diff --git a/images/ensemble_metrics/pareto_front/pareto_front.png b/images/ensemble_metrics/pareto_front/pareto_front.png new file mode 100644 index 000000000..185716265 Binary files /dev/null and b/images/ensemble_metrics/pareto_front/pareto_front.png differ diff --git a/scripting_documentation/RosettaScripts/EnsembleMetrics/EnsembleMetrics.md b/scripting_documentation/RosettaScripts/EnsembleMetrics/EnsembleMetrics.md new file mode 100644 index 000000000..6be54516c --- /dev/null +++ b/scripting_documentation/RosettaScripts/EnsembleMetrics/EnsembleMetrics.md @@ -0,0 +1,351 @@ +# EnsembleMetrics +*Back to main [[RosettaScripts|RosettaScripts]] page.* + +Page created Wed, 9 February 2022 by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org). + +[[_TOC_]] + +## 1. Description + +Just as [[SimpleMetrics]] measure some property of a pose, EnsembleMetrics measure some property of a group (or _ensemble_) of poses. They are designed to be used in two phases. In the _accumulation_ phase, an EnsembleMetric is applied to each pose in an ensemble in sequence, allowing it to store any relevant measurements from that pose that will later be needed to calculate properties of the ensemble. In the _reporting_ phase, the EnsembleMetric generates a report about the properties of the ensemble and writes this report to disk or to tracer. Following reporting, an EnsembleMetric may be _interrogated_ by such modules as the [[EnsembleFilter]], allowing retrieval of any floating-point values computed by the EnsembleMetric for filtering. Alternatively, the EnsembleMetric may be _reset_ for re-use (meaning that accumulated data, but not configuration settings, are wiped). + +##Available EnsembleMetrics + +EnsembleMetric | Description | MPI support? +-------------- | ----------- | ------------ +**[[CentralTendency]]** | Takes a [[real-valued SimpleMetric|SimpleMetrics]], applies it to each pose in an ensemble, and returns measures of central tendency (mean, median, mode) and other measures of the distribution (standard deviation, standard error, etc.). | YES +**[[ParetoFront]]** | Takes a set of [[real-valued SimpleMetrics|SimpleMetrics]], applies them to each pose in an ensemble, and returns a list of poses that are at the Pareto front, optimizing all of the properties measured by the [[SimpleMetrics]]. | YES + +## 2. Usage modes + +EnsembleMetrics have three intended usage modes in [[RosettaScripts]]: + +Mode | Setup | Accumulation Phase | Reporting Phase | Subsequent Interrogation | Subsequent Resetting +---- | ----- | ------------------ | --------------- | ------------------------ | -------------------- +Basic accumulator mode | Added to a protocol at point of accumulation. | The EnsembleMetric is applied to each pose that the RosettaScripts script handles, in sequence. | The EnsembleMetric produces its report at termination of the RosettaScripts application. This report covers all poses seen during this RosettaScripts run. | None. | None. +Internal generation mode | Provided with a ParsedProtocol for generating the ensemble of poses from the input pose, and a number to generate. Added to protocol at point where ensemble should be generated from pose at that point. | Accumulates information about each pose in the ensemble it generates. Poses are then discaded. | The report is provided immediately once the ensemble has been generated. The script then continues with the input pose. | After reporting. | On next nstruct (repeat) or next job. +Multiple pose mover mode | Set to use input from a mover that produces many outputs (a [[MultiplePoseMover]]). Placed in script after such a mover. | Collects data from each pose produced by previous mover. | Reports immediately after collecting data on all poses produced by previous mover. The script then continues on. | After reporting. | On next nstruct (repeat) or next job. + +### 2.1 Example of basic usage + +In this example, the input is a cyclic peptide (provided with the `-in:file:s` commandline option). This script perturbs the peptide backbone, relaxes the peptide, and then applies a [[CentralTendency EnsembleMetric|CentralTendency]] that in turn applies a [[TotalEnergyMetric]], measuring total score. At the end of execution (after repeat execution, a number of times set with the `-nstruct` commandline option), the EnsembleMetric produces a report about the mean, median, mode, etc. of the samples. + +```xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +``` + +### 2.2 Example of internal generation mode + +This example is similar to the example above, only this time, we load one or more cyclic peptides (provided with the `-in:file:s` or `-in:file:l` commandline