Path2pdb.py

path.info file can be easy converted to the PDB file using Python program presented below. PDB file can be loaded to VMD and you can visualize your path. To do this save the code in path2pdb.py file, next change privileges of this file:

chmod 777 path2pdb.py

and type:

./path2pdb.py

---

#!/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.pdb
## ./path2pdb.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.pdb','w')

for i in range(len(ff)/(2+2*atomNumber)):
    m = atomNumber*2+2
    mm = 1
    for j in range(atomNumber):
        x = float(string.split(ff[m*i+85+j])[0])
        y = float(string.split(ff[m*i+85+j])[1])
        z = float(string.split(ff[m*i+85+j])[2])
        if (atomName[j]=='N' and atomName[j+1]=='H'):
            mm = mm+1
        else:
            xyz.write("%4s%7d %-4s %4s%5d%12.3f%8.3f%8.3f\n" % ('ATOM', j+1, atomName[j], 'ALA', mm, x, y, z))

    xyz.write("END\n")

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