Difference between revisions of "Related Projects"
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==Programs Using Open Babel== | ==Programs Using Open Babel== | ||
* [http://avogadro.sourceforge.net/wiki/ Avogadro] - Flexible, cross-platform 3D molecular editor | * [http://avogadro.sourceforge.net/wiki/ Avogadro] - Flexible, cross-platform 3D molecular editor | ||
| − | * [ | + | * [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:// | + | * [http://brabosphere.sf.net Brabosphere] - Brabosphere, a molecular visualization tool for the quantum mechanics package BRABO |
| − | * [http://www.cse.scitech.ac.uk/ | + | * [http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/ CCP1GUI] - Free, extensible molecular viewer and editor, including GUI for GAMESS-UK |
| + | * [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://www.chemeo.com/ Cheméo] - Web search for high quality chemical properties | ||
* [http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ Chemtool] - 2D molecular drawing tool using GTK toolkit | * [http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ Chemtool] - 2D molecular drawing tool using GTK toolkit | ||
| − | * [http:// | + | * [http://chemspotlight.openmolecules.net/ ChemSpotlight] - Chemical indexing for Mac OS X |
* [http://chem-file.sourceforge.net/ Chemical Structure Project] - Open Source Chemical Structure Database | * [http://chem-file.sourceforge.net/ Chemical Structure Project] - Open Source Chemical Structure Database | ||
| + | * [http://opentox.informatik.uni-freiburg.de/ches-mapper-wiki CheS-Mapper] - Open Source 3D-viewer for chemical datasets of small molecules | ||
* [http://www.emolecules.com/ eMolecules] - World-wide chemical search | * [http://www.emolecules.com/ eMolecules] - World-wide chemical search | ||
| − | * [http:// | + | * [http://github.com/amaunz/fminer2 fminer2] - Molecular subgraph mining |
* [http://www.nongnu.org/gchempaint/ GChemPaint] - 2D molecular drawing tool for GNOME environment | * [http://www.nongnu.org/gchempaint/ GChemPaint] - 2D molecular drawing tool for GNOME environment | ||
* [http://www.uku.fi/~thassine/ghemical/ Ghemical] - Molecular editor for GNOME environment | * [http://www.uku.fi/~thassine/ghemical/ Ghemical] - Molecular editor for GNOME environment | ||
* [http://www.nongnu.org/gchemutils/ Gnome Chemistry Utils] - GTK/Gnome based tools for chemistry software development | * [http://www.nongnu.org/gchemutils/ Gnome Chemistry Utils] - GTK/Gnome based tools for chemistry software development | ||
| + | * [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. | ||
* [http://edu.kde.org/kalzium/ Kalzium] - KDE Chemistry Education project | * [http://edu.kde.org/kalzium/ Kalzium] - KDE Chemistry Education project | ||
* [http://mitglied.lycos.de/PageOfMH/ KMovisto] - 3D molecular viewer for Linux | * [http://mitglied.lycos.de/PageOfMH/ KMovisto] - 3D molecular viewer for Linux | ||
| + | * [http://www.knime.org/ KNIME] - Modular data processing (pipeline) environment | ||
* [http://www.predictive-toxicology.org/lazar/ lazar] - Lazy Structure-Activity Relationships (prediction of toxicity data) | * [http://www.predictive-toxicology.org/lazar/ lazar] - Lazy Structure-Activity Relationships (prediction of toxicity data) | ||
| − | * [http:/ | + | * [http://molekel.cscs.ch Molekel] - Advanced multiplatform 3D molecular viewer |
* [http://molsketch.sourceforge.net/ molsketch] - 2D molecular drawing tool for Qt/KDE environment (in development) | * [http://molsketch.sourceforge.net/ molsketch] - 2D molecular drawing tool for Qt/KDE environment (in development) | ||
* [http://mychem.sourceforge.net/ MyChem] - MySQL extension for chemical databases | * [http://mychem.sourceforge.net/ MyChem] - MySQL extension for chemical databases | ||
