Generating Ramachandran plot and statistics.
Project description
Ramachandran
Ramachandran plot visualizes energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. This Python package provides the implementations to crawling PDB/PDBx files from RCSB PDB Bank, parse PDB/PDBx files to extract geometric information, computing the torsion angles of residues from atom coordinates and the Ramachandran favorable regions from the reference PDB/PDBx files selected, and creating Ramachandran plots for user-provided PDB/PDBx files.
Dependencies
- Python 3.8+
- Numpy 1.20.1+
- Matplotlib 3.3.4+
Usages
It is recommended to use Docker container to run the program.
Build Docker Image
$ docker build -f docker/ramachandran.Dockerfile --no-cache --tag=ramachandran:0.0.1 .
Run Docker Container
$ docker run -it --rm --gpus device=0 -v $(pwd):/mnt ramachandran:0.0.1
Install
$ pip install ramachandran
Create Ramachandran Plots
$ ramachandran_plot --help
usage: ramachandran_plot [-h] --file-path FILE_PATH
[--save-dir-path SAVE_DIR_PATH]
[--protein-name PROTEIN_NAME]
Ramachandran Plot Tool. Plots for GLY, PRO, pre-PRO, and Other residues will
be created.
optional arguments:
-h, --help show this help message and exit
--file-path FILE_PATH
PDB/PDBx file path. (default: None)
--save-dir-path SAVE_DIR_PATH
Directory path for saving the Ramachandran plots for
the PDB/PDBx file. (default: .)
--protein-name PROTEIN_NAME
Protein name. (default: None)
Demo
$ ramachandran_plot --file-path 1AXC.cif --save-dir-path 1AXC --protein-name 1AXC
References
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
ramachandran-0.0.1.tar.gz
(3.7 MB
view hashes)
Built Distribution
Close
Hashes for ramachandran-0.0.1-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d8282ca99c468085be965e72f652760ce6de07449d1fa2906bc4daec4748a669 |
|
MD5 | a8c518fbfc489226005df5642432b130 |
|
BLAKE2b-256 | 2e9401a6c7354a16c73a41e33cbe4e9afef54901b28c2fd646aee6f8bd6e0465 |