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The code is a molecular dynamics code used to simulate etch and deposition processes. During the process, the structure of the surface will change on a larger length scale.
BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original sourcecode and to build a Python interface on top of it.
Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Sourcecode is contained in jar files. Download contains GSH reactivity plugin.
Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.
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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 sourcecode repository can be found on https://jchempaint.github.io
dmcut2 is a scientific program designed to simulate chemical reactions at surfaces using Metropolis and Monte-Carlo methods. Short ranged interactions between adsorbates may be taken into account. Emphasis was put on code readability and usability.