structuraldynamicslab/correlationplus repository overview

⁠correlationplus

A Python package to calculate, visualize and analyze dynamical correlations of proteins.

correlationplus contains four scripts that you can use to calculate, visualize and analyze dynamical correlations of proteins. These correlations can be dynamical cross-correlations, linear mutual information or generalized correlations.

⁠Video Tutorials

• Installation: https://www.youtube.com/watch?v=Fc_xpnrbbWU⁠
• Calculate Module: https://www.youtube.com/watch?v=HG8Mzmy1IOM⁠
• Visualize Module: https://www.youtube.com/watch?v=HgUVAV1unXs⁠
• Analyze Module: https://www.youtube.com/watch?v=04BwJDauOn4⁠
• Sequence Conservation Analysis with CoeViz and correlationplus (Part 1): https://www.youtube.com/watch?v=ieu91glEd0s⁠
• Sequence Conservation Analysis with CoeViz and correlationplus (Part 2): https://www.youtube.com/watch?v=BuxQNFoid1A⁠

⁠Home page

The project is available on github : https://github.com/tekpinar/correlationplus⁠

⁠Docker

The computation are perform under correlationplus user in /home/correlationplus inside the container. So You have to mount a directory from the host in the container to exchange data (inputs data, and results) from the host and the container. The shared directory must be writable by the correlationplus user or overwrite the user in the container by your id (see example below)

mkdir shared_dir
cp  6lu7_dimer_with_N3_protein_sim1_ca.pdb shared_dir
cd shared_dir
docker run -v $PWD:/home/correlationplus:latest -u $(id -u ${USER}):$(id -g ${USER}) structuraldynamicslab/correlationplus:latest  calculate -p 6lu7_dimer_with_N3_protein_sim1_ca.pdb -m GNM -o dcc-6lu7-gnm.dat

⁠Quickstart

There are four main scrips:

• calculate
• visualize
• analyze
• paths

You can find details of each script with the following commands:

docker run -v $PWD:/home/correlationplus -u $(id -u ${USER}):$(id -g ${USER}) structuraldynamicslab/correlationplus:latest  calculate -h
docker run -v $PWD:/home/correlationplus -u $(id -u ${USER}):$(id -g ${USER}) structuraldynamicslab/correlationplus:latest visualize -h
docker run -v $PWD:/home/correlationplus -u $(id -u ${USER}):$(id -g ${USER}) structuraldynamicslab/correlationplus:latest analyze -h
docker run -v $PWD:/home/correlationplus -u $(id -u ${USER}):$(id -g ${USER}) structuraldynamicslab/correlationplus:latest paths -h

Go to our readthedocs⁠ for detailed usage examples for each script.

⁠Licensing

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