SampleSequenceFromProbabilities

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SampleSequenceFromProbabilities

General description

Sample whole sequences or a specified number of mutations from a PerResidueProbabilitiesMetric and thread them onto the pose.

Autogenerated Tag Syntax Documentation:

A class to sample sequences from a PerResidueProbabilitiesMetric and thread them onto the pose.

References and author information for the SampleSequenceFromProbabilities mover:

SampleSequenceFromProbabilities Mover's author(s): Moritz Ertelt, University of Leipzig moritz.ertelt@gmail.com

<SampleSequenceFromProbabilities name="(&string;)" metric="(&string;)"
        pos_temp="(1 &real;)" aa_temp="(1 &real;)" prob_cutoff="(0.0001 &real;)"
        delta_prob_cutoff="(0 &real;)"
        max_mutations="(10000 &non_negative_integer;)" packing="(true &bool;)"
        use_cached_data="(false &bool;)" cache_prefix="(&string;)"
        cache_suffix="(&string;)" fail_on_missing_cache="(true &bool;)"
        task_operations="(&task_operation_comma_separated_list;)"
        packer_palette="(&named_packer_palette;)" />

metric: (REQUIRED) A PerResidueProbabilitiesMetric to calculate the pseudo-perplexity from.
pos_temp: Sampling temperature for choosing positions. T greater 1 is more deterministic, T smaller 1 increases diversity. Defaults to 1
aa_temp: Sampling temperature for choosing amino acids. T greater 1 is more deterministic, T smaller 1 increases diversity. Defaults to 1
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 (at least as likely as the current)
max_mutations: The maximal amount of mutations allowed. Defaults to basically unlimited (10000)
packing: Whether to do any packing at all, if set to false results in basic rotamers. You might want to set this to false if you e.g. relax after this mover anyways. (Default true)
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?
task_operations: A comma-separated list of TaskOperations to use.
packer_palette: A previously-defined PackerPalette to use, which specifies the set of residue types with which to design (to be pruned with TaskOperations).

Example

In this example, we sample ten mutations from ESM predicted probabilities, where each mutation needs have at least a probability of 0.0001 and a delta probability to current of 0.0 (meaning at least as likely as the current amino acid at a particular position). There is a temperature option for both the choice of position and amino acids, where T<1 leads to more deterministic behavior and T>1 to more diversity. We also restrict the choice of mutations with a resfile specifying packing behavior of residues and/or amino acids.

<ROSETTASCRIPTS>
    <TASKOPERATIONS>
        <ReadResfile name="rrf" filename="./resfile.resfile"/>
    </TASKOPERATIONS>
    <RESIDUE_SELECTORS>
        <Chain name="res" chains="A" />
    </RESIDUE_SELECTORS>
    <SIMPLE_METRICS>
        ----------------- Define model to use for prediction -----------------------------
        <PerResidueEsmProbabilitiesMetric name="esm" residue_selector="res" model="esm2_t30_150M_UR50D" write_pssm="" multirun="true"/>
    </SIMPLE_METRICS>
    <FILTERS>
    </FILTERS>
    <MOVERS>
        ----------------------- Sample mutations ------------------------------------------
        <SampleSequenceFromProbabilities name="sample" metric="esm" pos_temp="1.0" aa_temp="1.0" prob_cutoff="0.0001" delta_prob_cutoff="0.0" max_mutations="10" task_operations="rrf" use_cached_data="true"/>
        <RunSimpleMetrics name="run" metrics="esm"/>
    </MOVERS>
    <PROTOCOLS>
        <Add mover_name="run"/>
        <Add mover_name="sample"/>
    </PROTOCOLS>
</ROSETTASCRIPTS>

Reference

This is currently unpublished.

SampleSequenceFromProbabilities