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Difference between revisions of "Iterate State"

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(space argument)
 
(ARGUMENTS)
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===USAGE===
 
===USAGE===
iterate_state state,(selection),expression
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iterate_state state, (selection), expression
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=== ARGUMENTS ===
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* state = integer: state-index if positive number or any of these:
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** state = 0: all states
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** state = -1: current state
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* selection = string: atom selection
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* expression = string: expression in valid [http://en.wikipedia.org/wiki/Python_syntax_and_semantics python syntax]
  
 
===EXAMPLES===
 
===EXAMPLES===

Revision as of 11:09, 5 July 2011

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

ARGUMENTS

  • state = integer: state-index if positive number or any of these:
    • state = 0: all states
    • state = -1: current state
  • selection = string: atom selection
  • expression = string: expression in valid python syntax

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

# either with global stored object
from pymol import stored
stored.pos = []
cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))')

# or with local object, passed with space argument
pos = []
cmd.iterate_state(1, 'all', 'pos.append((x,y,z))', space={'pos': pos})

SEE ALSO

iterate, alter, Alter_State