Path2xyz.py

path.info file can be easy converted also to xyz format using Python program presented below. To do this save the code in path2xyz.py file, next change privileges of this file:

chmod 755 path2xyz.py

and type:

./path2xyz.py

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#!/usr/bin/env python

import sys
import string

###############################################################
##                                                            #
## Edyta Malolepsza                                           #
## David Wales' group, University of Cambridge                #
## in case of problems please send email: em427@cam.ac.uk     #
##                                                            #
###############################################################
##
## transform path.info into path_all.xyz
## ./path2xyz.py
##
###############################################################

prmtop = open("coords.prmtop").read()
f = string.split(prmtop, "\n")

q0 = f.index("%FLAG POINTERS                                                                  ")
q1 = f.index("%FLAG ATOM_NAME                                                                 ")
q2 = f.index("%FLAG RESIDUE_LABEL                                                             ")
q3 = f.index("%FLAG RESIDUE_POINTER                                                           ")

## names of tables are related to names in prmtop file

atomNumber = int(string.split(f[q0+2])[0])

atomName = []
residueLabel = []

an = 0
line = 0
while (an<atomNumber):
  for j in range(20):
    if (an<atomNumber):
      an = an+1
      atomName.append(f[q1+2+line][j*4:(j+1)*4].strip())
    else:
      break
  line = line+1

for i in range(q3-q2-2):
  for j in range((len(f[q2+2+i])+1)/4):
    residueLabel.append(string.strip(f[q2+2+i][j*4:4*(j+1)]))

info = open("path.info").read()
ff = string.split(info, "\n")

xyz = open('path_all.xyz','w')

for i in range(len(ff)/(2+2*atomNumber)):
    m = atomNumber*2+2
#    xyz.write("%d\n%s %s\n" % (atomNumber, ff[m*i], ff[m*i+1])) # energy and symmetry
    xyz.write("%d\n%s\n" % (atomNumber, ff[m*i])) # energy
    for j in range(atomNumber):
        xyz.write("%-4s %s\n" % (atomName[j], ff[m*i+85+j]))

xyz.write("\n")
xyz.close()