#!/usr/bin/env python3

# feel free to clean up the imports
import MDAnalysis
from MDAnalysis.coordinates.memory import MemoryReader
from MDAnalysis.analysis.base import AnalysisFromFunction
from MDAnalysis.analysis import align, rms
from MDAnalysis.analysis.dihedrals import *
from MDAnalysis.analysis import contacts

import matplotlib.pyplot as plt
import numpy as np
import sys, argparse


parser = argparse.ArgumentParser(description='Analyze a MD trajectory using MDAnalysis')
parser.add_argument("topology",help="Topology PDB file from OpenMM")
parser.add_argument("trajectory",help="Trajectory file")
args = parser.parse_args()

# KEEP all the hardcoded output file names as this is how your script will be graded.

# Preprocess trajectory



# RMSD Calculations



np.save('rmsd_first.npy',rmsd_first)
np.save('rmsd_last.npy',rmsd_last)

# RMSF Calculations



np.save('ca_rmsf.npy',ca_rmsf) #alpha carbon only rmsf


protein.atoms.write('rmsf.pdb') # must write pdb with tempfactors set for every atom

# Ramachandran 


np.save('ramachandran.npy',rama.results['angles'])

# Janin


np.save('janin.npy',janin.results['angles'])