Add documentation for EnsembleMetrics

scripting_documentation/RosettaScripts/EnsembleMetrics/ensemble_metric_pages/CentralTendency.md

@@ -0,0 +1,40 @@
+# CentralTendency Ensemble Metric
+*Back to [[SimpleMetrics]] page.*
+## CentralTendency Ensemble Metric
+
+[[_TOC_]]
+
+### Description
+
+The Central Tendency metric accepts as input a real-valued [[SimpleMetric|SimpleMetrics]].  It then applies it to each pose in an ensemble, collecting a series of values.  At reporting time, the metric computes measures of central tendency (mean, median, and mode), plus other descriptive statistics about the distribution of the measured value over the ensemble (standard deviation, standard error, min, max, range).
+
+### Author and history
+
+Created Tuesday, 8 February 2022 by Vikram K. Mulligan, Center for Computational Biology, Flatiron Institute ([email protected]).  This was the first [[EnsembleMetric|EnsembleMetrics]] implemented
+
+### Interface
+
+[[include:ensemble_metric_CentralTendency_type]]
+
+### Named values produced
+
+Measure | Name (used for the [[EnsembleFilter]]) | Description
+--------|----------------------------------------|------------
+Mean    | mean | The average of the values measured for the poses in the ensemble.
+Median  | median | When values measured from all of hte poses in the ensemble are listed in increasing order, this is the middle value.  If the number of poses in the ensemble is even, the middle two values are averaged.
+Mode    | mode | The most frequently seen value in the values measured from the poses in the environment.  If more than one value appears with equal frequency and this frequency is highest, the values are averaged.
+Standard Deviation    | stddev | Estimate of the standard deviation of the mean, defined as the sqrt( sum_i( S_i - mean )^2 / N ), where S_i is the ith sample, mean is the average of all the samples, and N is the number of samples.
+Standard Error    | stderr | Estimate of the standard error of the mean, defined by stddev / sqrt(N), where N is the number of samples.
+Min | min | The minimum value seen.
+Max | max | The maximum value seen.
+Range | range | the largest value seen minus the smallest.
+
+#### Note about mode
+
+The mode of a set of floating-point numbers can be thrown off by floating-point error.  For instance, two poses may have energies of -3.7641 kJ/mol, but the process of computing that energy may result in slightly different values at the 15th decimal point.  This could prevent the filter from recognizing this is at the most frequent value.  Mode is most useful as a metric when the "floating-point" values are actually integers (for instance, given a [[SimpleMetric|SimpleMetrics]] like the [[SelectedResidueCountMetric]], which returns integer counts).
+
+##See Also
+
+* [[SimpleMetrics]]: Available SimpleMetrics.
+* [[EnsembleMetrics]]: Available EnsembleMetrics.
+* [[I want to do x]]: Guide to choosing a tool in Rosetta.

scripting_documentation/RosettaScripts/FeaturesReporter/_Sidebar.md

@@ -20,6 +20,8 @@
 
    * [[Simple Metrics | SimpleMetrics]]
 
+   * [[Ensemble Metrics|EnsembleMetrics]]
+
    * [[Filters|Filters-RosettaScripts]]
 
    * [[FeaturesReporters|Features-reporter-overview]]

scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/_Sidebar.md

@@ -14,6 +14,10 @@
 
    * [[Filters|Filters-RosettaScripts]]
 
+   * [[Simple Metrics|SimpleMetrics]]
+
+   * [[Ensemble Metrics|EnsembleMetrics]]
+
    * [[Residue Selectors|ResidueSelectors]]
 
    * [[PackerPalettes|PackerPalette]]

scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/_Sidebar.md

@@ -14,6 +14,10 @@
 
    * [[Residue Selectors|ResidueSelectors]]
 
+   * [[Simple Metrics|SimpleMetrics]]
+
+   * [[Ensemble Metrics|EnsembleMetrics]]
+
    * [[PackerPalettes|PackerPalette]]
 
    * [[Filters|Filters-RosettaScripts]]

scripting_documentation/RosettaScripts/Filters/Filters-RosettaScripts.md

@@ -37,6 +37,7 @@ Filter  | Description
 **[[CompoundStatement|CompoundStatementFilter]]** | Uses previously defined filters with logical operations to construct a compound filter.
 **[[CombinedValue|CombinedValueFilter]]** | Weighted sum of multiple filters.
 **[[CalculatorFilter]]** | Combine multiple filters with a mathematical expression.
+**[[EnsembleFilter]]** | Filter based, not on a property of a single pose, but on a property of an _ensemble_ of many poses.
 **[[ReplicateFilter]]** | Repeat a filter multiple times and average.
 **[[Boltzmann|BoltzmannFilter]]** | Boltzmann weighted sum of positive/negative filters.
 **[[MoveBeforeFilter]]** | Apply a mover before applying the filter.

