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(use chempy instead of numpy)
Line 13: Line 13:
  
 
# move some 'ligand' to the origin
 
# move some 'ligand' to the origin
COM ligand, center=True
+
COM ligand, center=1
 
</source>
 
</source>
  
Line 41: Line 41:
 
# DATE  : 2008-09-26
 
# DATE  : 2008-09-26
 
# REV  : 1
 
# REV  : 1
# REQUIREMENTS: numpy
 
  
 
from pymol import cmd
 
from pymol import cmd
 
from pymol import stored
 
from pymol import stored
import numpy
+
from chempy import cpv
  
def COM(selection, center=False):
+
def COM(selection='all', center=0, quiet=1):
 
         """
 
         """
         centerOfMass: get the center of mass of selection or move selection to the origin.
+
DESCRIPTION
         param: selection -- a valid PyMOL selection
+
 
         param: center    -- (boolean) if (False) return the center of mass, else if (True) center the selection
+
         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 ]
 
         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)
 
         model = cmd.get_model(selection)
 
         nAtom = len(model.atom)
 
         nAtom = len(model.atom)
  
         COM = numpy.array([0.,0.,0.])
+
         COM = cpv.get_null()
        stored.curLoc = []
 
  
 
         for a in model.atom:
 
         for a in model.atom:
                 COM += numpy.array(a.coord)
+
                 COM = cpv.add(COM, a.coord)
                if ( center ):
+
        COM = cpv.scale(COM, 1./nAtom)
                        stored.curLoc.append( a.coord )
+
 
        COM /= float(nAtom)
+
        if not int(quiet):
 +
                print ' COM: [%8.3f,%8.3f,%8.3f]' % tuple(COM)
  
         if ( center ):
+
         if int(center):
                stored.curLoc = (numpy.array(stored.curLoc) - COM).tolist()
+
                 cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), COM)",
                 cmd.alter_state(1, selection, "(x,y,z)=stored.curLoc.pop(0)")
+
                        space={'COM': COM, 'sub': cpv.sub})
  
         return COM.tolist()
+
         return COM
  
 
cmd.extend("COM", COM)
 
cmd.extend("COM", COM)

Revision as of 08:52, 15 August 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
COM polymer

# move some 'ligand' to the origin
COM ligand, center=1


# @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)

See Also

Center_Of_Mass