options), generate a conformational ensemble for each peptide _in memory_, without writing all structures to disk, and perform ensemble analysis on that ensemble, filtering on the results with the [[EnsembleFilter]]. + +```xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +``` + +#### 2.2.1 Multi-threading + +When used in internal generation mode, the EnsembleMetric can generate members of the ensemble in [[parallel threads|Multithreading]]. This uses the [[RosettaThreadManager]], assigning work to available threads up to a user-specied maximum number to request. To set the maximum number of threads to request, use the `n_threads` option (where a setting of zero means to request all available threads). This functionality is only available in multi-threaded builds of Rosetta (built using `extras=cxx11thread` in the `scons` command), and requires that the total number of Rosetta threads be set at the command line using the `-multithreading:total_threads` commandline option. Note that an EnsembleMetric may be assigned fewer than the requested number of threads if other modules are using threads; at a minimum, it is guaranteed to be assigned the calling thread. **Note: this is a _highly_ experimental feature that can fail for many ensemble-generating protocols. When in doubt, it is safest to set `n_threads` to 1 (the default) for an EnsembleMetric.** + +### 2.3 Example of multiple pose mover mode + +The following example uses the [[BundleGridSampler]] mover to grid-sample helical bundle conformations parametrically. For each conformation sampled, the protocol then uses the [[Disulfidize]] mover to generate all possible disulfides joining the helices as an ensemble of poses. It then computes the median disulfide pair energy, and discards conformations for which this energy is above a cutoff. + +```xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +``` + +## 3. Interrogating EnsembleMetric floating-point values by name + +Each EnsembleMetric can return one or more floating-point values describing different features of the ensemble. Each of these has a name associated with it. + +### 3.1 From C++ or Python code + +From C++ (or Python) code, after an EnsembleMetric produces its final report, these values can be interrogated with the `get_metric_by_name()` method. To see all names offered by a particular EnsembleMetric, call `real_valued_metric_names()`: + +```C++ + // C++ pseudo-code: + + // Create an EnsembleMetric: + CentralTendencyEnsembleMetric my_ensemble_metric; + // Configure this EnsembleMetric here. This particular + // example would require a SimpleMetric to be passed to + // it, though in general the setup for EnsembleMetrics + // will vary from EnsembleMetric subclass to subclass. + + for( core::Size i=1; i<=nstruct; ++i ) { + // Generate a pose here. + // ... + + // Collect data from it: + my_ensemble_metric.apply( pose ); + } + + // Produce final report (to tracer or disk, + // depending on configuration): + my_ensemble_metric.produce_final_report(); + + // Get the names of floating point values + // that the EnsembleMetric has calculated: + utility::vector1< std::string > const value_names( + my_ensemble_metric.real_valued_metric_names() + ); + + // Confirm that "median" is a name of a value + // returned by this particular metric: + runtime_assert( value_names.has_value( "median" ) ); //This passes. + + // Get the median value from the ensemble: + core::Real const median_value( + my_ensemble_metric.get_metric_by_name( "median" ) + ); +``` + +### 3.2 Using filters + +In RosettaScripts (or in PyRosetta or even C++ code), when an EnsembleMetric is used in internal generator mode or multiple pose mover mode (_i.e._ it applies itself to an ensemble of poses that it either generates internally or receives from a previous mover) a subsequent [[EnsembleFilter]] may be used to interrogate a named value computed by the EnsembleMetric, and to cause the protocol to pass or fail depending on that property of the ensemble. + +Why would someone want to do this? One example would be if one wanted to write a script that would design a protein, generate for each design a conformational ensemble, and score the propensity to favour the designed conformation (_e.g._ with the planned [[PNear]] EnsembleMetric), then discard those designs that have poor propensity to favour the designed state based on the ensemble analysis. This would ensure that one could produce thousands or tens of thousands of designs in memory, analyze them all, and only write to disk the ones worth carrying forward. Variant patterns include generating initial designs using a low-cost initial design protocol, doing moderate-cost ensemble