scripting_documentation/RosettaScripts/Filters/_Sidebar.md

@@ -20,6 +20,8 @@
 
    * [[Simple Metrics | SimpleMetrics]]
 
+   * [[Ensemble Metrics | EnsembleMetrics]]
+
    * [[Filters|Filters-RosettaScripts]]
 
    * [[FeaturesReporters|Features-reporter-overview]]

scripting_documentation/RosettaScripts/Filters/filter_pages/EnsembleFilter.md

@@ -0,0 +1,132 @@
+# EnsembleFilter
+*Back to [[SimpleMetrics]] page.*
+*Back to [[Filters | Filters-RosettaScripts]] page.*
+## EnsembleFilter
+
+Created by Vikram K. Mulligan ([email protected]) on 10 February 2022.
+
+[[_TOC_]]
+
+### Description
+
+This filter takes as input an [[EnsembleMetric|EnsembleMetrics]] that has been used to evaluate some set of properties of an ensemble of filters, retrives a named floating-point value from the metric, and filters based on whether that value is greater than, equal to, or less than some threshold.  (Note that [[EnsembleMetrics]] evaluate a property of a collection or _ensemble_ poses, not of a single pose.  This makes this filter unusual: where most discard a trajectory based on the state of a single pose, this can discard a trajectory based on the state of large ensemble of poses -- for example, based on many sampled conformatinos of a single design.)
+
+
+### Options
+
+[[include:filter_SimpleMetricFilter_type]]
+
+### Example: 
+
+In this example,  we load one or more cyclic peptides (provided with the `-in:file:s` or `-in:file:l` commandline options), generate a conformational ensemble of slightly perturbed conformations for each peptide _in memory_, without writing all structures to disk, and perform ensemble analysis on that ensemble with the [[CentralTendency EnsembleMetric|CentralTendency]], filtering on the results with the EnsembleFilter.  Only those peptides that have low-energy ensembles of perturbed conformations pass the filter.
+
+```xml
+<ROSETTASCRIPTS>
+	<!-- Example of using the EnsembleFilter to filter based on the properties of an ensemble of poses
+	generated from the current pose. -->
+	<SCOREFXNS>
+		<ScoreFunction name="r15" weights="ref2015.wts" />
+	</SCOREFXNS>
+	<MOVERS>
+		<!-- The movers that set up, perturb, and relax a cyclic peptide are set up here.  We
+			later bundle the perturbation protocol in a ParsedProtocol: -->
+		<DeclareBond name="connect_termini" res1="8" res2="1" atom1="C" atom2="N" add_termini="true" />
+		<GeneralizedKIC name="perturb1" selector_scorefunction="r15" closure_attempts="200"
+			stop_when_n_solutions_found="1" selector="lowest_rmsd_selector"
+		>
+			<AddResidue res_index="3"/>
+			<AddResidue res_index="4"/>
+			<AddResidue res_index="5"/>
+			<AddResidue res_index="6"/>
+			<AddResidue res_index="7"/>
+			<SetPivots res1="3" atom1="CA" res2="5" atom2="CA" res3="7" atom3="CA" />
+			<AddPerturber effect="perturb_dihedral" >
+				<AddAtoms res1="3" atom1="N" res2="3" atom2="CA" />
+				<AddAtoms res1="3" atom1="CA" res2="3" atom2="C" />
+				<AddAtoms res1="4" atom1="N" res2="4" atom2="CA" />
+				<AddAtoms res1="4" atom1="CA" res2="4" atom2="C" />
+				<AddAtoms res1="5" atom1="N" res2="5" atom2="CA" />
+				<AddAtoms res1="5" atom1="CA" res2="5" atom2="C" />
+				<AddAtoms res1="6" atom1="N" res2="6" atom2="CA" />
+				<AddAtoms res1="6" atom1="CA" res2="6" atom2="C" />
+				<AddAtoms res1="7" atom1="N" res2="7" atom2="CA" />
+				<AddAtoms res1="7" atom1="CA" res2="7" atom2="C" />
+				<AddValue value="5.0"/>
+			</AddPerturber>
