Extractedmin2pdb.py

1. !/usr/bin/env python

import sys import string

1. 2. #
   3. Edyta Malolepsza #
   4. David Wales' group, University of Cambridge #
   5. in case of problems please send email: em427@cam.ac.uk #
   6. #
   8. transform path.info into path_all.pdb
   9. ./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 ")

1. 1. 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("extractedmin").read() ff = string.split(info, "\n")

xyz = open('points.min.pdb','w')

for i in range(len(ff)/(atomNumber)):

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

   xyz.write("END\n")

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