Difference between revisions of "Iterate State"

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(DESCRIPTION)
(Made this useful)
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===DESCRIPTION===
 
===DESCRIPTION===
'''iterate_state''' is to '''alter_state''' as '''iterate''' is to '''alter'''.
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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===
 
===USAGE===
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===EXAMPLES===
 
===EXAMPLES===
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==From PyMOL command line==
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To get the sum of x coordinates:
 
<source lang="python">
 
<source lang="python">
 
stored.sum_x = 0.0
 
stored.sum_x = 0.0
iterate 1,(all),stored.sum_x = stored.sum_x + x
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iterate_state 1,(all),stored.sum_x = stored.sum_x + x
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</source>
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To get a list of the positions in a selection
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<source lang="python">
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stored.pos = []
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iterate_state 1, (all), stored.pos.append((x,y,z))
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</source>
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==From Python==
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To get a list of positions
 +
<source lang="python">
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stored.pos = []
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cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))')
 
</source>
 
</source>
  

Revision as of 07:39, 6 July 2006

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

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

SEE ALSO

Cmd iterate, Cmd alter, Cmd alter_state