#  ============================================================================
#
#  This script reads in the following input parameters:
#  a. The atomic structure of a component (PDB format) fitted in a cryo-EM map
#  and its length
#  b. The cryo-EM density map (includeing origin, format, size)
#  c. The name of the directory that contains all "fits"
#  d. The list containing the names of all "fits"
#  and calculate the energy of each fit (CCF, stereo-chemical
#  and non-bonded interactions terms).
#
#  =======================  Maya Topf, 19 Dec 2008 ============================

from modeller import *
import shutil
import sys, os, os.path    
import string 
import math

from score import energy

env = environ()  

############### INPUT PARAMETERS ##################

path = './'                             # directory path
em_map_file = 'map.mrc'                 # name of EM density map (mrc)
format='MRC'                            # map format: MRC or XPLOR
apix=1.0                                # voxel size: A/pixel
box_size=86                             # size of the density map (cubic)
resolution=10.0                         # resolution
x=-31.00; y=-36.0; z=-11.00             # origin of the map
results_dir = 'final/'                  # a directory for the PDB files of all fits

code = 'mdl1'                           # 4 letter code of the structure
list_pdb_file = 'list_pdbs.txt'         # a file containing the names the above files

############### RUN OPTIMIZATION ##################

list_pdbs = []
in_file = open(list_pdb_file ,'U')
num=0
while True:
    in_line = in_file.readline()
    if len(in_line) == 0:
        break
    in_line = in_line[:-1]
    list_pdbs.append(in_line)
print list_pdbs

# calculate score  for each model: 
i=0
for input_pdb_file in list_pdbs: 
    if input_pdb_file == "":
     break
    file_name = results_dir + input_pdb_file
    i+=1
    energy(path, code, str(i), 9*i, em_map_file, file_name, format, apix, box_size, resolution, x, y, z)