OpenScience / Software / Chemistry



OpenBabel

Posted on March 26, 2002 by Dan Gezelter

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Find … Continue reading →

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JOELib

Posted on March 26, 2002 by Dan Gezelter

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available. Find JOELib at: http://sourceforge.net/projects/joelib/

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ScrumPy

Posted on March 26, 2002 by Dan Gezelter

A package of Python modules that allows you to do metabolic modelling. Find ScrumPy at: http://mudshark.brookes.ac.uk/ScrumPy

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VEGa

Posted on October 28, 2001 by Dan Gezelter

VEGA was developed to create a bridge between most of the molecular software packages. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules. Find VEGa at: http://users.unimi.it/~ddl

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Chemistry::MolecularMass.pm

Posted on April 4, 2001 by Dan Gezelter

A Perl module for calculating molecular mass of chemical compounds. Find Chemistry::MolecularMass.pm at: http://www.cpan.org/modules/by-module/Chemistry/

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XVibs

Posted on March 24, 2001 by Dan Gezelter

A utility for animating molecular vibrations. Find XVibs at: http://xvibs.sourceforge.net/

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TheRate

Posted on March 1, 2001 by Dan Gezelter

TheRate stands for Theoretical Rates. TheRate allows thermal rate constants for unimolecular and bimolecular gas-phase reactions to be calculated directly from an electronic structure molecular orbital and density functional theory. Find TheRate at: http://therate.hec.utah.edu/

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XLOGP

Posted on March 1, 2001 by Dan Gezelter

XLOGP is a method which can calculate the logP value for an organic compound from its topological structure Find XLOGP at: http://mdl.ipc.pku.edu.cn/drug_design/work/xlogp.html

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XMakemol

Posted on March 1, 2001 by Dan Gezelter

XMakemol is a program written for UN*X operating systems in ANSI C using the X, Xt and Motif libraries. It can be used to view and manipulate atomic and molecular data given in xyz format. Find XMakemol at: http://www.nongnu.org/xmakemol/

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XBS

Posted on March 1, 2001 by Dan Gezelter

XBS is a simple but very useful program for plotting ball-and-sticks models of molecules or crystals under the X Window system. Find XBS at: http://www.ccl.net/chemistry/resources/software/X-WINDOW/xbs/index.shtml

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