Metadata-Version: 2.1
Name: backmap
Version: 0.0.1.post0.dev12
Summary: Shows protein backbone structures in compact graphical form using Ramachandran numbers
Home-page: http://www.github.com/ranjanmannige/backmap
Author: ranjanmannige
Author-email: ranjanmannige@gmail.com
License: mit
Description: ```
          ____             _    __  __          _____  
         |  _ \           | |  |  \/  |   /\   |  __ \ 
         | |_) | __ _  ___| | _| \  / |  /  \  | |__) |
         |  _ < / _` |/ __| |/ / |\/| | / /\ \ |  ___/ 
         | |_) | (_| | (__|   <| |  | |/ ____ \| |     
         |____/ \__,_|\___|_|\_\_|  |_/_/    \_\_|     
                               (Multi-angle Picture)                                             
        ```
        
        This tool provides easily readable "pictures" of protein conformations, 
        ensembles, and trajectories saved as either a combined protein databank 
        (PDB) structure file, or a directory of such files, and produces graphs.
        
        # Installation
        ```
        pip install backmap
        ```
        
        # RE-installation
        ```
        pip install -I backmap
        ```
        
        # Usage
        
        ## Module Usage 
        
        ```python
        import backmap
        print backmap.R(phi=0,psi=0)
        ```
        See the manuscript for more information regarding uses.
        
        ## Stand-alone Usage 
        
        ```
        python -m backmap.__init__ -pdb ./pdbs/ProteinDatabankStructureFilename.pdb
        python -m backmap.__init__ -pdb /directory/containing/pdbs/
        ```
        
        The `.__init__` is needed because the main file we are referencing is `backmap/__init__.py`.
        
        ### Expected output to the stand alone mode
        
        Three graphs (in both png/raster and pdf/vector format)
        ```
        ./pdbs/reports/filename.rcode.pdf/png      (y-axis: residue #; color: R number based on "-signed" and <rcode_cmap>)
        ./pdbs/reports/filename.rcode.his.pdf/png  (y-axis: Ramachandran number (R); color: frequency of R in model)
        ./pdbs/reports/filename.rcode.rmsf.pdf/png (y-axis: residue #; color: RMSF in R from the previous model)
        ./pdbs/reports/filename.rcode.rmsd.pdf/png (y-axis: residue #; color: RMSD in R from the previous model)
        ```
        (the last two files may not be created if only one model exists in the PDB file.)
        
        ## Additional tags
        ```
        -h       -     Prints a help file
        -ss      -     Color the ramachandran number codes (R-codes) by 
                       secondary structure (default: color by chirality and sign)
        -signed  -     Use the signed version of the ramachandran number
        ```
        
        # Publications
        
        The Ramachandran number concept is discussed in the following manuscripts (this tool is discussed in the first reference):
        
        1. Mannige (2018) "The Backmap Python Module: How a Simpler Ramachandran Number Can Simplify the Life of a Protein Simulator" Manuscript Prepared. Preprint available 
        the [manuscript/manuscript](manuscript/manuscript/plotmap.pdf) subdirectory of this repo.
        2. Mannige, Kundu, Whitelam (2016) "The Ramachandran Number: An Order Parameter for Protein Geometry" PLoS ONE 11(8): e0160023. 
        Full Text: https://doi.org/10.1371/journal.pone.0160023
        
Platform: any
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: License :: OSI Approved :: MIT License
Description-Content-Type: text/markdown