analysis, discarding poor designs with the EnsembleFilter, and refining those designs that pass the filter using higher-cost refinement protocols. Other similar usage patterns are possible. + +Note that if one simply wants the value produced by the EnsembleMetric to be recorded in the pose, the EnsembleFilter can be used for that purpose as well by setting `confidence="0"` (so that the filter never rejects anything, but only reports). At some point, a SimpleMetric may be written for that purpose. For more information, see the page for the [[EnsembleFilter]]. + +## 4. Note about running in MPI mode + +The [[Message Passing Interface (MPI)|MPI]] permits massively parallel execution of a Rosetta protocol. If an EnsembleMetric is used in basic mode (Section 2.1) using the [[MPI build|Build-Documentation]] of Rosetta, all poses seen _by all processes_ are considered part of the ensemble that is being analysed. At the end of the protocol, all of the instances of the EnsembleMetric on worker processes will report back to the director process with the measurements needed to allow the director process to perform the analysis on the whole ensemble. This can be convenient for rapidly analysing very large ensembles generated in memory across a large cluster, without needing to write thousands or millions of structuers to disk. This functionality is currently only available in the [[JD2]] version of the [[RosettaScripts]] application, and only when the [[MPIWorkPoolJobDistributor|JD2]] (the default MPI JD2 job distributor) or the MPIFileBufJobDistributor (the default MPI JD2 job distributor for use with Rosetta silent files) is used. Support for [[JD3|RosettaScripts-JD3]] is planned. + +Note that EnsembleMetrics that run in different MPI processes, and which generate ensembles internally using either a generating protocol (Section 2.2) or a multiple pose mover (Section 2.3), report immediately on the ensemble seen locally _in that process_. In this case, no information is shared between processes. + +As a final note, some EnsembleMetrics may not support MPI job collection. These should tell you so with a suitable error message at parse time (i.e. before you run an expensive protocol and try to collect in results). See the table of EnsembleMetrics for MPI support. + +## 5. See Also + +* [[SimpleMetrics]]: Measure a property of a single pose. +* [[Filters|Filters-RosettaScripts]]: Filter on a measured feature of a pose. +* [[EnsembleFilter]]: Filter on a property of an ensemble of poses. +* [[Movers|Movers-RosettaScripts]]: Modify a pose. +* [[I want to do x]]: Guide to choosing a Rosetta protocol. diff --git a/scripting_documentation/RosettaScripts/EnsembleMetrics/ensemble_metric_pages/CentralTendency.md b/scripting_documentation/RosettaScripts/EnsembleMetrics/ensemble_metric_pages/CentralTendency.md new file mode 100644 index 000000000..2901acadf --- /dev/null +++ b/scripting_documentation/RosettaScripts/EnsembleMetrics/ensemble_metric_pages/CentralTendency.md @@ -0,0 +1,41 @@ +# 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 (vmulligan@flatironinstitute.org). 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. +* [[ParetoFront ensemble metric|ParetoFront]]: An ensemble metric that allows identification of poses at the Pareto front, given some [[simple metrics|SimpleMetrics]]. +* [[I want to do x]]: Guide to choosing a tool in Rosetta. \ No newline at end of file diff --git a/scripting_documentation/RosettaScripts/EnsembleMetrics/ensemble_metric_pages/ParetoFront.md b/scripting_documentation/RosettaScripts/EnsembleMetrics/ensemble_metric_pages/ParetoFront.md new file mode 100644 index 000000000..fe0aa9270 --- /dev/null +++ b/scripting_documentation/RosettaScripts/EnsembleMetrics/ensemble_metric_pages/ParetoFront.md @@ -0,0 +1,274 @@ +# ParetoFront Ensemble Metric +*Back to [[SimpleMetrics]] page.* +## ParetoFront Ensemble Metric + +[[_TOC_]] + +### Author and history + +Created Friday, 8 April 2022 by Vikram K. Mulligan, Center for Computational Biology, Flatiron Institute (vmulligan@flatironinstitute.org). This was the fourth [[EnsembleMetric|EnsembleMetrics]] completed. + +### Description + +The Pareto front is the subset of elements in a set that are optimal for more than one property, in the sense that no element in the set has a value that is more optimal for one property without also having a value that is less optimal for another property. In other words, you can't make one property better without sacrificing another property. When plotted in N-dimensional space (where N is the number of properties), the Pareto front is the "rim" of the point cloud, as shown below. The ParetoFront ensemble metric