Center of mass: Difference between revisions
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(catch get_unused_name error for backwards compatibility; Remove redundant previous implementation) |
(see also centerofmass) |
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{{Infobox script-repo | |||
|type = script | |||
|filename = center_of_mass.py | |||
|author = [[User:Henschel|Henschel]] | |||
|license = | |||
}} | |||
===Description=== | ===Description=== | ||
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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 | ||
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#Create a single pseudoatom containing the COM for each state found in 1c3y and store it as "COM" | #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! | #The "COM" object will contain MULTIPLE states! | ||
</source> | </source> | ||
=== See Also === | === See Also === | ||
* [[centerofmass]] (new command in PyMOL 1.7.2) | |||
* [[COM]] | * [[COM]] | ||
* [[get_extent]] | * [[get_extent]] | ||
| Line 125: | Line 49: | ||
[[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
- centerofmass (new command in PyMOL 1.7.2)
- COM
- get_extent
- get_position