+		</GeneralizedKIC>
+		<GeneralizedKIC name="perturb2" selector_scorefunction="r15" closure_attempts="200"
+			stop_when_n_solutions_found="1" selector="lowest_rmsd_selector"
+		>
+			<AddResidue res_index="7"/>
+			<AddResidue res_index="1"/>
+			<AddResidue res_index="2"/>
+			<AddResidue res_index="3"/>
+			<AddResidue res_index="4"/>
+			<SetPivots res1="7" atom1="CA" res2="2" atom2="CA" res3="4" atom3="CA"></SetPivots>
+			<AddPerturber effect="perturb_dihedral" >
+				<AddAtoms res1="7" atom1="N" res2="7" atom2="CA" />
+				<AddAtoms res1="7" atom1="CA" res2="7" atom2="C" />
+				<AddAtoms res1="1" atom1="N" res2="1" atom2="CA" />
+				<AddAtoms res1="1" atom1="CA" res2="1" atom2="C" />
+				<AddAtoms res1="2" atom1="N" res2="2" atom2="CA" />
+				<AddAtoms res1="2" atom1="CA" res2="2" atom2="C" />
+				<AddAtoms res1="3" atom1="N" res2="3" atom2="CA" />
+				<AddAtoms res1="3" atom1="CA" res2="3" atom2="C" />
+				<AddAtoms res1="4" atom1="N" res2="4" atom2="CA" />
+				<AdmoverdAtoms res1="4" atom1="CA" res2="4" atom2="C" />
+				<AddValue value="5.0"/>
+			</AddPerturber>
+		</GeneralizedKIC>
+		<FastRelax name="frlx" repeats="1" scorefxn="r15" />
+		<!-- Bundling the perturbation steps together so that they can be passed
+			to the CentralTendency EnsembleMetric: -->
+		<ParsedProtocol name="ensemble_generating_protocol" >
+			<Add mover="perturb1" />
+			<Add mover="perturb2" />
+			<Add mover="frlx" />
+		</ParsedProtocol>
+	</MOVERS>
+	<SIMPLE_METRICS>
+		<!-- The SimpleMetric that will be passed to the CentralTendency EnsembleMetric: --> 
+		<TotalEnergyMetric name="total_energy" scorefxn="r15" />
+	</SIMPLE_METRICS>
+	<ENSEMBLE_METRICS>
+		<!-- Setting up the EnsembleMetric with both a SimpleMetric and a
+			ParsedProtocol for generating the ensemble from a given pose: -->
+		<CentralTendency name="avg_energy" n_threads="0" real_valued_metric="total_energy"
+			output_mode="tracer_and_file" output_filename="report.txt"
+			ensemble_generating_protocol="ensemble_generating_protocol"
+			ensemble_generating_protocol_repeats="20"
+		/>
+	</ENSEMBLE_METRICS>
+	<FILTERS>
+		<!-- Set up the filter that can discard those peptides that yield an
+			ensemble with energy above a cutoff threshold: -->
+		<EnsembleFilter name="filter_on_avg_energy" ensemble_metric="avg_energy"
+			named_value="mean" filter_acceptance_mode="less_than_or_equal"
+			threshold="4.0"
+		/>
+	</FILTERS>
+	<PROTOCOLS>
+		<!-- Set up the peptide, but don't perturb it yet: -->
+		<Add mover="connect_termini" />
+		<!-- Accumulate data with the EnsembleMetric for every replicate of the
+			peturbation protocol (which in this case is run by the EnsembleMetric,
+			generating each member of the ensemble internally, in memory, without
+			exporting them): -->
+		<Add ensemble_metrics="avg_energy" />
+		<!-- Abandon the jobs that produce bad ensemble properties prior to
+			writing the structure back to disk: -->
+		<Add filter="filter_on_avg_energy" />
+	</PROTOCOLS>
+	<OUTPUT scorefxn="r15" />
+</ROSETTASCRIPTS>
+```
+
+### See also
+
+* [[EnsembleMetrics]]: Available SimpleMetrics
+* [[SimpleMetrics]]: Available SimpleMetrics
+* [[SimpleMetricFilter]]: Filter on an arbitrary SimpleMetric
+* [[Movers|Movers-RosettaScripts]]: Available Movers
+* [[I want to do x]]: Guide to choosing a Rosetta protocol.

scripting_documentation/RosettaScripts/Movers/_Sidebar.md

@@ -20,6 +20,8 @@
 
    * [[Simple Metrics | SimpleMetrics]]
 
