JED is a program for performing Essential Dynamics of protein trajectories written in Java. JED is a powerful tool for examining the dynamics of proteins from trajectories derived from MD or Geometric simulations. Currently, there are two types of PCA: distance-pair and Cartesian, and three models: COV, CORR, and PCORR.
When I am using the FES_Driver.jar file, no matter which DVPs I use the program only shows the first two. I am using files from the most recent update form this Github account.
I am requesting a code review of the formulae used to compute the reduced c-matrices and reduced dynamical matrices. The two methods are in the class PCA.java: static Matrix get_reduced_C_matrix(Matrix Q), and static Matrix get_reduced_DYN_matrix(Matrix DYN). The key lines of code are: double cov = (Q.get(a1, b1) + Q.get(a2, b2) + Q.get(a3, b3)); double dyn = -(DYN.get(a1, b1) + DYN.get(a2, b2) + DYN.get(a3, b3));
The original formulae were written in a vectorized form for Matlab, so I want to be sure that the conversion to the component version here is correct.