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# Polarpairs

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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

```'''
(c) 2011 Thomas Holder, MPI for Developmental Biology
'''

from pymol import cmd

def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name='', 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

cmd.find_pairs, cmd.distance
'''
cutoff = float(cutoff)
quiet = int(quiet)
if angle == 'default':
angle = cmd.get('h_bond_max_angle', cmd.get_object_list(sel1)[0])
angle = float(angle)
mode = 1 if angle > 0 else 0
x = cmd.find_pairs('(%s) and donors' % sel1, '(%s) and acceptors' % sel2,
cutoff=cutoff, mode=mode, angle=angle) + \
cmd.find_pairs('(%s) and acceptors' % sel1, '(%s) and donors' % sel2,
cutoff=cutoff, mode=mode, angle=angle)
x = sorted(set(x))
if not quiet:
print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
print 'Found %d polar contacts' % (len(x))
if len(name) > 0:
for p in x:
cmd.distance(name, '(%s`%s)' % p[0], '(%s`%s)' % p[1])
return x

cmd.extend('polarpairs', polarpairs)
```