Back to SimpleMetrics page.

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:


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.

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