Metadata-Version: 2.1
Name: ramachandran
Version: 0.0.1
Summary: Generating Ramachandran plot and statistics.
Home-page: https://github.com/leimao/Ramachandran
Author: Lei Mao
Author-email: dukeleimao@gmail.com
License: UNKNOWN
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
        ```
        
        ![1AXC](./demo/1AXC/general.svg)
        
        
        ## References
        
        * [Ramachandran Plot](https://en.wikipedia.org/wiki/Ramachandran_plot)
        * [PyRAMA](https://github.com/gerdos/PyRAMA)
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
