Polarpairs - Revision history

Cchem: 1 revision

2019-04-01T03:11:57Z

1 revision

Speleo3: 2to3

2019-03-12T18:53:18Z

2to3

Bell: 3 revisions

2014-03-28T03:08:45Z

3 revisions

Speleo3: state argument added

2011-09-10T19:54:22Z

state argument added

Speleo3: plugins category

2011-06-24T09:01:43Z

plugins category

Speleo3: Created page with "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 [[distance|cmd.distance(m..."

2011-06-24T09:00:13Z

Created page with "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 [[distance|cmd.distance(m..."

New page

Find polar pairs with the [[find_pairs|cmd.find_pairs]] function and return them as a list of atom pairs. It finds (more or less) the same contacts like [[distance|cmd.distance(mode=2)]].

== Example ==

<source lang="python">
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)
</source>

== 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='', 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)
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)
</source>

[[Category:Biochemical_Scripts]]

← Older revision		Revision as of 09:01, 24 June 2011
Line 58:		Line 58:
	</source>		</source>

		+	[[Category:Plugins]]
	[[Category:Biochemical_Scripts]]		[[Category:Biochemical_Scripts]]

← Older revision	Revision as of 03:11, 1 April 2019
(No difference)

@@ Line 7: / Line 7: @@
 for p in pairs:
      dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
-     print p, 'Distance: %.2f' % (dist)
+     print(p, 'Distance: %.2f' % (dist))
 </source>
@@ Line 51: / Line 51: @@
      x = sorted(set(x))
      if not quiet:
-         print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
+         print('Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle))
-         print 'Found %d polar contacts' % (len(x))
+         print('Found %d polar contacts' % (len(x)))
      if len(name) > 0:
          for p in x:

← Older revision	Revision as of 03:08, 28 March 2014
(No difference)

@@ Line 19: / Line 19: @@
 from pymol import cmd
-def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name='', quiet=1):
+def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name='', state=1, quiet=1):
      '''
 ARGUMENTS
@@ Line 38: / Line 38: @@
      cutoff = float(cutoff)
      quiet = int(quiet)
      if angle == 'default':
          angle = cmd.get('h_bond_max_angle', cmd.get_object_list(sel1)[0])
@@ Line 43: / Line 44: @@
      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))