2.2 Rho matrix

** Calculation of Rho matrix **

The goal of this tool is to identify residue pairs contributing to the conformational change described by the geometric vector g.

The Rho matrix is a matrix of correlation coefficients calculated between the sum of non-bonded interaction energies (nbe) from dyno_pwie.py and a time series vector describing a geometric property (g).

rho<sub>ij</sub> is the correlation coefficient between the g and non-bonded interaction energy between residue's i and j (nbe<sub>ij</sub>)

g can be time series data from (and not limited to the list below):

• Projection on any of the principal components
• Distance between any two points
• Angle between any three points
• Dihedral angle between any four points
• Solvent accessible surface area
• Radius of gyration
• RMSF/RMSD
• Pocket/Cavity volume

Format of the file with g (should have same number of time frames as the data from dyno_pwie.py):

#time_stamp g
0 0
100 9.1
200 267.10
300 3.392
400 320.300  

input arguments:

-g GEM, --gem GEM     File with geometrical variables, e.g. vectors.txt
-i FIEX, --fiex FIEX  Folder with interaction energy files iedata/
-f FST, --fst FST     First residue
-l LST, --lst LST     last residue
-n NREP, --nrep NREP  Number of replicas [NOT FUNCTIONAL]
-e FENE, --fene FENE  energy files label used during PWIE calculation
-o LABEL, --label LABEL label for output file
-t TMAX, --tmax TMAX  Number of threads. By default will use 80% of the available threads
-m CORR, --corr CORR  Type of correlation method 0: Pearson; 1: Spearmen; 2: NMI
-v NVEC, --nvec NVEC  Number of Geom vectors to use 1...N default 1

sample usage:

dyno_2_dmatrix.py -g vectors.txt -i iexvg/ -f 1 -l 10 -n 1 -e label_of_energy_files