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...PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/

...This software allows collecting individual data files from in situ experiment into one dataset. After that this data set can be visualized, edited, normalized and averaged. Resulted data can be saved as one flat file (FLT-format) which can be used for PSD/MED calculations via 2DMED software (http://sourceforge.net/projects/twodmed/?source=directory). 2DFLT specifically was written to target in situ X-ray Powder Diffraction data from synchrotron measurements. Hence it can read CHI, XYE (TOPAS), FXYE(GSAS/ GSASII) and XY- files formats. However it can read general in situ data written into individual TXT or XY – files.

PLEASE NOTE ORBKIT HAS BEEN MOVED TO https://github.com/orbkit/orbkit orbkit is a parallel Python program package for post-processing wave function data extracted from output files of MOLPRO (Molden File Format), TURBOMOLE (AOMix file format), GAMESS-US, PROAIMS/AIMPAC (wfn/wfx file format), and Gaussian (Output File and Formatted Checkpoint File) output files. Futhermore, an interface to cclib, a parser for quantum chemical logfiles, is provided. If you use orbkit in your work, please cite it as follows: Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay, Beate Paulus, Hans-Christian Hege, and Axel Schild, "ORBKIT: A Modular Python Toolbox for Cross-Platform Postprocessing of Quantum Chemical Wavefunction Data", J. ...

...Includes among others * a multiscale particle tracking algorithm [1] whose C++ implementation is optimised for 3D confocal data. Python implementation is more versatile (2D and 3D data). * a Leica file reader, * Steindhard bond orientational order calculation * a VTK file writer 1. Leocmach, M. & Tanaka, H. A novel particle tracking method with individual particle size measurement and its application to ordering in glassy hard sphere colloids. Soft Matter 9, 1447–1457 (2013). https://dx.doi.org/10.1039/C2SM27107A (http://arxiv.org/pdf/1301.7237.pdf)

MePrId is a Python program which can be used to classify a protein, depending whether it is a membrane or a globular protein. Download link: http://meprid.svn.sourceforge.net/viewvc/meprid.tar.gz?view=tar