Difference between revisions of "Iterate State"
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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 08:39, 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))')