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 [,name=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, name=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, name=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, name=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,name=None):
   
   """
   Author: Sean Law
   Michigan State University
   slaw (at) msu . edu
   """
   if (name == None):
      name=selection+"_COM"
   cmd.delete(name)
   
   if (state != None):
      x, y, z=get_com(selection,mass=mass)
      print "%f %f %f" % (x, y, z)
      cmd.pseudoatom(name,pos=[x, y, z])
      cmd.show("spheres",name)
   else:
      for i in range(cmd.count_states()):
         x, y, z=get_com(selection,mass=mass,state=i+1)
         print "State %d:%f %f %f" % (i+1, x, y, z)
         cmd.pseudoatom(name,pos=[x, y, z],state=i+1)
         cmd.show("spheres",name)
   
   return
 
cmd.extend("com",com)

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

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

   atmass={'H':1.00800000000000, 'C':12.0110000000000, \
              'N':14.0070000000000, 'O':15.9994000000000, \
              'P':30.9740000000000, 'S':32.0600000000000, \
              'F':18.9980000000000
           }
   
   totmass=0.0
   if (mass!=None):
      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):
         if (a.name[0] in atmass):
            x+= a.coord[0]*atmass[a.name[0]]
            y+= a.coord[1]*atmass[a.name[0]]
            z+= a.coord[2]*atmass[a.name[0]]
            totmass+=atmass[a.name[0]]
         else:
            print "Please add atomic mass for "+a.name+" to atmass"
            return
      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)

Previous Implementation

Here is a script that calculates the center of geometry from a selection. It gets hold of the coordinates with cmd.get_model. Make sure the atoms in the selection are of equal weight.

For a sample application, see: "Convergent Evolution Examples"

## Author: Andreas Henschel 2006

from pymol import cmd
from pymol.cgo import *

def centerOfMass(selection):
   ## assumes equal weights (best called with "and name ca" suffix)
   model = cmd.get_model(selection)
   x,y,z=0,0,0
   for a in model.atom:
       x+= a.coord[0]
       y+= a.coord[1]
       z+= a.coord[2]
   return (x/len(model.atom), y/len(model.atom), z/len(model.atom))

cmd.load("/group/bioinf/Data/PDBLinks/1c7c.pdb")
cmd.select("domain", "/1c7c//A/143-283/ and name ca") ## selecting a domain

domainCenter=centerOfMass("domain")

print "Center of mass: (%.1f,%.1f,%.1f)"% domainCenter
cmd.as("cartoon", "all")
cmd.show("spheres", "domain")

## Creating a sphere CGO
com = [COLOR, 1.0, 1.0, 1.0, SPHERE]+list(domainCenter) + [3.0] ## white sphere with 3A radius
cmd.load_cgo(com, "CoM")

cmd.zoom("1c7c", 1.0)
cmd.center("domain")

#ah@bioinfws19:~/Projects/PyMOL$ pymol -qc centerOfMass4.py
#Center of mass: (-1.0,24.5,48.2)
#ah@bioinfws19:~/Projects/PyMOL$