COM

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

# get the COM of the polymer
COM polymer
 
# move some 'ligand' to the origin
COM ligand, center=True

# @AUTHOR: Jason Vertrees
# Copyright (c) 2008, Jason Vertrees
# All rights reserved.
#
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#     * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to endorse or promote products derived
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#
# DATE  : 2008-09-26
# REV   : 1
# REQUIREMENTS: numpy
 
from pymol import cmd
from pymol import stored
import numpy
 
def COM(selection, center=False):
        """
        centerOfMass: get the center of mass of selection or move selection to the origin.
        param: selection -- a valid PyMOL selection
        param: center    -- (boolean) if (False) return the center of mass, else if (True) center the selection
        returns: center of mass: [ xCOM, yCOM, zCOM ]
        """
        model = cmd.get_model(selection)
        nAtom = len(model.atom)
 
        COM = numpy.array([0.,0.,0.])
        stored.curLoc = []
 
        for a in model.atom:
                COM += numpy.array(a.coord)
                if ( center ):
                        stored.curLoc.append( a.coord )
        COM /= float(nAtom)
 
        if ( center ):
                stored.curLoc = (numpy.array(stored.curLoc) - COM).tolist()
                cmd.alter_state(1, selection, "(x,y,z)=stored.curLoc.pop(0)")
 
        return COM.tolist()
 
cmd.extend("COM", COM)

Category: Script Library