CorrelationPlus

A Python API to plot and analyze dynamical correlations of proteins.

CorrelationPlus contains three scripts that you can use to plot and analyze dynamical correlations for proteins and biological macromolecules. These correlations can be dynamical cross-correlations or linear mutual information.

mapAnalysis app plots and produces analysis scripts for correlation maps. It can be more useful if your structure contains multiple chains. The program will produce an output for overall structure and all individual intra-chain correlations, if exist. Moreover, the program will give you inter-chain correlations, if you have more than one chain. The program only requires a pdb file and a correlation data matrix. The correlation data has to be in matrix format, where only A(i,j) values are listed in a square matrix format. You can analyze the correlations with VMD just by loading the tcl files produced by mapAnalysis module.

A Quick Start with correlationPlus Scripts

To run a simple example, go to examples folder and then run:

correlationPlus mapAnalysis -i 6fl9_just_prot_anm_100_modes_rc_15_cross-correlations.txt -p 6fl9_centeredOrientedAligned2Z.pdb -t absndcc

This will produce plots of absolute values of dynamical cross correlations.

Sometimes, we may need to plot difference map of two correlation maps. For example, you may want to see the differences of linear mutual information maps of produced with two different methods, conditions etc. This can be produced with diffMap app as follows:

correlationPlus diffMap -i 6fl9_rc15_scalCoeff1_100_modes_lmi_v2.dat -j zacharias_rc15_scalCoeff15_100_modes_lmi.dat -p 6fl9_centeredOrientedAligned2Z.pdb -t lmi

Finally, correlationPlus can do centrality analysis for your protein via its centralityAnalysis app.

It computes degree, closeness, betweenness, current flow closeness, current flow betweenness and eigenvector centrality.

correlationPlus centralityAnalysis -i 6fl9_just_prot_anm_100_modes_rc_15_cross-correlations.txt -p 6fl9_centeredOrientedAligned2Z.pdb -t absndcc

Ipython Interface

For a detailed analysis, script interfaces provided by mapAnalysis, diffMap and centralityAnalysis apps may not be sufficient. Therefore, you can use IPython to load the functions and do a detailed analysis as follows.

from correlationPlus.mapAnalysis import *

You can get help for individual functions with

help(intraChainCorrelationMaps) 

You can check different valueFilters, distanceFilters for your analysis. Even you can scan a range of values by calling the functions in a loop.

Installation

for users

We recommend to use pip

pip install correlationPlus

or if you do not have administration rights

pip install --user correlationPlus

If you prefer to use a virtualenv

python3.8 -m venv correlationPlus
cd correlationPlus
source bin/activate
pip install correlationPlus

for developers

We recommend to use pip and a virtualenv

python3.8 -m venv correlationPlus
cd correlationPlus
source bin/activate
mkdir src
cd src
git clone https://github.com/tekpinar/correlationPlus.git # or git@github.com:tekpinar/correlationPlus.git
cd correlationPlus
pip install -e .

Licensing

correplationPlus is developed and released under GNU Lesser GPL Licence. Please read to the COPYING and COPYING.LESSER files to know more.