+   * [[Ensemble Metrics|EnsembleMetrics]]
+
    * [[Filters|Filters-RosettaScripts]]
 
    * [[FeaturesReporters|Features-reporter-overview]]

scripting_documentation/RosettaScripts/RosettaScripts.md

@@ -19,6 +19,7 @@ Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, et al. (2011) Rosetta
 -   [[JumpSelectors |JumpSelectors]]
 -   [[PackerPalettes|PackerPalette]]
 -   [[SimpleMetrics]]
+-   [[EnsembleMetrics]]
 
 ---------------------
 

scripting_documentation/RosettaScripts/SimpleMetrics/_Sidebar.md

@@ -14,6 +14,10 @@
 
    * [[Residue Selectors|ResidueSelectors]]
 
+   * [[Simple Metrics|SimpleMetrics]]
+
+   * [[Ensemble Metrics|EnsembleMetrics]]
+
    * [[PackerPalettes|PackerPalette]]
 
    * [[Task Operations|TaskOperations-RosettaScripts]]

scripting_documentation/RosettaScripts/TaskOperations/_Sidebar.md

@@ -19,6 +19,8 @@
    * [[Task Operations|TaskOperations-RosettaScripts]]
 
    * [[Simple Metrics | SimpleMetrics]]
+
+   * [[Ensemble Metrics|EnsembleMetrics]]
 
    * [[Filters|Filters-RosettaScripts]]
 

scripting_documentation/RosettaScripts/_Sidebar.md

@@ -22,6 +22,8 @@
 
    * [[Simple Metrics | SimpleMetrics]]
 
+   * [[Ensemble Metrics|EnsembleMetrics]]
+
    * [[Filters|Filters-RosettaScripts]]
 
    * [[FeaturesReporters|Features-reporter-overview]]

scripting_documentation/RosettaScripts/composite_protocols/_Sidebar.md

@@ -20,6 +20,8 @@
 
    * [[Simple Metrics | SimpleMetrics]]
 
+   * [[Ensemble Metrics|EnsembleMetrics]]
+
    * [[Filters|Filters-RosettaScripts]]
 
    * [[Features Reporters|Features-reporter-overview]]

scripting_documentation/RosettaScripts/xsd/ensemble_metric_CentralTendency_type.md

@@ -0,0 +1,33 @@
+<!-- THIS IS AN AUTOGENERATED FILE: Don't edit it directly, instead change the schema definition in the code itself. -->
+
+_Autogenerated Tag Syntax Documentation:_
+
+---
+An ensemble metric that takes a real-valued simple metric, applies it to all poses in an ensemble, and calculates measures of central tendency (mean, median, mode) and other statistics about the distribution (standard deviation, standard error of the mean, min, max, range, etc.).  Values that this ensemble metric returns are referred to in scripts as: mean, median, mode, stddev, stderr, min, max, and range.
+
+References and author information for the CentralTendency ensemble metric:
+
+CentralTendencyEnsembleMetric SimpleMetric's author(s):
+Vikram K. Mulligan, Systems Biology group, Center for Computational Biology, Flatiron Institute [[email protected]]  (Created the ensemble metric framework and wote the CentralTendency ensemble metric.)
+
+```xml
+<CentralTendency name="(&string;)" label_prefix="(&string;)"
+        label_suffix="(&string;)" output_mode="(tracer &string;)"
+        output_filename="(&string;)" ensemble_generating_protocol="(&string;)"
+        ensemble_generating_protocol_repeats="(1 &non_negative_integer;)"
+        n_threads="(1 &non_negative_integer;)"
+        use_additional_output_from_last_mover="(false &bool;)"
+        real_valued_metric="(&string;)" />
+```
+
+-   **label_prefix**: If provided, this prefix is prepended to the label for this ensemble metric (with an underscore after the prefix and before the ensemble metric name).
+-   **label_suffix**: If provided, this suffix is appended to the label for this ensemble metric (with an underscore after the ensemble metric name and before the suffix).
+-   **output_mode**: The output mode for reports from this ensemble metric.  Default is 'tracer'.  Allowed modes are: 'tracer', 'tracer_and_file', or 'file'.
+-   **output_filename**: The file to which the ensemble metric report will be written if output mode is 'tracer_and_file' or 'file'.  Note that this filename will have the job name and number prepended so that each report is unique.
+-   **ensemble_generating_protocol**: An optional ParsedProtocol or other mover for generating an ensemble from the current pose.  This protocol will be applied repeatedly (ensemble_generating_protocol_repeats times) to generate the ensemble of structures.  Each generated pose will be measured by this metric, then discarded.  The ensemble properties are then reported.  If not provided, the current pose is measured and the report will be produced later (e.g. at termination with the JD2 rosetta_scripts application).
+-   **ensemble_generating_protocol_repeats**: The number of times that the ensemble_generating_protocol is applied.  This is the maximum number of structures in the ensemble (though the actual number may be smaller if the protocol contains filters or movers that can fail for some attempts).  Only used if an ensemble-generating protocol is provided with the ensemble_generating_protocol option.  Defaults to 1.
+-   **n_threads**: The number of threads to request for generating ensembles in parallel.  This is only used in multi-threaded compilations of Rosetta (compiled with extras=cxx11thread), and only when an ensemble-generating protocol is provided with the ensemble_generating_protocol option.  A value of 0 means to use all available threads.  In single-threaded builds, this must be set to 0 or 1.  Defaults to 1.  NOTE THAT MULTI-THREADING IS HIGHLY EXPERIMENTAL AND LIKELY TO FAIL FOR MANY ENSEMBLE-GENERATING PROTOCOLS.  When in doubt, leave this set to 1.
+-   **use_additional_output_from_last_mover**: If true, this ensemble metric will use the additional output from the previous pose (assuming the previous pose generates multiple outputs) as the ensemble, analysing it and producing a report immediately.  If false, then it will behave normally.  False by default.
+-   **real_valued_metric**: (REQUIRED) The name of a real-valued simple metric defined previously.  Required input.
+
+---

