Center of mass - Revision history

Cchem: 1 revision

2016-10-17T00:06:56Z

1 revision

2016-10-12T19:53:00Z

2014-03-28T01:43:00Z

18 revisions

2012-01-15T15:02:15Z

2011-12-11T21:32:14Z

2011-12-09T11:39:02Z

2011-12-09T11:38:32Z

2011-12-09T11:34:48Z

Examples

2011-08-15T09:10:03Z

catch get_unused_name error for backwards compatibility; Remove redundant previous implementation

2011-03-31T19:11:05Z

name -> object

@@ Line 42: / Line 42: @@
 === See Also ===
 * [[COM]]
 * [[get_extent]]

← Older revision		Revision as of 15:02, 15 January 2012
Line 48:		Line 48:
	[[Category:Script_Library\|Center of Mass]]		[[Category:Script_Library\|Center of Mass]]
	[[Category:Math_Scripts]]		[[Category:Math_Scripts]]
		+	[[Category:Pymol-script-repo]]

@@ Line 1: / Line 1: @@
 {{Infobox script-repo
-|type      = Python Module
+|type      = script
 |filename  = center_of_mass.py
 |author    = [[User:Henschel|Henschel]]

@@ Line 1: / Line 1: @@
 ===Description===
@@ Line 31: / Line 38: @@
 #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!
 </source>

← Older revision	Revision as of 00:06, 17 October 2016
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← Older revision	Revision as of 01:43, 28 March 2014
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← Older revision	Revision as of 11:39, 9 December 2011
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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.
 ===Usage===
@@ Line 55: / Line 53: @@
     quiet = int(quiet)
     if (object == None):
-       object = cmd.get_legal_name(selection)
+       try:
-      object = cmd.get_unused_name(object + "_COM", 0)
+         object = cmd.get_legal_name(selection)
     cmd.delete(object)
@@ Line 116: / Line 117: @@
 </source>
+* [[COM]]
-===Previous Implementation===
+* [[get_extent]]
+* [[get_position]]
 [[Category:Script_Library|Center of Mass]]
 [[Category:Math_Scripts]]

@@ Line 8: / Line 8: @@
 <source lang="python">
-com selection [,state=None [,mass=None [,name=None]]]
+com selection [,state=None [,mass=None [,object=None]]]
 </source>
@@ Line 21: / Line 21: @@
 #The "1c3y_COM" object will contain 1 state only
-com 1c3y, state=1, name=COG
+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, name=COM, mass=1
+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, name=COM, mass=1
+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!