* [http://www.nanoengineer-1.net/ NanoEngineer-1] - Open source 3D molecular modeler for Windows, Mac and Linux. | * [http://www.nanoengineer-1.net/ NanoEngineer-1] - Open source 3D molecular modeler for Windows, Mac and Linux. | ||
* [http://www.nano-hive.org/ NanoHive-1 Nanospace Simulator] - Modular simulator for modeling nanometer scale physics and chemistry | * [http://www.nano-hive.org/ NanoHive-1 Nanospace Simulator] - Modular simulator for modeling nanometer scale physics and chemistry | ||
| − | * [http:// | + | * [http://openmd.net OpenMD] - Open source molecular dynamics engine |
| + | * [http://open3dalign.org/ Open3DALIGN] - Conformational search and unsupervised molecular alignment | ||
| + | * [http://www.open3dqsar.org/ Open3DQSAR] - High-throughput computation and chemometric analysis of molecular interaction fields | ||
* [http://cactus.nci.nih.gov/osra/ OSRA] - Optical Structure Recognition (graphics into [[SMILES]]) | * [http://cactus.nci.nih.gov/osra/ OSRA] - Optical Structure Recognition (graphics into [[SMILES]]) | ||
* [http://pgfoundry.org/projects/pgchem/ pgchem::tigress] - PostgreSQL database engine for molecules | * [http://pgfoundry.org/projects/pgchem/ pgchem::tigress] - PostgreSQL database engine for molecules | ||
| + | * [http://www.silicos.com Pharao] - Open source pharmacophore generation and alignment | ||
| + | * [http://www.silicos.com Piramid] - Open source shape-based alignment using Gaussian volumes | ||
| + | * [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). | ||
| + | * [http://sdf2xyz2sdf.sourceforge.net/ SDF2XYZ2SDF] - How to exploit TINKER power in cheminformatics projects | ||
* [http://code.google.com/p/semanticwebopenbabel/ Semantic Web Open Babel] - Using Open Babel for a chemical Semantic Web | * [http://code.google.com/p/semanticwebopenbabel/ Semantic Web Open Babel] - Using Open Babel for a chemical Semantic Web | ||
| + | * [http://www.silicos.com/ Sieve] - Filtering molecule files based on calculated molecular properties, topologies and fragments | ||
* [http://www.karwath.org/systems/smirep/ SMIREP] - [[SMILES]] based structure-activity relationship rules | * [http://www.karwath.org/systems/smirep/ SMIREP] - [[SMILES]] based structure-activity relationship rules | ||
* [http://www.freebase.com/view/en/sporcalc SPORCalc] - Substrate Product Occurrence Ratio Calculator - Fingerprint Probabilistic Scoring of Sites of Metabolism | * [http://www.freebase.com/view/en/sporcalc SPORCalc] - Substrate Product Occurrence Ratio Calculator - Fingerprint Probabilistic Scoring of Sites of Metabolism | ||
| + | * [http://www.silicos.com Stripper] - Scaffold extraction tool following a number of published scaffold-extraction approaches, including Schuffenhauer, Oprea and Murcko | ||
| + | * [http://toxtree.sourceforge.net/ Toxtree] - Estimate toxicity activity using decision trees | ||
* [http://inac.cea.fr/L_Sim/V_Sim/index.en.html V-Sim] Visualizes atomic structures such as crystals, grain boundaries, etc. | * [http://inac.cea.fr/L_Sim/V_Sim/index.en.html V-Sim] Visualizes atomic structures such as crystals, grain boundaries, etc. | ||
* [http://viewmol.sourceforge.net/ ViewMol] - Molecular viewer and graphical front end for computational chemistry programs | * [http://viewmol.sourceforge.net/ ViewMol] - Molecular viewer and graphical front end for computational chemistry programs | ||
| + | * [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. | ||
* [http://xdrawchem.sourceforge.net/ XDrawChem] - XWindows/Qt-based 2D molecular drawing tool | * [http://xdrawchem.sourceforge.net/ XDrawChem] - XWindows/Qt-based 2D molecular drawing tool | ||
