A Python-based script for optimal reaction coordinate search. The method requires that projections of the trajectory (trajectories) onto a N-dimensional vector basis (e.g., obtained by Principal Component Analysis) be provided.
The script is Python-based -- hence, no istallation is needed. However, some dependencies are needed:
numpyscipymatplotliboverlap_NEW.so
The library overlap_NEW.so has to be compiled from the Cython module overlap_NEW.pyx manually prior to the script usage.
python setup_overlap_NEW.py build_ext --inplace