Path2pdb.py
Revision as of 16:30, 30 April 2008 by import>Em427
Script useful for AMBER9 and NAB users
path.info file can be easy converted to the PDB format 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, change privileges of this file:
chmod 755 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()