Difference between revisions of "Centroid"

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(see also centerofmass)
 
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{{Infobox script-repo
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|type      = module
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|filename  = centroid.py
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|author    = [[User:Inchoate|Jason Vertrees]]
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|license  = BSD
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}}
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== 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.
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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]
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centroid (selection=PyMOLSelection), [center=boolean]
 
</source>
 
</source>
  
 
== Examples ==
 
== Examples ==
 
<source lang="python">
 
<source lang="python">
# get the COM of the polymer
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# get the centroid of the polymer
COM polymer
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import centroid
 +
fetch 4ins, async=0
 +
centroid polymer
  
 
# move some 'ligand' to the origin
 
# move some 'ligand' to the origin
COM ligand, center=True
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centroid ligand, center=1
 
</source>
 
</source>
  
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===See Also===
  
<source lang="python">
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* [[centerofmass]] (new command in PyMOL 1.7.2)
# @AUTHOR: Jason Vertrees
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* [[Center_Of_Mass]]
# 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>
 
  
 
[[Category:Script_Library|CenterOfMass]]
 
[[Category:Script_Library|CenterOfMass]]
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[[Category:Structural_Biology_Scripts]]
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[[Category:Pymol-script-repo]]

Latest revision as of 15:53, 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