http://www.blueobelisk.org/ Blue Obelisk Movement]
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==Programs Using Open Babel==
* [http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml Blue Obelisk - Chemoinformatics Algorithm Dictionary]
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* [http://avogadro.sourceforge.net/wiki/ Avogadro] - Flexible, cross-platform 3D molecular editor
* [http://www.blueobelisk.org/dokuwiki/doku.php?id=wiki:datarepository Blue Obelisk - Chemoinformatics Data Repository]
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* [https://wiki.fysik.dtu.dk/ase/ ASE] - Atomic Simulation Environment, a Python framework for building simulation codes, as well as pre- and post-processing tools.
* [http://cdk.sourceforge.net/ Chemical Development Kit (CDK)]
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* [http://brabosphere.sf.net Brabosphere] - Brabosphere, a molecular visualization tool for the quantum mechanics package BRABO
* [http://cml.sourceforge.net/ Chemistry Markup Language (CML)]
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* [http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/ CCP1GUI] - Free, extensible molecular viewer and editor, including GUI for GAMESS-UK
* [http://jchempaint.sourceforge.net/ JChemPaint]
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* [https://sourceforge.net/projects/chemaztech/ ChemAzTech] - Web/database solution. Manage your chemical database, with product's properties. Draw, edit molecules and interact with common chemical software.
* [http://jmol.sourceforge.net/ JMol]
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* [http://www.chemeo.com/ Cheméo] - Web search for high quality chemical properties
* [http://joelib.sourceforge.net/ JOELib]
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* [http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ Chemtool] - 2D molecular drawing tool using GTK toolkit
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* [http://chemspotlight.openmolecules.net/ ChemSpotlight] - Chemical indexing for Mac OS X
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* [http://chem-file.sourceforge.net/ Chemical Structure Project] - Open Source Chemical Structure Database
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* [http://opentox.informatik.uni-freiburg.de/ches-mapper-wiki CheS-Mapper] - Open Source 3D-viewer for chemical datasets of small molecules
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* [http://www.emolecules.com/ eMolecules] - World-wide chemical search
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* [http://github.com/amaunz/fminer2 fminer2] - Molecular subgraph mining
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* [http://www.nongnu.org/gchempaint/ GChemPaint] - 2D molecular drawing tool for GNOME environment
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* [http://www.uku.fi/~thassine/ghemical/ Ghemical] - Molecular editor for GNOME environment
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* [http://www.nongnu.org/gchemutils/ Gnome Chemistry Utils] - GTK/Gnome based tools for chemistry software development
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* [http://www.hbar-lab.com hBar Lab: Computer-aided Chemistry On Demand] - First web application for performing molecular modeling calculations including quantum chemistry calculations online.
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* [http://edu.kde.org/kalzium/ Kalzium] - KDE Chemistry Education project
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* [http://mitglied.lycos.de/PageOfMH/ KMovisto] - 3D molecular viewer for Linux
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* [http://www.knime.org/ KNIME] - Modular data processing (pipeline) environment
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* [http://www.predictive-toxicology.org/lazar/ lazar] - Lazy Structure-Activity Relationships (prediction of toxicity data)
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* [http://molekel.cscs.ch Molekel] - Advanced multiplatform 3D molecular viewer
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* [http://molsketch.sourceforge.net/ molsketch] - 2D molecular drawing tool for Qt/KDE environment (in development)
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* [http://mychem.sourceforge.net/ MyChem] - MySQL extension for chemical databases
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* [http://www.nanoengineer-1.net/ NanoEngineer-1] - Open source 3D molecular modeler for Windows, Mac and Linux.
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* [http://www.nano-hive.org/ NanoHive-1 Nanospace Simulator] - Modular simulator for modeling nanometer scale physics and chemistry
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* [http://openmd.net OpenMD] - Open source molecular dynamics engine
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* [http://open3dalign.org/ Open3DALIGN] - Conformational search and unsupervised molecular alignment
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* [http://www.open3dqsar.org/ Open3DQSAR] - High-throughput computation and chemometric analysis of molecular interaction fields
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* [http://cactus.nci.nih.gov/osra/ OSRA] - Optical Structure Recognition (graphics into [[SMILES]])
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* [http://pgfoundry.org/projects/pgchem/ pgchem::tigress] - PostgreSQL database engine for molecules
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* [http://www.silicos.com Pharao] - Open source pharmacophore generation and alignment
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* [http://www.silicos.com Piramid] - Open source shape-based alignment using Gaussian volumes
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* [http://pyrx.scripps.edu/ PyRx] - Virtual Screening tool that includes Open Babel widget (watch [http://www.youtube.com/watch?v=niw6gHDLfO4 PyRx Screencast - Open Babel] to learn more).
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* [http://sdf2xyz2sdf.sourceforge.net/ SDF2XYZ2SDF] - How to exploit TINKER power in cheminformatics projects
