Find polar pairs with the
cmd.find_pairs function and return them as a list of atom pairs. It finds (more or less) the same contacts like
cmd.distance(mode=2).
Example
pairs = polarpairs('chain A', 'chain B')
for p in pairs:
dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
print(p, 'Distance: %.2f' % (dist))
The Script
<source lang="python">
(c) 2011 Thomas Holder, MPI for Developmental Biology
from pymol import cmd
def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name=, state=1, quiet=1):
ARGUMENTS
sel1, sel2 = string: atom selections
cutoff = float: distance cutoff
angle = float: h-bond angle cutoff in degrees. If angle="default", take
"h_bond_max_angle" setting. If angle=0, do not detect h-bonding.
name = string: If given, also create a distance object for visual representation
SEE ALSO
cmd.find_pairs, cmd.distance
cutoff = float(cutoff)
quiet = int(quiet)
state = ..→
