#!/usr/bin/python
# takes the coordinates from the arg specified file
# and substitutes them for the coordinates in the
# std input pdb file
# the results is out via std out as a pdb file

# example:
# replace_coords.py adjusted.pdb < original.pdb > new.pdb

import sys
import string

adjusted = sys.argv[1]

"""
0123456789012345678901234567890123456789012345678901234567890123456
ATOM      1  N   SER     1      23.567  14.160  40.755  1.00  0.00
ATOM      2  H1  SER     1      23.583  13.893  41.098  1.00  0.00
ATOM      3  H2  SER     1      23.327  14.269  41.142  1.00  0.00

ATOM    717  CG2 THR A  95      17.091  15.628  45.440  1.00  0.00
"""
f = open(adjusted)
db = {}
# build the database of coords
for line in f.readlines():
	if line[:4]<>"ATOM": continue
	if line[17:20]=='SOL': continue
	atom = line[12:16]
	if atom==' O1 ':
		atom = ' O  '
	# this next one is due to differences between 3.2.1 and 3.3.1
	if atom==' CD ':
		atom = ' CD1'
	if atom==' O2 ':
		atom = ' OXT'
	residueIndex = line[22:26]
	db[atom+residueIndex] = line[29:66]
f.close()

lines = sys.stdin.readlines()

for line in lines:
	if line[:4]<>"ATOM":
		print line,
		continue
	atom = line[12:16]
	if atom==' O1 ':
		atom = ' O  '
	# this next one is due to differences between 3.2.1 and 3.3.1
	if atom==' CD ':
		atom = ' CD1'
	if atom==' O2 ':
		atom = ' OXT'
	coords = db[atom+line[22:26]]
	print line[:29]+coords+line[66:],