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* [http://code.google.com/p/semanticwebopenbabel/ Semantic Web Open Babel] - Using Open Babel for a chemical Semantic Web
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* [http://www.silicos.com/ Sieve] - Filtering molecule files based on calculated molecular properties, topologies and fragments
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* [http://www.karwath.org/systems/smirep/ SMIREP] - [[SMILES]] based structure-activity relationship rules
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* [http://www.freebase.com/view/en/sporcalc SPORCalc] - Substrate Product Occurrence Ratio Calculator - Fingerprint Probabilistic Scoring of Sites of Metabolism
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* [http://www.silicos.com Stripper] - Scaffold extraction tool following a number of published scaffold-extraction approaches, including Schuffenhauer, Oprea and Murcko
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* [http://toxtree.sourceforge.net/ Toxtree] - Estimate toxicity activity using decision trees
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* [http://inac.cea.fr/L_Sim/V_Sim/index.en.html V-Sim] Visualizes atomic structures such as crystals, grain boundaries, etc.
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* [http://viewmol.sourceforge.net/ ViewMol] - Molecular viewer and graphical front end for computational chemistry programs
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* [http://webbabel.wiki.sourceforge.net/ WebBabel] - WebBabel is a web application that uses OpenBabel to convert files from one format to another, or browse for files containing molecular structures.
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* [http://xdrawchem.sourceforge.net/ XDrawChem] - XWindows/Qt-based 2D molecular drawing tool
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* [http://www.yasara.com/ YASARA - Yet Another Scientific Artificial Reality Application]
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* [http://www.zeden.org Zodiac] - Cross-platform suite for Rational drug design
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==Front Ends==
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* [http://homepage.mac.com/swain/Macinchem/page6/page6.html iBabel] - Mac OS X interface to Open Babel (see also [[iBabel]] documentation)
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* [http://kemistry.sourceforge.net/ Kemistry] - Collection of chemical applications for the KDE environment
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* [http://kopenbabel.sourceforge.net/ KOpenBabel] - A KDE interface of Open Babel
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* [http://code.google.com/p/pygtk-openbabel/ PyGTK-Open Babel] - A GTK interface to Open Babel using Python
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* [http://kopenbabel.sourceforge.net/ QOpenBabel] - A Qt interface of Open Babel
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* [http://vcclab.org/ Virtual Computational Chemistry Laboratory] - Web based services for computational chemistry
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* [http://wwmm-svc.ch.cam.ac.uk/wwmm/html/observer.html World Wide Molecular Matrix] - Web based services for chemoinformatics
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==Related Open Chemistry Projects==
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* [http://www.bioclipse.net/ Bioclipse] - Java based bioinformatics and cheminformatics tools
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* [http://www.autistici.org/interzona/index.php?mod=03_Bist Bist] 2D drawing tool for Qt/KDE (in development)
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* [http://www.blueobelisk.org/ Blue Obelisk Movement] - A group of open source chemistry and chemoinformatics projects
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** [http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml Blue Obelisk - Chemoinformatics Algorithm Dictionary]
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** [http://www.blueobelisk.org/dokuwiki/doku.php?id=wiki:datarepository Blue Obelisk - Chemoinformatics Data Repository]
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** [http://cb.openmolecules.net/posts.php?category=Blue%20Obelisk Planet BO - Personal blogs of Blue Obelisk contributors]
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** [http://cb.openmolecules.net/ Chemical Blogosphere]
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* [http://cdk.sourceforge.net/ Chemical Development Kit (CDK)] - Java library for structural chemo- and bioinformatics.
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* [http://chem-file.sourceforge.net/ ChemFile - Open Chemical Structures Library]
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* [http://cml.sourceforge.net/ Chemistry Markup Language (CML)] - A standardized XML file format for chemistry and molecular science
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* [http://www.crystallography.net/ Crystallography Open Database] - An open crystallography database using Open Babel for structure and substructure search
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* [http://depth-first.com/ Depth First] - Cheminformatics blog using open source chemistry tools.
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* [http://gabedit.sf.net Gabedit] - Molecular editor for GNOME environment
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* [http://jchempaint.sourceforge.net/ JChemPaint] - A 2D molecular drawing package based on CDK.
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* [http://jmol.sourceforge.net/ Jmol] - Java molecular viewer for desktop or web visualization
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* [http://joelib.sourceforge.net/wiki/ JOELib] - Java version of OpenBabel, and like OpenBabel also a OELib successor
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* [http://nmrshiftdb.org/ NMRShiftDB] - Open database of molecular NMR data
 
