Centroid

Overview

COM is a small script that returns the value of the center of mass of your selection. It also can translate the object of that selection to the origin.

Syntax

COM (selection=PyMOLSelection), [center=boolean]

Examples

# get the COM of the polymer
COM polymer

# move some 'ligand' to the origin
COM ligand, center=1

# @AUTHOR: Jason Vertrees
# Copyright (c) 2008, Jason Vertrees
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# DATE  : 2008-09-26
# REV   : 1

from pymol import cmd
from pymol import stored
from chempy import cpv

def COM(selection='all', center=0, quiet=1):
        """
DESCRIPTION

        get the center of mass of selection or move selection to the origin.

ARGUMENTS

        selection = string: a valid PyMOL selection {default: all}
        center = 0 or 1: if center=1 center the selection {default: 0}

        returns: center of mass: [ xCOM, yCOM, zCOM ]

SEE ALSO

        get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass
        """
        model = cmd.get_model(selection)
        nAtom = len(model.atom)

        COM = cpv.get_null()

        for a in model.atom:
                COM = cpv.add(COM, a.coord)
        COM = cpv.scale(COM, 1./nAtom)

        if not int(quiet):
                print ' COM: [%8.3f,%8.3f,%8.3f]' % tuple(COM)

        if int(center):
                cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), COM)",
                        space={'COM': COM, 'sub': cpv.sub})

        return COM

cmd.extend("COM", COM)

See Also

Center_Of_Mass