https://github.com/ijpulidos/mdcli

Some tools for the analysis and pre/post-processing of molecular dynamics data.
https://github.com/ijpulidos/mdcli

bioinformatics biophysics molecular-dynamics

Last synced: 24 days ago
JSON representation

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

• Host: GitHub
• URL: https://github.com/ijpulidos/mdcli
• Owner: ijpulidos
• License: mit
• Created: 2019-03-28T01:30:08.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2021-02-25T05:21:54.000Z (almost 4 years ago)
• Last Synced: 2023-09-21T13:53:49.096Z (over 1 year ago)
• Topics: bioinformatics, biophysics, molecular-dynamics
• Language: Jupyter Notebook
• Size: 323 KB
• Stars: 3
• Watchers: 2
• Forks: 3
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# 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:

```bash

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:

```bash

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.