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(Replaced content with "Find polar pairs")
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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)]].
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Find polar pairs
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== Example ==
 
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<source lang="python">
 
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pairs = polarpairs('chain A', 'chain B')
 
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for p in pairs:
 
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    dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
 
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    print p, 'Distance: %.2f' % (dist)
 
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</source>
 
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== The Script ==
 
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<source lang="python">
 
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'''
 
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(c) 2011 Thomas Holder, MPI for Developmental Biology
 
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'''
 
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from pymol import cmd
 
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def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name='', state=1, quiet=1):
 
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    '''
 
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ARGUMENTS
 
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    sel1, sel2 = string: atom selections
 
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    cutoff = float: distance cutoff
 
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    angle = float: h-bond angle cutoff in degrees. If angle="default", take
 
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    "h_bond_max_angle" setting. If angle=0, do not detect h-bonding.
 
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    name = string: If given, also create a distance object for visual representation
 
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SEE ALSO
 
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    cmd.find_pairs, cmd.distance
 
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    '''
 
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    cutoff = float(cutoff)
 
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    quiet = int(quiet)
 
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    state = int(state)
 
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    if angle == 'default':
 
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        angle = cmd.get('h_bond_max_angle', cmd.get_object_list(sel1)[0])
 
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    angle = float(angle)
 
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    mode = 1 if angle > 0 else 0
 
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    x = cmd.find_pairs('(%s) and donors' % sel1, '(%s) and acceptors' % sel2,
 
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            state, state,
 
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            cutoff=cutoff, mode=mode, angle=angle) + \
 
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        cmd.find_pairs('(%s) and acceptors' % sel1, '(%s) and donors' % sel2,
 
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            state, state,
 
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            cutoff=cutoff, mode=mode, angle=angle)
 
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    x = sorted(set(x))
 
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    if not quiet:
 
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        print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
 
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        print 'Found %d polar contacts' % (len(x))
 
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    if len(name) > 0:
 
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        for p in x:
 
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            cmd.distance(name, '(%s`%s)' % p[0], '(%s`%s)' % p[1])
 
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    return x
 
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cmd.extend('polarpairs', polarpairs)
 
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</source>
 
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[[Category:Plugins]]
 
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[[Category:Biochemical_Scripts]]
 

Revision as of 20:26, 23 April 2015

Find polar pairs

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