sannevandalen/pamm

Tools for the Probabilistic Analysis of Molecular Motifs method

PAMM library and tools

This repository contains a simple Fortran90 implementation of the Probabilistic Analysis of Molecular Motifs algorithm. It contains a library to compute PAMM structure counts, a tool to perform the analysis on an arbitrary set of structural descriptors, and an example application to the automatic definition of hydrogen bond descriptors.

Source code is stored in the src/ directory, and the executables will be generated inside bin/. test/ contains a simple example of the usage of these programs.

Compilation and installation

Compilation should be trivial, requiring only a recent version of gfortran and LAPACK libraries. You can adjust the compiler and the path of the libraries modifying src/Makefile. You should then be able to compile the library with the commands

cd src/
make

The executables will be generated inside the bin/ directory. Make sure to copy them in your path, or to add the folder to your path environment variable:

export PATH=$PATH:$PWD/bin/

Getting started

An example of the usage of pamm and hbpamm can be found in the test/ directory.