Difference between revisions of "Centroid"

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{{Infobox script-repo
 +
|type      = Python Module
 +
|filename  = com.py
 +
|author    = [[User:Inchoate|Jason Vertrees]]
 +
|license  = -
 +
}}
 +
 
== Overview ==  
 
== 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.
 
[[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.
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# move some 'ligand' to the origin
 
# move some 'ligand' to the origin
 
COM ligand, center=1
 
COM ligand, center=1
</source>
 
 
 
<source lang="python">
 
# @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.
 
#
 
# 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
 
# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
#
 
# 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)
 
 
</source>
 
</source>
  

Revision as of 06:49, 9 December 2011

Type Python Module
Download com.py
Author(s) Jason Vertrees
License -
This code has been put under version control in the project Pymol-script-repo

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
import com
fetch 4ins, async=0
COM polymer

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

See Also

Center_Of_Mass