C++ Libraries and Software for Molecular Modeling (Erik Santiso)
Latest change: 07-27-11 - most packages are in this link: projects.tgz , including a bash script to build all the projects in the right order. Below is a description of the different projects.
common: Contains basic types and base class definitions for all the other libraries - a copy of this directory must be in the same path as each one of the libraries below (only one copy is necessary if you keep all the projects in the same directory).
mymath: Contains classes for vector, matrix and quaternion operations, calculation of special functions, sorting, matching problems, root finding, optimization, linear and orientational statistics, and numerical integration.
mymol: Contains classes to deal with atoms, molecules, lattices, and various molecule file formats (xyz, pdb, psf, dcd, and mol2).
crystdist: Contains classes to do positional and orientational statistics on molecular geometries, and to calculate crystal order parameters.
getpeaks: A utility to find peaks in the distribution function of distances, bond orientations, relative orientations and internal degrees of freedom for a given geometry.
cryststat: A utility to find averages and concentration parameters for a model of the pair distribution function of distances, bond orientations, relative orientations and internal degrees of freedom given a reference set of peaks (from getpeaks) and a molecular dynamics trajectory.
copcalc: A utility to calculate crystal order parameters for a given geometry.
cop2pdb: A visualization tool for crystal order parameters.
pkt2pdb: A visualization tool for the pair distribution function obtained by getpeaks.
smcv: Contains classes to use the string method in collective variables using crystal order parameters.
restforce: A utility to calculate the average restraint forces from a restrained molecular dynamics simulation using crystal order parameters.
smcvstep: A utility to carry out steps of the string method in collective variables. Originally written to work with crystal order parameters, but can be easily modified to use any set of order parameters by changing the definition of the class opdfile (see smcv).
opd2cop: A visualization tool for restraint forces from restrained molecular dynamics simulations using crystal order parameters.
stringcurv: A utility to compute the curvature of a path in crystal order parameter space (useful for Voronoi-tesselated milestoning).
stringpca: A utility to compute the principal components of a path in crystal order parameter space (useful for Voronoi-tesselated milestoning).
peakdist: A utility to find averages and concentration parameters for a model of the pair distribution function of distances, bond orientations, relative orientations and internal degrees of freedom in partially ordered systems. This replaces the combination of getpeaks and crystat when it is difficult to obtain a good reference structure. This requires the randomc library (see below).
The following can be downloaded separately:
evolve: A tool to evolve populations with members described by genomes. Erik Santiso, with modifications for length limits by N. Musolino.
Download: evolve_limits.tar
gnugen.py: A python script to construct gnuplot input from the output of the triangle package (see below).
Download: gnugen.py
randomc: A library of random-number generators. This code belongs to Agner Fog, I've only added a Makefile to it. This code is required for the peakdist package. The link to the original library is here.
Download: randomc.tgz
Triangle: A code to generate 2D meshes. This code belongs to Jonathan Richard Shewchuk. Triangle is useful to visualize Voronoi tesselations in combination with stringpca and gnugen.py. The link to the original code is here.
Download: triangle.tgz