Sidechaincenters

sidechain centers

Included in psico This command or function is available from psico, which is a PyMOL extension.
Module	psico.creating

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

Example

fetch 2x19
sidechaincenters scc, 2x19

The Script

'''
(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 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

    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

    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:', method)
        return

    model = models.Indexed()
    for centeratoms in atmap.values():
        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']:
            setattr(atom, key, getattr(at, 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 sidechaincentroids(object='scc', selection='all', name='PS1'):
    '''
DESCRIPTION

    Sidechain centroids. Works like "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:

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

SEE ALSO

    sidechaincenters
    '''
    return sidechaincenters(object, selection, name, method='centroid')

cmd.extend('sidechaincenters', sidechaincenters)
cmd.extend('sidechaincentroids', sidechaincentroids)

cmd.auto_arg[1].update({
    'sidechaincenters'     : [ cmd.selection_sc           , 'selection'       , ''   ],
    'sidechaincentroids'   : [ cmd.selection_sc           , 'selection'       , ''   ],
})

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