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SequenceMetric

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com)

Modified 20 December 2018 by Vikram K. Mulligan (vmulligan@flatironinstitute.org) to add more output options.

Autogenerated Tag Syntax Documentation:


Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) A metric for measuring ... and adding it to the resulting score file.

<SequenceMetric name="(&string;)" custom_type="(&string;)"
        three_letter="(false &bool;)"
        output_mode="(oneletter &SequenceMetric_output_modes;)"
        residue_selector="(&string;)" />
  • custom_type: Allows multiple configured SimpleMetrics of a single type to be called in a single RunSimpleMetrics and SimpleMetricFeatures. The custom_type name will be added to the data tag in the scorefile or features database.
  • three_letter: DEPRECATED. Use of this option will trigger a runtime error. Use the output_mode option instead.
  • output_mode: The format for the sequence. Allowed output formats are: oneletter, threeletter, basename, or fullname.
  • residue_selector: Output the sequence of only the selected residues. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.

Note that the three_letter option has been deprecated in favour of the output_mode option, which provides the options "oneletter", "threeletter", "basename", or "fullname". Examples of each are given below. Note that the distinctions are particularly important for noncanonicals: some noncanonicals, such as ornithine, don't have a separate three-letter code for the D-equivalent.

Output type Example
oneletter RSTLNEXXYYS
threeletter ARG,SER,THR,LEU,ASN,GLU,ORN,ORN,DTY,TYR,DSE
basename ARG,SER,THR,LEU,ASN,GLU,ORN,DORN,DTYR,TYR,DSER
fullname ARG:NtermProteinFull,SER,THR,LEU,ASN,GLU,ORN,DORN,DTYR,TYR,DSER:CtermProteinFull

See Also