Re: [ccp4bb] PDB data mining

[Christian Fufezan]

Hi Cale,

this could be done equally with a python module called p3d.
A script would look like this

#!/usr/bin/env python3.1
'''Calculate ND1pairwise distances by Ch. Fufezan 2011

usage: ND1_pairs.py <pdb file>

see online documentation http://p3d.fufezan.net 
'''
import sys
import p3d
import itertools

if (__name__ == '__main__'):
    if (len(sys.argv) != 2):
        print (__doc__)
        sys.exit(1)
        
    pdb  = p3d.protein.Protein(sys.argv[1])
    ND1s = pdb.query("protein and resname HIS and atom type ND1")
    for atom1,atom2 in itertools.combinations(ND1s,2):
        print("{atom1_info} {atom2_info} {distance}".format(
            atom1_info = atom1.info(lvl='min'),
            atom2_info = atom2.info(lvl='min'),
            distance   = atom1.distanceTo(atom2)
        ))
     
Cheers :)