SequenceRecovery

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SequenceRecovery

Calculates the fraction sequence recovery of a pose compared to a reference pose. This is similar to the InterfaceRecapitulationMover mover, but does not require a design mover. Instead, the user can provide a list of task operations that describe which residues are designable in the pose. Works with symmetric poses and poses with symmetric "building blocks". Can also filter based on/report to the scorefile the number of mutations rather than the recovery rate if desired by using the report_mutations and mutation_threshold options. Will output the specific mutations to the tracer if the option verbose=1. The reference pose against which the recovery rate will be computed can be defined using the -in:file:native command-line flag. If that flag is not defined, the starting pose will be used as a reference.

<SequenceRecovery name="(&string)" rate_threshold="(0.0 &Real)" task_operations="(comma-delimited list of operations &string)" mutation_threshold="(100 &Size)" report_mutations="(0 &bool)" scorefxn="('talaris2013' &string)" verbose="(0 &bool)" />

rate_threshold: Lower cutoff for the acceptable recovery rate for a passing design. Will fail if actual rate is below this threshold.
task_operations: Define the designable residues.
scorefxn: Define the score function used to score the mutations listed in the reports.
mutation_threshold: Upper cutoff for the number of mutations for an acceptable design. Only matters if report_mutations is set to true.
report_mutations: Defaults to false. If set to true, then will act as a filter for the number of mutations rather than the rate.
verbose: Defaults to false. If set to true, then will output the mutated positions and identities to the tracer.

SequenceRecovery

SequenceRecovery

See also