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Difference between revisions of "Iterate State"
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| − | + | #REDIRECT [[iterate]] | |
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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. | 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=== | ||
| − | iterate_state state,(selection),expression | + | 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 [http://en.wikipedia.org/wiki/Python_syntax_and_semantics python syntax] | ||
| + | * space = dict: namespace dictionary (API only) {default: pymol namespace} | ||
| + | * atomic = 0/1: provide atomic properties as variables if 1, or only x/y/z if 0 (atomic=0 gives some speed improvement) {default: 1} | ||
===EXAMPLES=== | ===EXAMPLES=== | ||
| Line 18: | Line 29: | ||
</source> | </source> | ||
==From Python== | ==From Python== | ||
| − | To get a list of positions | + | To get a list of positions |
<source lang="python"> | <source lang="python"> | ||
| + | # either with global stored object | ||
from pymol import stored | from pymol import stored | ||
| − | |||
stored.pos = [] | stored.pos = [] | ||
cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))') | 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}) | ||
</source> | </source> | ||
Latest revision as of 07:02, 3 January 2016
Redirect to:
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
- space = dict: namespace dictionary (API only) {default: pymol namespace}
- atomic = 0/1: provide atomic properties as variables if 1, or only x/y/z if 0 (atomic=0 gives some speed improvement) {default: 1}
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})