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=True

# @AUTHOR: Jason Vertrees
# Copyright (c) 2008, Jason Vertrees
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following
# conditions are met:
#
#     * Redistributions of source code must retain the above copyright notice, this list of conditions and the following
#     * disclaimer.
#     * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
#     * disclaimer in the documentation and/or other materials provided with the distribution.
#     * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to endorse or promote products derived
#     * from this software without specific prior written permission.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
# THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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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)