* [http://www.perlmol.org/ PerlMol - Perl Modules for Molecular Chemistry]
 
* [http://www.perlmol.org/ PerlMol - Perl Modules for Molecular Chemistry]
* [http://octetsource.com/ Octet]
 
 
* [http://qsar.sourceforge.net/ Open Source QSAR]
 
* [http://qsar.sourceforge.net/ Open Source QSAR]
  
=See Also=
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[[Category:Capabilities]]
* [[Programs|Programs Using Open Babel]]
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Latest revision as of 04:50, 24 May 2012

There are many projects which use Open Babel code internally, including several easy-to-use "front end" interfaces, as well as a variety of related open source chemistry projects.

Programs Using Open Babel

  • Avogadro - Flexible, cross-platform 3D molecular editor
  • ASE - Atomic Simulation Environment, a Python framework for building simulation codes, as well as pre- and post-processing tools.
  • Brabosphere - Brabosphere, a molecular visualization tool for the quantum mechanics package BRABO
  • CCP1GUI - Free, extensible molecular viewer and editor, including GUI for GAMESS-UK
  • ChemAzTech - Web/database solution. Manage your chemical database, with product's properties. Draw, edit molecules and interact with common chemical software.
  • Cheméo - Web search for high quality chemical properties
  • Chemtool - 2D molecular drawing tool using GTK toolkit
  • ChemSpotlight - Chemical indexing for Mac OS X
  • Chemical Structure Project - Open Source Chemical Structure Database
  • CheS-Mapper - Open Source 3D-viewer for chemical datasets of small molecules
  • eMolecules - World-wide chemical search
  • fminer2 - Molecular subgraph mining
  • GChemPaint - 2D molecular drawing tool for GNOME environment
  • Ghemical - Molecular editor for GNOME environment
  • Gnome Chemistry Utils - GTK/Gnome based tools for chemistry software development
  • hBar Lab: Computer-aided Chemistry On Demand - First web application for performing molecular modeling calculations including quantum chemistry calculations online.
  • Kalzium - KDE Chemistry Education project
  • KMovisto - 3D molecular viewer for Linux
  • KNIME - Modular data processing (pipeline) environment
  • lazar - Lazy Structure-Activity Relationships (prediction of toxicity data)
  • Molekel - Advanced multiplatform 3D molecular viewer
  • molsketch - 2D molecular drawing tool for Qt/KDE environment (in development)
  • MyChem - MySQL extension for chemical databases
  • NanoEngineer-1 - Open source 3D molecular modeler for Windows, Mac and Linux.
  • NanoHive-1 Nanospace Simulator - Modular simulator for modeling nanometer scale physics and chemistry
  • OpenMD - Open source molecular dynamics engine
  • Open3DALIGN - Conformational search and unsupervised molecular alignment
  • Open3DQSAR - High-throughput computation and chemometric analysis of molecular interaction fields
  • OSRA - Optical Structure Recognition (graphics into SMILES)
  • pgchem::tigress - PostgreSQL database engine for molecules
  • Pharao - Open source pharmacophore generation and alignment
  • Piramid - Open source shape-based alignment using Gaussian volumes
  • PyRx - Virtual Screening tool that includes Open Babel widget (watch PyRx Screencast - Open Babel to learn more).
  • SDF2XYZ2SDF - How to exploit TINKER power in cheminformatics projects
  • Semantic Web Open Babel - Using Open Babel for a chemical Semantic Web
  • Sieve - Filtering molecule files based on calculated molecular properties, topologies and fragments
  • SMIREP - SMILES based structure-activity relationship rules
  • SPORCalc - Substrate Product Occurrence Ratio Calculator - Fingerprint Probabilistic Scoring of Sites of Metabolism
  • Stripper - Scaffold extraction tool following a number of published scaffold-extraction approaches, including Schuffenhauer, Oprea and Murcko
  • Toxtree - Estimate toxicity activity using decision trees
  • V-Sim Visualizes atomic structures such as crystals, grain boundaries, etc.
  • ViewMol - Molecular viewer and graphical front end for computational chemistry programs
  • WebBabel - WebBabel is a web application that uses OpenBabel to convert files from one format to another, or browse for files containing molecular structures.
  • XDrawChem - XWindows/Qt-based 2D molecular drawing tool
  • YASARA - Yet Another Scientific Artificial Reality Application
  • Zodiac - Cross-platform suite for Rational drug design

Front Ends

Related Open Chemistry Projects