* [http://www.yasara.com/ YASARA - Yet Another Scientific Artificial Reality Application] | * [http://www.yasara.com/ YASARA - Yet Another Scientific Artificial Reality Application] | ||
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==Related Open Chemistry Projects== | ==Related Open Chemistry Projects== | ||
* [http://www.bioclipse.net/ Bioclipse] - Java based bioinformatics and cheminformatics tools | * [http://www.bioclipse.net/ Bioclipse] - Java based bioinformatics and cheminformatics tools | ||
| + | * [http://www.autistici.org/interzona/index.php?mod=03_Bist Bist] 2D drawing tool for Qt/KDE (in development) | ||
* [http://www.blueobelisk.org/ Blue Obelisk Movement] - A group of open source chemistry and chemoinformatics projects | * [http://www.blueobelisk.org/ Blue Obelisk Movement] - A group of open source chemistry and chemoinformatics projects | ||
** [http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml Blue Obelisk - Chemoinformatics Algorithm Dictionary] | ** [http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml Blue Obelisk - Chemoinformatics Algorithm Dictionary] | ||
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* [http://www.crystallography.net/ Crystallography Open Database] - An open crystallography database using Open Babel for structure and substructure search | * [http://www.crystallography.net/ Crystallography Open Database] - An open crystallography database using Open Babel for structure and substructure search | ||
* [http://depth-first.com/ Depth First] - Cheminformatics blog using open source chemistry tools. | * [http://depth-first.com/ Depth First] - Cheminformatics blog using open source chemistry tools. | ||
| + | * [http://gabedit.sf.net Gabedit] - Molecular editor for GNOME environment | ||
* [http://jchempaint.sourceforge.net/ JChemPaint] - A 2D molecular drawing package based on CDK. | * [http://jchempaint.sourceforge.net/ JChemPaint] - A 2D molecular drawing package based on CDK. | ||
* [http://jmol.sourceforge.net/ Jmol] - Java molecular viewer for desktop or web visualization | * [http://jmol.sourceforge.net/ Jmol] - Java molecular viewer for desktop or web visualization | ||
Latest revision as of 05:50, 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
- iBabel - Mac OS X interface to Open Babel (see also iBabel documentation)
- Kemistry - Collection of chemical applications for the KDE environment
- KOpenBabel - A KDE interface of Open Babel
- PyGTK-Open Babel - A GTK interface to Open Babel using Python
- QOpenBabel - A Qt interface of Open Babel
- Virtual Computational Chemistry Laboratory - Web based services for computational chemistry
- World Wide Molecular Matrix - Web based services for chemoinformatics
Related Open Chemistry Projects
- Bioclipse - Java based bioinformatics and cheminformatics tools
- Bist 2D drawing tool for Qt/KDE (in development)
- Blue Obelisk Movement - A group of open source chemistry and chemoinformatics projects
- Chemical Development Kit (CDK) - Java library for structural chemo- and bioinformatics.
- ChemFile - Open Chemical Structures Library
- Chemistry Markup Language (CML) - A standardized XML file format for chemistry and molecular science
- Crystallography Open Database - An open crystallography database using Open Babel for structure and substructure search
- Depth First - Cheminformatics blog using open source chemistry tools.
- Gabedit - Molecular editor for GNOME environment
- JChemPaint - A 2D molecular drawing package based on CDK.
- Jmol - Java molecular viewer for desktop or web visualization
- JOELib - Java version of OpenBabel, and like OpenBabel also a OELib successor
- NMRShiftDB - Open database of molecular NMR data
- PerlMol - Perl Modules for Molecular Chemistry
- Open Source QSAR
