#!/usr/bin/env python

# The name of this file
__name__ = "General OptCDR Functions"
# Documentation
__doc__ = """
Written in 2014 by Matthew Grisewood of the Costas Maranas Lab in the Chemical
Engineering Department of the Pennsylvania State University.

This file contains functions for running OptCDR. Each of the main functions
requires an Experiment class object as its input."""

# Include the PYTHON modules
import os
import sys
# Include the IPRO Suite STANDARDS module
from STANDARDS import *
# And include other IPRO Suite modules
import EXPERIMENT
import MOLECULES

# Load canonicals, clashes, average positions, clusters, antigens

# Center antigens at the center

# Output the antigens and canonical structures for positioning calculations

# Generate the movements

# Run the CPP program


# Load the scores


