Difference between revisions of "Centroid"

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

Revision as of 11:49, 9 December 2011

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

@@ Line 1: / Line 1: @@
+{{Infobox script-repo
+|type      = Python Module
+|filename  = com.py
+|author    = [[User:Inchoate|Jason Vertrees]]
+|license   = -
+}}
 == 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.
@@ Line 16: / Line 23: @@
 # move some 'ligand' to the origin
 COM 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
-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:
-                COM = cpv.add(COM, a.coord)
-        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)",
-                        space={'COM': COM, 'sub': cpv.sub})
-        return COM
-cmd.extend("COM", COM)
 </source>

Difference between revisions of "Centroid"

Revision as of 11:49, 9 December 2011

Contents

Overview

Syntax

Examples

See Also

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