Iterate State: Difference between revisions
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===DESCRIPTION=== | ===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=== | ===USAGE=== | ||
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===EXAMPLES=== | ===EXAMPLES=== | ||
==From PyMOL command line== | |||
To get the sum of x coordinates: | |||
<source lang="python"> | <source lang="python"> | ||
stored.sum_x = 0.0 | stored.sum_x = 0.0 | ||
iterate_state 1,(all),stored.sum_x = stored.sum_x + x | |||
</source> | |||
To get a list of the positions in a selection | |||
<source lang="python"> | |||
stored.pos = [] | |||
iterate_state 1, (all), stored.pos.append((x,y,z)) | |||
</source> | |||
==From Python== | |||
To get a list of positions | |||
<source lang="python"> | |||
stored.pos = [] | |||
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))')