Centroid: Difference between revisions

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{{Infobox script-repo
|type      = module
|filename  = centroid.py
|author    = [[User:Inchoate|Jason Vertrees]]
|license  = BSD
}}
== 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.
Centroid is a small script that returns the value of the geometric center (or centroid) of your selection.  It also can translate the object of that selection to the origin.


== Syntax ==
== Syntax ==
<source lang="python">
<source lang="python">
COM (selection=PyMOLSelection), [center=boolean]
centroid (selection=PyMOLSelection), [center=boolean]
</source>
</source>


== Examples ==
== Examples ==
<source lang="python">
<source lang="python">
# get the COM of the polymer
# get the centroid of the polymer
COM polymer
import centroid
fetch 4ins, async=0
centroid polymer


# move some 'ligand' to the origin
# move some 'ligand' to the origin
COM ligand, center=True
centroid 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
# 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)
</source>
</source>


===See Also===
===See Also===


[[Center_Of_Mass]]
* [[centerofmass]] (new command in PyMOL 1.7.2)
* [[Center_Of_Mass]]


[[Category:Script_Library|CenterOfMass]]
[[Category:Script_Library|CenterOfMass]]
[[Category:Structural_Biology_Scripts]]
[[Category:Structural_Biology_Scripts]]
[[Category:Pymol-script-repo]]

Latest revision as of 14:53, 12 October 2016

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

Overview

Centroid is a small script that returns the value of the geometric center (or centroid) of your selection. It also can translate the object of that selection to the origin.

Syntax

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

Examples

# get the centroid of the polymer
import centroid
fetch 4ins, async=0
centroid polymer

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

See Also

Retrieved from "https://pymolwiki.org/index.php?title=Centroid&oldid=12460"