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Difference between revisions of "Iterate State"

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===SEE ALSO===
 
===SEE ALSO===
[[Cmd iterate]], [[Cmd alter]], [[Cmd alter_state]]
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[[iterate]], [[alter]], [[Alter_State]]
  
[[Category:Commands|iterate_state]]
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[[Category:Commands|Iterate State]]
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[[Category:States|Iterate State]]

Revision as of 14:09, 20 June 2009

DESCRIPTION

Iterate state can be used to extract position data from an object or selection. The expression can use the variables x, y, and z which are the position of the current atom. One common usage is to extract the positions as a python list to alter then write back to the molecule using alter_state.

USAGE

iterate_state state,(selection),expression

EXAMPLES

From PyMOL command line

To get the sum of x coordinates:

stored.sum_x = 0.0
iterate_state 1,(all),stored.sum_x = stored.sum_x + x

To get a list of the positions in a selection

stored.pos = []
iterate_state 1, (all), stored.pos.append((x,y,z))

From Python

To get a list of positions (import stored first)

from pymol import stored

stored.pos = []
cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))')

SEE ALSO

iterate, alter, Alter_State