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">
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# get the COM of the polymer
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# get the centroid of the polymer
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import com
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import centroid
−
COM polymer
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fetch 4ins, async=0
 +
centroid polymer
  
 
# move some 'ligand' to the origin
 
# move some 'ligand' to the origin
−
COM ligand, center=1
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centroid ligand, center=1
−
</source>
 
−
 
 
−
 
 
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<source lang="python">
 
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# @AUTHOR: Jason Vertrees
 
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# Copyright (c) 2008, Jason Vertrees
 
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# All rights reserved.
 
−
#
 
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# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following
 
−
# conditions are met:
 
−
#
 
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#    * 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
 
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#    * disclaimer in the documentation and/or other materials provided with the distribution.
 
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#    * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to endorse or promote products derived
 
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#    * 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
 
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# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
 
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# THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 
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# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 
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# 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.
 
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#
 
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# DATE  : 2008-09-26
 
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# REV  : 1
 
−
 
 
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from pymol import cmd
 
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from pymol import stored
 
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from chempy import cpv
 
−
 
 
−
def COM(selection='all', center=0, quiet=1):
 
−
        """
 
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DESCRIPTION
 
−
 
 
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        get the center of mass of selection or move selection to the origin.
 
−
 
 
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ARGUMENTS
 
−
 
 
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        selection = string: a valid PyMOL selection {default: all}
 
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        center = 0 or 1: if center=1 center the selection {default: 0}
 
−
 
 
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        returns: center of mass: [ xCOM, yCOM, zCOM ]
 
−
 
 
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SEE ALSO
 
−
 
 
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        get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass
 
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        """
 
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        model = cmd.get_model(selection)
 
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        nAtom = len(model.atom)
 
−
 
 
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        COM = cpv.get_null()
 
−
 
 
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        for a in model.atom:
 
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                COM = cpv.add(COM, a.coord)
 
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        COM = cpv.scale(COM, 1./nAtom)
 
−
 
 
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        if not int(quiet):
 
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                print ' COM: [%8.3f,%8.3f,%8.3f]' % tuple(COM)
 
−
 
 
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        if int(center):
 
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                cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), COM)",
 
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                        space={'COM': COM, 'sub': cpv.sub})
 
−
 
 
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        return COM
 
−
 
 
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cmd.extend("COM", COM)
 
 
</source>
 
</source>
  
 
===See Also===
 
===See Also===
  
−
[[Center_Of_Mass]]
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* [[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 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

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