mdcli

Some tools for the analysis and pre/post-processing of molecular dynamics data.

Requirements

It is recommended that you use an anaconda/conda environment, since it would allow to install many of the needed libs and tools in an easier way (they are already included in some conda channels).

Adding conda channels

Add salilab conda channel to install Modeller which is a required tool and schrodinger channel for pymol (as a python lib), as follows:

conda config --add channels conda-forge
conda config --add channels salilab
conda config --add channels schrodinger

Building environment from file

The environment.yml file allows to build an anaconda environment that will be named mdcli-env by default, with all the required packages. To build it just use:

conda env create -f environment.yml

Features - capabilities

The current capabilities of the tools in this repository are the following.

Completing residues

The script complete_residues.py is a friendly tool that completes a PDB structure with both missing residues and atoms. Example of usage is as follows:

python complete_residues.py -i /path/to/input/PDB --pdbcode PDBcode

And it will return a pdb fill structure (see output for exact name).

Extract helical residues

Using the script get_helices.py you can extract the ids from residues belonging to helical structure given a PDB file. It also outputs a PDB file with the structure of only the helical residues. Example of its usage is:

python get_helices.py --pdbfile ../../datafiles/conf.pdb -o /tmp/helices.pdb

For example using the conf.pdb file in the datafiles.