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Jamberoo (former JMolEditor) is a library of algorithms for structural Computational Chemistry implemented in the Java programming language. The Jamberoo classes can be integrated into other Java applications.
Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.
This application is intended to help students with the basics of chemistry. It can solve basic gas laws equations, and find the molar mass of a compound or element. These tasks allow students to cut the repetition out of basic chemistry.
The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!
JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.
The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io
Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.