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===DESCRIPTION=== | ===DESCRIPTION=== | ||
| + | '''iterate''' iterates over an expression with a separate name space for each atom. However, unlike the "alter" command, atomic properties can not be altered. Thus, '''iterate''' is more efficient than '''alter'''. | ||
| − | + | It can be used to perform operations and aggregations using atomic selections, and store the results in any global object, such as the predefined '''stored''' object. | |
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| + | The local namespace for "iterate" contains the following names: | ||
| + | *name | ||
| + | *resn | ||
| + | *resi | ||
| + | *chain | ||
| + | *alt | ||
| + | *elem | ||
| + | *q | ||
| + | *b | ||
| + | *segi | ||
| + | *type (ATOM,HETATM) | ||
| + | *formal_charge | ||
| + | *partial_charge | ||
| + | *numeric_type | ||
| + | *text_type | ||
| + | *ID | ||
| + | *vdw | ||
| + | |||
| + | All strings in the expression must be explicitly quoted. This operation typically takes a second per thousand atoms. | ||
| + | |||
| + | ===USAGE=== | ||
| + | iterate (selection),expression | ||
| + | |||
===EXAMPLES=== | ===EXAMPLES=== | ||
| − | + | *The following example calculates the net charge on an object. | |
| − | + | <source lang="python"> | |
| − | + | stored.net_charge = 0 | |
| − | + | iterate (all),stored.net_charge = stored.net_charge + partial_charge | |
| − | + | </source> | |
| − | + | ||
| − | + | ||
| + | *The following example fills an array, '''stored.names''' with the names of all the residues. | ||
| + | <source lang="python"> | ||
| + | stored.names = [] | ||
| + | iterate (all),stored.names.append(name) | ||
| + | </source> | ||
| + | |||
| + | |||
| + | *The following prints the b-factors for all atoms around residue #1. | ||
| + | <source lang="python"> | ||
| + | iterate resi 1, print round(b,2) | ||
| + | </source> | ||
| + | |||
===SEE ALSO=== | ===SEE ALSO=== | ||
| − | + | [[Cmd iterate_state]], [[Cmd alter]], [[Cmd alter_state]] | |
| − | |||
[[Category:Commands|iterate]] | [[Category:Commands|iterate]] | ||
Revision as of 08:49, 16 January 2007
DESCRIPTION
iterate iterates over an expression with a separate name space for each atom. However, unlike the "alter" command, atomic properties can not be altered. Thus, iterate is more efficient than alter.
It can be used to perform operations and aggregations using atomic selections, and store the results in any global object, such as the predefined stored object.
The local namespace for "iterate" contains the following names:
- name
- resn
- resi
- chain
- alt
- elem
- q
- b
- segi
- type (ATOM,HETATM)
- formal_charge
- partial_charge
- numeric_type
- text_type
- ID
- vdw
All strings in the expression must be explicitly quoted. This operation typically takes a second per thousand atoms.
USAGE
iterate (selection),expression
EXAMPLES
- The following example calculates the net charge on an object.
stored.net_charge = 0
iterate (all),stored.net_charge = stored.net_charge + partial_charge
- The following example fills an array, stored.names with the names of all the residues.
stored.names = []
iterate (all),stored.names.append(name)
- The following prints the b-factors for all atoms around residue #1.
iterate resi 1, print round(b,2)