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ResidueSummaryMetric

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com)

The ResidueSummaryMetric takes a PerResidueRealMetric and summarizes the data in various ways, such as the mean, sum, or the number of residues above, below, or equal to a certain value. This Metric is itself a RealMetric and can be used as such in filters, features reporters, etc.

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Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) A SimpleMetric that takes a PerResidueRealMetric and calculates different summaries of the overall data. This metric can calculate means, totals, or the number of residues (n_res) matching certain criteria. Useful for summarizing metrics or using more complex functionality in the SimpleMetricFilter

Be sure to set a custom_type to label the summary type in which you are calculating!.

<ResidueSummaryMetric name="(&string;)" custom_type="(&string;)"
        epsilon="(.0001 &real;)" metric="(&string;)"
        action="(mean &summary_types;)" action_value="(&real;)"
        use_cached_data="(false &bool;)" cache_prefix="(&string;)"
        cache_suffix="(&string;)" fail_on_missing_cache="(true &bool;)" />
  • 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.
  • epsilon: Significant digits used for equal operators

    IE: The absolute value of the difference between two numbers, below which they will be considered to be equal. Used when comparing numbers if action = n_res_eq or n_res_ne.

  • metric: The PerResidueRealMetric that we will summarize
  • action: Summary type that this metric should calculate. Current choices are: [mean, n_res_eq, n_res_gt, n_res_gt_or_eq, n_res_lt, n_res_lt_or_eq, n_res_ne, sum]
  • action_value: Number to use for any summary metrics that calculate N residues based on a value.
  • 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?

See Also