correlationplus 0.1.9

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

correlationplus

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

correlationplus contains three main 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. You can use elastic network models or your your molecular dynamics trajectories for these visualizations and analyses.

Installation

We recommend one of the installation methods for regular users:

with pip

The pip version required by some dependencies is >= 21.0.1 which is not the pip version bundle with python 3.(6,7,8) So you have to update pip before to install correlationplus. Otherwise you will have trouble during MDAnalysis dependency installation. For this reason we strongly encourage you to install correlation plus in a virtualenv.

python3 -m venv correlationplus
cd correlationplus
source bin/activate
python3 -m pip install -U pip
python3 -m pip install correlationplus

if you still want to install it without using a virtualenv you hate to upgrade pip version to a version >=21.0.1 or install numpy==1.16 and the install correlationplus

We recommend to use pip as follows:

python3 -m pip install numpy==1.16.1
python3 -m pip install correlationplus

or if you do not have administration rights

python3 -m pip install --user numpy==1.16.1
python3 -m pip install --user correlationplus

with conda

conda install -c bioconda correlationplus

Most of the time, at least one these methods will be sufficient for the installation. However, if these two methods didn't work for any reason, you can take a look to 'Advanced Installation' instructions at https://correlationplus.readthedocs.io/en/latest/installation.html#advanced-installation.

Quickstart

There are three main scrips:

• calculate
• visualize
• analyze

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

correlationplus calculate -h
correlationplus visualize -h
correlationplus analyze -h

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

Licensing

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