import sys
from MMTK import *
from Bio import PDB
import numpy

listnames = open(sys.argv[1],'r')

listnames = listnames.readlines()

def calc_atom_dist(atom_one, atom_two) :
    """Returns the C-alpha distance between two atoms"""
    diff_vector  = atom_one.coord - atom_two.coord
    return numpy.sqrt(numpy.sum(diff_vector * diff_vector))


def check_bondlengths(pdbfile):
        """checks for bond lengths shorter than forcefield cutoff of 0.277908 nm"""
        parser = PDB.PDBParser()
	f = open(pdbfile,'r')
        o = parser.get_structure(pdbfile, f)
        f.close()
	out = open(pdbfile.replace(".pdb","_atombondlengths.txt"),"w")
        list_atoms=[]
        error=[]
        dist = []
        for r in o.get_atoms():
                list_atoms.append(r)
        for i in range(len(list_atoms)):
		for j in range(len(list_atoms)):
                	dist = calc_atom_dist(list_atoms[i],list_atoms[j])
			out.write(str((i,j))+"\t"+str(dist)+"\n")
for l in listnames:
        l = l.rstrip()
	l = l.split("\t")
	filename=l[1]+"_allatom"
	#filename=l.split("/")[3].replace(".mode","")
	modes = load(l[0]) #should have the input modes file for the TIM barrel structure in question
	universe = modes.universe
	protein = universe.protein
	protein.normalizeConfiguration('Ir')
	protein.writeToFile(filename+"_modes.pdb")
        check_bondlengths(filename+"_modes.pdb")