Iterate: Difference between revisions
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'''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'''. | '''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'''. | ||
Iterate is a powerful toold that 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. For example, one could iterate over all of the alpha carbons and record their B Factors, or print out all of the secondary structure classifications of all the residues. | |||
The | The '''iterate''' command only has access to certain properties. Those properties are: | ||
*name | *'''name''': the atom name | ||
*resn | *'''resn''': the residue name | ||
*resi | *'''resi''': the residue identifier (residue number) | ||
*chain | *'''chain''': the chain name | ||
*alt | *'''alt''': | ||
*elem | *'''elem''': the chemical element | ||
*q | *'''q''' | ||
*b | *'''b''': the B Factor | ||
*segi | *'''segi''': | ||
*type (ATOM,HETATM) | *'''type''' (ATOM,HETATM): the atom type | ||
*formal_charge | *'''formal_charge''': the formal charge of the atom | ||
*partial_charge | *'''partial_charge''': the partial charger of the ato | ||
*numeric_type | *'''numeric_type''' | ||
*text_type | *'''text_type ''' | ||
*ID | *'''ID''' | ||
*vdw | *'''vdw''' | ||
All strings in the expression must be explicitly quoted. This operation typically takes a second per thousand atoms. | All strings in the expression must be explicitly quoted. This operation typically takes a second per thousand atoms. | ||
Revision as of 16:16, 18 February 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.
Iterate is a powerful toold that 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. For example, one could iterate over all of the alpha carbons and record their B Factors, or print out all of the secondary structure classifications of all the residues.
The iterate command only has access to certain properties. Those properties are:
- name: the atom name
- resn: the residue name
- resi: the residue identifier (residue number)
- chain: the chain name
- alt:
- elem: the chemical element
- q
- b: the B Factor
- segi:
- type (ATOM,HETATM): the atom type
- formal_charge: the formal charge of the atom
- partial_charge: the partial charger of the ato
- 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)