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 :)
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