Getting Started

Build Documentation

Rosetta Basics

Application Documentation

Scripting Interfaces

Development Documentation

Internal Documentation

How to Write Documentation

FAQ

Glossary

Options list

Back to Mover page.

ParsedProtocol (formerly DockDesign)

Autogenerated Tag Syntax Documentation:

This is a special mover that allows making a single compound mover and filter vector (just like protocols). The optional option mode changes the order of operations within the protocol, as defined by the option. If undefined, mode defaults to the historical functionality, which is operation of the Mover/Filter pairs in the defined order.

<ParsedProtocol name="(&string;)" mode="(sequence &mode_types;)"
        filter_name="(true_filter &string;)" filter="(true_filter &string;)"
        apply_probability="(&real;)" resume_support="(false &bool;)" >
    <Add mover_name="(&string;)" mover="(&string;)" filter_name="(&string;)"
            filter="(&string;)" metrics="(&string;)" labels="(&string;)"
            apply_probability="(&real;)" report_at_end="(true &bool;)"
            never_rerun_filter="(false &bool;)" />
    <Filter Tag ... />
    <Mover Tag ... />
</ParsedProtocol>
  • mode: "sequence" (default) - perform the Mover/Filter pair in the specified sequence; "random_order" - perform EACH of the defined Mover/Filter pairs one time in a random order; "single_random" - randomly pick a SINGLE Mover/Filter pair from the list
  • filter_name: XSD XRW: TO DO
  • filter: XSD XRW: TO DO
  • apply_probability: by default equal probability for all tags
  • resume_support: XSD XRW: TO DO

Subtag Add: The steps to be applied.

  • mover_name: The mover whose execution is desired
  • mover: The mover whose execution is desired
  • filter_name: The filter whose execution is desired
  • filter: The filter whose execution is desired
  • metrics: A comma-separated list of metrics to run at this point.
  • labels: A comma-separated list of labels to use for the provided metrics in the output. If empty/missing, use the metric names from the metrics setting. If '-', use the metric's default.
  • apply_probability: by default equal probability for all tags
  • report_at_end: Report filter value via filter re-evaluation on final pose after conclusion of protocol. Otherwise report filter value as evaluated mid-protocol.
  • never_rerun_filter: Never run this filter after the original apply-time run. Use this option to avoid expensive re-runs when reporting

"Filter Tag": Any of the RosettaScripts Filters tags

"Mover Tag": Any of the RosettaScripts Mover tags

  • apply_probabilities: This only works in mode single_random. You can set the probability that an individual submover will be called 0-1. The probabilities must sum to 1.0, or you'll get an error message. Notice that this is used by GenericMonteCarlo in its adaptive_movers mode to adjust the probabilities of movers dynamically during a sampling trajectory.

See Also