Sidechaincenters

Pseudo single-atom representation of sidechains. Usefull for pair potential calculation for example.

Example

fetch 2x19
pseudo_sidechaincenters scc, 2x19

The Script

<source lang="python"> (c) 2010 Thomas Holder

from pymol import cmd from chempy import Atom, cpv, models

sidechaincenteratoms = {

   'GLY': ('CA',),
   'ALA': ('CB',),
   'VAL': ('CG1', 'CG2'),
   'ILE': ('CD1',),
   'LEU': ('CD1', 'CD2'),
   'SER': ('OG',),
   'THR': ('OG1', 'CG2'),
   'ASP': ('OD1', 'OD2'),
   'ASN': ('OD1', 'ND2'),
   'GLU': ('OE1', 'OE2'),
   'GLN': ('OE1', 'NE2'),
   'LYS': ('NZ',),
   'ARG': ('NE', 'NH1', 'NH2'),
   'CYS': ('SG',),
   'MET': ('SD',),
   'MSE': ('SE',),
   'PHE': ('CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ'),
   'TYR': ('CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ', 'OH'),
   'TRP': ('CG', 'CD1', 'CD2', 'NE1', 'CE2', 'CE3', 'CZ2', 'CZ3'),
   'HIS': ('CG', 'ND1', 'CD2', 'CE1', 'NE2'),
   'PRO': ('CB', 'CG', 'CD'),

}

def pseudo_sidechaincenters(object='scc', selection='all', name='PS1', method='bahar1996'):

DESCRIPTION

   Creates an object with sidechain representing pseudoatoms for each residue
   in selection.

   Sidechain interaction centers as defined by Bahar and Jernigan 1996
   http://www.ncbi.nlm.nih.gov/pubmed/9080182

USAGE

   pseudo_sidechaincenters object [, selection]

ARGUMENTS

   object = string: name of object to create

   selection = string: atoms to consider {default: (all)}

   name = string: atom name of pseudoatoms {default: PS1}

SEE ALSO

   pseudo_sidechaincentroids, pseudoatom
   
   atmap = dict()
   if method == 'bahar1996':
       modelAll = cmd.get_model('(%s) and resn %s' % (selection, '+'.join(sidechaincenteratoms)))
       for at in modelAll.atom:
           if at.name in sidechaincenteratoms[at.resn]:
               atmap.setdefault((at.segi, at.chain, at.resn, at.resi), []).append(at)
   elif method == 'centroid':
       modelAll = cmd.get_model('(%s) and not (hydro or name C+N+O)' % selection)
       for at in modelAll.atom:
           atmap.setdefault((at.segi, at.chain, at.resn, at.resi), []).append(at)
   else:
       print 'Error: unknown method'
       return

   model = models.Indexed()
   for centeratoms in atmap.itervalues():
       center = cpv.get_null()
       for at in centeratoms:
           center = cpv.add(center, at.coord)
       center = cpv.scale(center, 1./len(centeratoms))
       atom = Atom()
       atom.coord = center
       atom.index = model.nAtom + 1
       atom.name = name
       for key in ['resn','chain','resi','resi_number','hetatm','ss','segi']:
           atom.__dict__[key] = at.__dict__[key]
       model.add_atom(atom)
   model.update_index()
   if object in cmd.get_object_list():
       cmd.delete(object)
   cmd.load_model(model, object)
   return model

def pseudo_sidechaincentroids(object='scc', selection='all', name='PS1'):

DESCRIPTION

   Sidechain centroids. Works like "pseudo_sidechaincenters", but the
   pseudoatom is the centroid of all atoms except hydrogens and backbone atoms
   (N, C and O).

NOTE

   If you want to exclude C-alpha atoms from sidechains, modify the selection
   like in this example:

   pseudo_sidechaincentroids newobject, all and (not name CA or resn GLY)

SEE ALSO

   pseudo_sidechaincenters
   
   return pseudo_sidechaincenters(object, selection, name, method='centroids')

cmd.extend('pseudo_sidechaincenters', pseudo_sidechaincenters) cmd.extend('pseudo_sidechaincentroids', pseudo_sidechaincentroids)

1. vi: ts=4:sw=4:smarttab:expandtab

</script>