Iterate

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)

SEE ALSO

Cmd iterate_state, Cmd alter, Cmd alter_state