Center of mass: Difference between revisions

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{{Infobox script-repo
|type      = script
|filename  = center_of_mass.py
|author    = [[User:Henschel|Henschel]]
|license  =
}}
===Description===
===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.
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.
Note: In order to use the [[Pseudoatom]] in your measurements (i.e. distance), you need to invoke the distance calculation directly via the command line using the [[Distance]] function and not via the Wizard!


===Usage===
===Usage===
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<source lang="python">
<source lang="python">
import center_of_mass
fetch 1c3y, finish=1, multiplex=0
fetch 1c3y, finish=1, multiplex=0


Line 34: Line 40:
</source>
</source>


===PyMOL API===
=== See Also ===
 
<source lang="python">
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):
      object = cmd.get_legal_name(selection)
      object = cmd.get_unused_name(object + "_COM", 0)
  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)
* [[centerofmass]] (new command in PyMOL 1.7.2)
 
* [[COM]]
def get_com(selection,state=1,mass=None, quiet=1):
* [[get_extent]]
  """
* [[get_position]]
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
</source>
 
 
 
===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: [http://yggdrasil.biotec.tu-dresden.de/abac/b.47.1.2___b.16.1.1___g.4.1.1.html "Convergent Evolution Examples"]
 
<source lang="python">
## 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$
</source>


[[Category:Script_Library|Center of Mass]]
[[Category:Script_Library|Center of Mass]]
[[Category:Math_Scripts]]
[[Category:Math_Scripts]]
[[Category:Pymol-script-repo]]

Latest revision as of 14:53, 12 October 2016

Type Python Script
Download center_of_mass.py
Author(s) Henschel
License
This code has been put under version control in the project Pymol-script-repo

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

import center_of_mass
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!

See Also

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