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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.

License: GNU General Public License v3.0

Java 26.07% HTML 71.18% JavaScript 0.04% CSS 0.55% Jupyter Notebook 2.16%
pca-analysis subspace-identification covariance-matrix correlation-matrices essentialmode principal-components dynamical-modeling correlation-measures pymol free-energy

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jed's Issues

FES Driver only inputs first two DVPs

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.

Code Review: Reduced C Matrix and Dynamical Matrix

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.

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