2.2 Rho matrix

Step 2. 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