Center of mass

Description

This script calculates the true center-of-mass (COM) or the center-of-geometry (COG) for a given selection and returns the x, y, z values in the form of a Pseudoatom (rather than a CGO sphere). The benefit of using a Pseudoatom is that it can be selected and used in calculations. In addition, this script also iteratively goes through all states of a selection if more than one state exists and appends the corresponding COM/COG values as states into the Pseudoatom. The script itself is quite simple yet robust enough to be applied in different settings. As well, the calculation of the COM/COG is handled independently from the formation of the Pseudoatom and can be called as an independent function where applicable.

Usage

com selection [,state=None [,mass=None [,object=None]]]

Examples

fetch 1c3y, finish=1, multiplex=0

com 1c3y, state=1
#Create a pseudoatom representing the 1c3y COG and store it as "1c3y_COM"
#The "1c3y_COM" object will contain 1 state only

com 1c3y, state=1, object=COG
#Create a pseudoatom representing the 1c3y COG and store it as "COG"
#The "COG" object will contain 1 state only

com 1c3y, state=1, object=COM, mass=1
#Create a pseudoatom representing the 1c3y COM and store it as "COM"
#The "COM" object will contain 1 state only

com 1c3y, object=COM, mass=1
#Create a single pseudoatom containing the COM for each state found in 1c3y and store it as "COM"
#The "COM" object will contain MULTIPLE states!

PyMOL API

from pymol import cmd

def com(selection,state=None,mass=None,object=None, quiet=1, **kwargs):
   """
DESCRIPTION

   Places a pseudoatom at the center of mass

   Author: Sean Law
   Michigan State University
   slaw (at) msu . edu

SEE ALSO

   pseudoatom, get_com
   """
   quiet = int(quiet)
   if (object == None):
      try:
         object = cmd.get_legal_name(selection)
         object = cmd.get_unused_name(object + "_COM", 0)
      except AttributeError:
         object = 'COM'
   cmd.delete(object)

   if (state != None):
      x, y, z=get_com(selection,mass=mass, quiet=quiet)
      if not quiet:
         print "%f %f %f" % (x, y, z)
      cmd.pseudoatom(object,pos=[x, y, z], **kwargs)
      cmd.show("spheres",object)
   else:
      for i in range(cmd.count_states()):
         x, y, z=get_com(selection,mass=mass,state=i+1, quiet=quiet)
         if not quiet:
            print "State %d:%f %f %f" % (i+1, x, y, z)
         cmd.pseudoatom(object,pos=[x, y, z],state=i+1, **kwargs)
         cmd.show("spheres", 'last ' + object)

cmd.extend("com",com)

def get_com(selection,state=1,mass=None, quiet=1):
   """
DESCRIPTION

   Calculates the center of mass

   Author: Sean Law
   Michigan State University
   slaw (at) msu . edu
   """
   quiet = int(quiet)

   totmass=0.0
   if mass!=None and not quiet:
      print "Calculating mass-weighted COM"

   state=int(state)
   model = cmd.get_model(selection,state)
   x,y,z=0,0,0
   for a in model.atom:
      if (mass != None):
         m = a.get_mass()
         x+= a.coord[0]*m
         y+= a.coord[1]*m
         z+= a.coord[2]*m
         totmass+=m
      else:
         x+= a.coord[0]
         y+= a.coord[1]
         z+= a.coord[2]

   if (mass!=None):
      return x/totmass, y/totmass, z/totmass
   else:
      return x/len(model.atom), y/len(model.atom), z/len(model.atom)

cmd.extend("get_com", get_com)

# vi:expandtab:sw=3

See Also

• COM
• get_extent
• get_position