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| | {{Infobox script-repo |
| | |type = module |
| | |filename = scripts/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. |
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| |
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| == Syntax == | | == Syntax == |
| <source lang="python"> | | <source lang="python"> |
| COM (selection=PyMOLSelection), [center=boolean]
| | centroid (selection=PyMOLSelection), [center=boolean] |
| </source> | | </source> |
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| |
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| == 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=1
| | centroid ligand, center=1 |
| </source>
| |
| | |
| | |
| <source lang="python">
| |
| # @AUTHOR: Jason Vertrees
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| # 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
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| # * 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:
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| COM = cpv.add(COM, a.coord)
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| 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)",
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| space={'COM': COM, 'sub': cpv.sub})
| |
| | |
| return COM
| |
| | |
| cmd.extend("COM", COM)
| |
| </source> | | </source> |
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| ===See Also=== | | ===See Also=== |
|
| |
|
| [[Center_Of_Mass]] | | * [[centerofmass]] (new command in PyMOL 1.7.2) |
| | * [[Center_Of_Mass]] |
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| |
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| [[Category:Script_Library|CenterOfMass]] | | [[Category:Script_Library|CenterOfMass]] |
| [[Category:Structural_Biology_Scripts]] | | [[Category:Structural_Biology_Scripts]] |
| | [[Category: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