Metadata-Version: 1.1
Name: proteingraph
Version: 0.1.1
Summary: A package for making graph representations of proteinstructures.
Home-page: http://github.com/ericmjl/protein-interaction-network/
Author: Eric J. Ma
Author-email: ericmajinglong@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: # protein-graph
        
        Computes a molecular graph for protein structures.
        
        ## why?
        
        Proteins fold into 3D structures, and have a natural graph representation: amino acids are nodes, and biochemical interactions are edges.
        
        I wrote this package as part of a larger effort to do graph convolutional neural networks on protein structures (represented as graphs). However, that's not the only thing I can foresee doing with this.
        
        One may be interested in the topology of proteins across species and over evolutionary time. This package can aid in answering this question.
        
        
        ## how do I use this package?
        
        This package assumes that you have a standard protein structure file (e.g. a PDB file). This may be a file generated after solving the NMR or crystal structure of a protein, or it may be generated from homology modelling.
        
        Once that has been generated, the molecular graph can be generated using Python code.
        
        ```python
        from pin import ProteinInteractionNetwork
        
        p = pin.ProteinInteractionNetwork('my_model.pdb')
        ```
        
        Because the `ProteinInteractionNetwork` class inherits from NetworkX's `Graph` class, all methods that `Graph` has are inherited by `ProteinInteractionNetwork`, and it behaves just as a NetworkX graph does.
        
        What this means is that all graph-theoretic metrics (e.g. degree centrality, betweenness centrality etc.) can be computed on the `ProteinInteractionNetwork` object.
        
        See the HIV1 homology model example in the `examples/` directory for a minimal example.
        
Keywords: protein,biochemistry,structural biology,graph theory
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