scripting_documentation/RosettaScripts/xsd/filter_EnsembleFilter_type.md

@@ -0,0 +1,26 @@
+<!-- THIS IS AN AUTOGENERATED FILE: Don't edit it directly, instead change the schema definition in the code itself. -->
+
+_Autogenerated Tag Syntax Documentation:_
+
+---
+A filter that filters based on some named float-valued property measured by an EnsembleMetric.  Note that the value produced by the EnsembleMetric is based on an ensemble generated earlier in the protocol, presumably from the pose on which we are currently filtering.
+
+References and author information for the EnsembleFilter filter:
+
+EnsembleFilter Filter's author(s):
+Vikram K. Mulligan, Systems Biology Group, Center for Computational Biology, Flatiron Institute. [[email protected]]  (Wrote the EnsembleFilter.)
+
+```xml
+<EnsembleFilter name="(&string;)" ensemble_metric="(&string;)"
+        named_value="(&string;)" threshold="(0.0 &real;)"
+        filter_acceptance_mode="(less_than_or_equal &string;)"
+        confidence="(1.0 &real;)" />
+```
+
+-   **ensemble_metric**: (REQUIRED) A previously-defined EnsembleMetric that produces at least one floating-point value.  This filter will filter a pose based on that value.
+-   **named_value**: (REQUIRED) A named floating-point value produced by the EnsembleMetric, on which this filter will filter.
+-   **threshold**: The threshold for rejecting a pose.
+-   **filter_acceptance_mode**: The criterion for ACCEPTING a pose.  For instance, if the value returned by the ensemble metric is greater than the threshold, and the mode is 'less_than_or_equal' (the default mode), then the pose is rejected.  Allowed modes are: 'greater_than', 'less_than', 'greater_than_or_equal', 'less_than_or_equal', 'equal', and 'not_equal'.
+-   **confidence**: Probability that the pose will be filtered out if it does not pass this Filter
+
+---

scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md

@@ -13,7 +13,7 @@ Filter based on any score that can be calculated in fragment_picker.
         outputs_name="(pose &string;)" csblast="(&string;)"
         blast_pgp="(&string;)" placeholder_seqs="(&string;)"
         sparks-x="(&string;)" sparks-x_query="(&string;)" psipred="(&string;)"
-        vall_path="(/scratch/benchmark/W.hojo-1/rosetta.Hojo-1/master/main/database//sampling/vall.jul19.2011.gz &string;)"
+        vall_path="(/home/vikram/rosetta_devcopy/Rosetta/main/database//sampling/vall.jul19.2011.gz &string;)"
         frags_scoring_config="(&string;)" n_frags="(200 &non_negative_integer;)"
         n_candidates="(1000 &non_negative_integer;)"
         print_to_pdb="(false &xs:boolean;)"