main_ens.py

import sys
import time
import json
import numpy as np
import pprint
import os

from informatics.rawretrievers import PDBData, PubMedData
from informatics.parsers import Parser
from informatics.summaries import StructureSummarizer
from informatics.presenter import Presenter, HowToViz
from informatics.database import DBHandler

def search_pdb():
    pdb_root = PDBData(save_to_disk=True)
    pdb_parser = Parser(pdb_root, 'xml_string')
    pdb_root.set_search_resolution(1.0, 1.2)
    pdb_root.set_search_title('sumo')
    pdb_root.search()
    for structure_root in pdb_root:
        structure_primitive = pdb_parser(structure_root)
        print (structure_primitive.label)
        summarizer = StructureSummarizer()
        summarizer.set_nresidues(structure_primitive)
        summarizer.set_nresidues_polarity(structure_primitive)
        summarizer.set_bfactor_chain_stat(structure_primitive)
        print (summarizer.unpack_nresidues())
        print (summarizer.unpack_nresidues_polarity())
        print (summarizer.unpack_bfactor_chain_stat())
#        vis = Visualizer()
#        vis.stacked_bars(summarizer.get_nresidues_polarity().unpack_value(),
#                         x_axis='chain', y_axis='residue_count', 
#                         stack='property', title=structure_primitive.label)
#        vis.make_html('/mnt/c/Users/Anders/Desktop/tmp2.html')
        print ('\n\n') 

def main(args):

#    search_pdb()
#    sys.exit() 

    data_parser = Parser(PDBData(), 'xml_file')

    path = os.getcwd() 
    db_handler = DBHandler('django', path + '/viz_output/', path + 'vizout.db',
                           table_name='presenter_files',
                           headers=['created_by','version',
                                 'created_time','id_label','entry_data_type',
                                 'viz_method', 'id_text', 'entry_data_text',
                                 'viz_text', 'file_path', 'file_namespace'])

    pdb_files = ['protein_3tv3.xml', 'protein_1wm3.xml',
    'protein_3a4r.xml','protein_3r0m.xml','protein_3d9a.xml']

    collector = []
    for pdb_file in pdb_files:
        structure = data_parser(path + '/' + pdb_file)
        print (structure.label)

        summarizer = StructureSummarizer(structure.label)
        summarizer.populate_nresidues(structure)
        print (summarizer.populate_nresidues)
        print (summarizer.entry_collector['nresidues'])
        raise AttributeError('Sean Connery')
        summarizer.populate_nresidues_polarity(structure)
        summarizer.populate_rresidues_polarity(structure)
        summarizer.populate_bfactor_chain_stat(structure)
        summarizer.populate_bb_torsions(structure)

        presenter = Presenter(summarizer, db_handler,
                              data_type_subset=['bb_torsions','nresidues_polarity'])
        presenter.produce_visualization(output_format='javascript')

        collector.append(summarizer)

    ht = HowToViz(default='summary structure')
    ht.add('bfactor_chain_stat', 'box_plot',
           {'values' : 'property statistics', 'label' : 'id'})
    presenter = Presenter(collector, db_handler, howtoviz=ht,
                          data_type_subset=['rresidues_polarity',
                                            'bb_torsions',
                                            'bfactor_chain_stat'])
    presenter.produce_visualization(output_format='javascript')



if __name__ == '__main__':
    sys.exit(main(sys.argv[1:]))