database.py

from __future__ import division

class MetrixDB(object):
  '''
  A high level class to perform operations on the metrix database

  '''

  def __init__(self, overwrite=False):
    '''
    Initialise the database

    '''
    from metrix_db.initialiser import Initialiser
    initialiser = Initialiser(overwrite=overwrite)
    self.handle = initialiser.handle

  def add_pdb_entry(self, pdb_id, filename):
    '''
    Add a pdb entry to the database

    '''
    from metrix_db.pdb_parser import PDBParser
    parser = PDBParser(self.handle)
    parser.add_entry(pdb_id, filename)

  def add_xia2_entry(self,
                     pdb_id,
                     xia2_txt_filename,
                     xia2_json_filename):
    '''
    Add a xia2 entry to the database

    '''
    from metrix_db.xia2_parser import XIA2Parser
    parser = XIA2Parser(self.handle)
    parser.add_entry(pdb_id, xia2_txt_filename, xia2_json_filename)

  def add_protein_entry(self, pdb_id, filename):
    '''
    Add a protein entry to the database

    '''
    from metrix_db.protein_parser import ProteinParser
    parser = ProteinParser(self.handle)
    parser.add_protein(pdb_id, filename)


  def write_csv(self, filename):
    '''
    Write a CSV file from the database

    '''
    from metrix_db.csv_writer import CSVWriter
    writer = CSVWriter(self.handle)
    writer.write(filename)