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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>
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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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| #
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| # Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following
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| # conditions are met:
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| #
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| # * Redistributions of source code must retain the above copyright notice, this list of conditions and the following
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| # * disclaimer.
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| # * 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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| #
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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
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| # 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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|
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| from pymol import cmd
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| from pymol import stored
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| from chempy import cpv
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|
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| def COM(selection='all', center=0, quiet=1):
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| """
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| DESCRIPTION
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|
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| get the center of mass of selection or move selection to the origin.
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|
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| ARGUMENTS
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|
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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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|
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| returns: center of mass: [ xCOM, yCOM, zCOM ]
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|
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| SEE ALSO
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|
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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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|
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| COM = cpv.get_null()
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|
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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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|
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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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|
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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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|
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| cmd.extend("COM", COM)
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| </source> | | </source> |
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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