RestrictAAsFromProbabilities

Back to TaskOperations page.

TaskOperation to restrict designable amino acids depending on the probabilities from a PerResidueProbabilitiesMetric. Does not modify which positions are designable.

Autogenerated Tag Syntax Documentation:

A TaskOperation to restrict designable amino acids depending on the probabilities from a PerResidueProbabilitiesMetric

<RestrictAAsFromProbabilities name="(&string;)" metric="(&string;)"
        prob_cutoff="(0.0001 &real;)" delta_prob_cutoff="(0 &real;)"
        use_cached_data="(false &bool;)" cache_prefix="(&string;)"
        cache_suffix="(&string;)" fail_on_missing_cache="(true &bool;)" />

metric: (REQUIRED) A PerResidueProbabilitiesMetric to restrict amino acid identities from.
prob_cutoff: Probability cutoff for amino acids to consider for sampling. Defaults to 0.0001
delta_prob_cutoff: Delta probability (current-proposed) cutoff for amino acids to consider for sampling. Defaults to 0 (as likely as the current)
use_cached_data: Use any data stored in the datacache that matches the set metrics name (and any prefix/suffix.) Data is stored during a SimpleMetric's apply function, which is called during RunSimpleMetrics
cache_prefix: Any prefix used during apply (RunSimpleMetrics), that we will match on if use_cache is true
cache_suffix: Any suffix used during apply (RunSimpleMetrics), that we will match on if use_cache is true
fail_on_missing_cache: If use_cached_data is True and cache is not found, should we fail?

Example

Load probabilities from a weights file and restrict to amino acids that have at least a probability of 0.0001 and a delta probability of 0 (meaning at least as likely as the current amino acid at that position).

<ROSETTASCRIPTS>
    <RESIDUE_SELECTORS>
    </RESIDUE_SELECTORS>
    <SIMPLE_METRICS>
        <LoadedProbabilitiesMetric name="loaded_probs" filename="probs.weights"/>
    </SIMPLE_METRICS>
    <TASKOPERATIONS>
        <RestrictAAsFromProbabilities name="restrict_to_probs" metric="loaded_probs" prob_cutoff="0.0001" delta_prob_cutoff="0.0" use_cached_data="true"/>
    </TASKOPERATIONS>
    <FILTERS>
    </FILTERS>
    <MOVERS>
        <PackRotamersMover name="design" scorefxn="beta" task_operations="restrict_to_probs" />
    </MOVERS>
    <PROTOCOLS>
        <Add mover_name="load"/>
        <Add mover_name="design"/>
    </PROTOCOLS>
</ROSETTASCRIPTS>

RestrictAAsFromProbabilities

Example

See Also