centroid.py

'''
See more here: http://www.pymolwiki.org/index.php/centroid

DESCRIPTION
        get the centroid (geometric center) of a 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: centroid: [ x, y, z ]

SEE ALSO
        get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass

# @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
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
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# DATE  : 2008-09-26
# REV   : 1

'''
from __future__ import print_function
from pymol import cmd
from pymol import stored
from chempy import cpv


def centroid(selection='all', center=0, quiet=1):

    model = cmd.get_model(selection)
    nAtom = len(model.atom)

    centroid = cpv.get_null()

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

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

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

    return centroid

cmd.extend("centroid", centroid)