Center of mass: Difference between revisions

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Here is a script that calculates the center of mass from a selection.  
{{Infobox script-repo
It gets hold of the coordinates with cmd.get_model.
|type      = script
Make sure the atoms in the selection are of equal weight.
|filename  = center_of_mass.py
|author    = [[User:Henschel|Henschel]]
|license  =
}}


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"]
===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===


<source lang="python">
<source lang="python">
## Author: Andreas Henschel 2006
com selection [,state=None [,mass=None [,object=None]]]
</source>
 
 
===Examples===


from pymol import cmd
<source lang="python">
from pymol.cgo import *
import center_of_mass
fetch 1c3y, finish=1, multiplex=0


def centerOfMass(selection):
com 1c3y, state=1
  ## assumes equal weights (best called with "and name ca" suffix)
#Create a pseudoatom representing the 1c3y COG and store it as "1c3y_COM"
  model = cmd.get_model(selection)
#The "1c3y_COM" object will contain 1 state only
  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")
com 1c3y, state=1, object=COG
cmd.select("domain", "/1c7c//A/143-283/ and name ca") ## selecting a domain
#Create a pseudoatom representing the 1c3y COG and store it as "COG"
#The "COG" object will contain 1 state only


domainCenter=centerOfMass("domain")
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


print "Center of mass: (%.1f,%.1f,%.1f)"% domainCenter
com 1c3y, object=COM, mass=1
cmd.as("cartoon", "all")
#Create a single pseudoatom containing the COM for each state found in 1c3y and store it as "COM"
cmd.show("spheres", "domain")
#The "COM" object will contain MULTIPLE states!
</source>


## Creating a sphere CGO
=== See Also ===
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)
* [[centerofmass]] (new command in PyMOL 1.7.2)
cmd.center("domain")
* [[COM]]
* [[get_extent]]
* [[get_position]]


#ah@bioinfws19:~/Projects/PyMOL$ pymol -qc centerOfMass4.py
[[Category:Script_Library|Center of Mass]]
#Center of mass: (-1.0,24.5,48.2)
[[Category:Math_Scripts]]
#ah@bioinfws19:~/Projects/PyMOL$
[[Category:Pymol-script-repo]]
</source>

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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