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Difference between revisions of "Center of mass"

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Here is a script that calculates the center of mass from a selection. It gets hold of the coordinates with cmd.get_model.
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{{Infobox script-repo
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Make sure the atoms in the selection are of equal weight.
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|type      = script
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|filename  = center_of_mass.py
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|author    = [[User:Henschel|Henschel]]
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|license  =
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}}
  
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===Description===
  
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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.
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===Usage===
  
 
<source lang="python">
 
<source lang="python">
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from pymol import cmd
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com selection [,state=None [,mass=None [,object=None]]]
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from pymol.cgo import *
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</source>
  
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def centerOfMass(selection):
 
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  ## assumes equal weights (best called with "and name ca" suffix)
 
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  model = cmd.get_model(selection)
 
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  x,y,z=0,0,0
 
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  for a in model.atom:
 
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      x+= a.coord[0]
 
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      y+= a.coord[1]
 
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      z+= a.coord[2]
 
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  return (x/len(model.atom), y/len(model.atom), z/len(model.atom))
 
  
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cmd.load("/group/bioinf/Data/PDBLinks/1c7c.pdb")
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===Examples===
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cmd.select("domain", "/1c7c//A/143-283/ and name ca") ## selecting a domain
 
  
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domainCenter=centerOfMass("domain")
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<source lang="python">
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import center_of_mass
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fetch 1c3y, finish=1, multiplex=0
  
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print "Center of mass: (%.1f,%.1f,%.1f)"% domainCenter
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com 1c3y, state=1
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cmd.as("cartoon", "all")
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#Create a pseudoatom representing the 1c3y COG and store it as "1c3y_COM"
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cmd.show("spheres", "domain")
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#The "1c3y_COM" object will contain 1 state only
  
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## Creating a sphere CGO
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com 1c3y, state=1, object=COG
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com = [COLOR, 1.0, 1.0, 1.0, SPHERE]+list(domainCenter) + [3.0] ## white sphere with 3A radius
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#Create a pseudoatom representing the 1c3y COG and store it as "COG"
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cmd.load_cgo(com, "CoM")
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#The "COG" object will contain 1 state only
  
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cmd.zoom("1c7c", 1.0)
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com 1c3y, state=1, object=COM, mass=1
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cmd.center("domain")
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#Create a pseudoatom representing the 1c3y COM and store it as "COM"
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#The "COM" object will contain 1 state only
  
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#ah@bioinfws19:~/Projects/PyMOL$ pymol -qc centerOfMass4.py
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com 1c3y, object=COM, mass=1
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#Center of mass: (-1.0,24.5,48.2)
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#Create a single pseudoatom containing the COM for each state found in 1c3y and store it as "COM"
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#ah@bioinfws19:~/Projects/PyMOL$
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#The "COM" object will contain MULTIPLE states!
 
</source>
 
</source>
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=== See Also ===
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* [[centerofmass]] (new command in PyMOL 1.7.2)
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* [[COM]]
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* [[get_extent]]
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* [[get_position]]
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[[Category:Script_Library|Center of Mass]]
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[[Category:Math_Scripts]]
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[[Category:Pymol-script-repo]]

Latest revision as of 00:06, 17 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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