identify the poses at the Pareto front for two or more properties (as measured by [[SimpleMetrics]]). This is useful in situations in which one is seeking diverse structures optimized for more than one property, and the optimal trade-off between one property and another is unknown. For example, if one were designing proteins to bind to a target, one might want the proteins to have low overall Rosetta scores in isolation, low interface interaction scores, and low numbers of buried unsatisfied hydrogen bond donors and acceptors. In this case, the Pareto optimal designs would be the ones in which, for instance, one couldn't improve the Rosetta score without worsening either the interface score or the number of buried unsatisfied hydrogen bond donors/acceptors. + +[[/images/ensemble_metrics/pareto_front/pareto_front.png]] + +In the plot above, a set of structures is plotted by Rosetta energy (horizontal axis) and solvent-exposed polar surface area (vertical axis). If low energy and high exposed polar surface area were both desirable properties, the set of orange points, lying at the Pareto front, would be the ones of interest, since these are the ones in which one of these properties cannot be made better without sacrificing the other property. + +#### Details + +The ParetoFront ensemble metric accepts as input two or more real-valued [[SimpleMetrics]], as well as a comma-separated list of Boolean values indicating whether it is desirable to have lower (true) or higher (false) value for each property measured by each [[SimpleMetric|SimpleMetrics]]. It then applies these [[SimpleMetrics]] to each pose in an ensemble, collecting a series of values. At reporting time, the metric returns three lists: + +- A table of those poses at the Pareto front, with the corresponding values of each [[SimpleMetric|SimpleMetrics]]. +- A table of _all_ poses seen with the values of each [[SimpleMetric|SimpleMetrics]] and a Boolean "TRUE" or "FALSE" indicating whether each is at the Pareto Front. +- Optionally, a list of binary silent strings representing those poses at the Pareto front. These can be copied into separate text files and converted to PDB files using Rosetta's [[extract_pdbs|Apps]] application. Note that if this option is used, more memory is required. + +### Usage + +#### Interface + +[[include:ensemble_metric_ParetoFront_type]] + +#### Example configuration in RosettaScripts + +In this example, an input PDB file containing a single 8-residue cyclic peptide is perturbed and redesigned. The score and polar solvent-exposed surface area of each design are measured using a [[TotalEnergyMetric]] and a [[SasaMetric]] (two [[SimpleMetrics]]), respectively. The ParetoFront ensemble metric then returns a list of the peptides that have high polar solvent-exposed surface area and low total score (i.e. those at the Pareto front for these two properties). + +```xml + + # Generate a bunch of perturbations of a cyclic peptide input, design each, and select + # designs at the Pareto front of low score and high polar SASA. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +``` + +#### Example output + +The output from the example above is shown below: + +``` +protocols.ensemble_metrics.metrics.ParetoFrontEnsembleMetric: (0) Report from ParetoFront: + MPI_process: 0 + poses_in_ensemble: 20 +Poses at Parteo front: +Pose Metric_1 Metric_2 +teststruct_0001 -10.9948 562.189 +teststruct_0010 -11.1487 561.375 +teststruct_0011 -14.4376 533.249 +teststruct_0014 -11.3264 538.945 +teststruct_0003 -15.1701 423.254 +teststruct_0009 -13.7229 536.632 +End poses at Parteo front +All poses: +Pose Metric_1 Metric_2 At_Pareto_front? +teststruct_0001 -10.9948 562.189 TRUE +teststruct_0004 -9.58659 464.091 FALSE +teststruct_0007 -7.11429 476.887 FALSE +teststruct_0010 -11.1487 561.375 TRUE +teststruct_0013 8.69142 460.517 FALSE +teststruct_0016 -7.30785 560.823 FALSE +teststruct_0019 -11.5179 475.092 FALSE +teststruct_0002 -5.46091 504.822 FALSE +teststruct_0005 -8.69703 536.107 FALSE +teststruct_0008 -11.6457 509.571 FALSE +teststruct_0011 -14.4376 533.249 TRUE +teststruct_0014 -11.3264 538.945 TRUE +teststruct_0017 -13.9076 524.441 FALSE +teststruct_0020 -13.8797 495.925 FALSE +teststruct_0003 -15.1701 423.254 TRUE +teststruct_0006 6.03388 470.449 FALSE +teststruct_0009 -13.7229 536.632 TRUE +teststruct_0012 -7.75434 546.179 FALSE +teststruct_0015 -6.62836 500.375 FALSE +teststruct_0018 -13.6551 526.151 FALSE +End all poses +Full poses at pareto front: +[BEGIN 1: teststruct_0001] +SEQUENCE: DXDXDXDX +SCORE: score fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref chainbreak rama_prepro description +REMARK BINARY SILENTFILE +ANNOTATED_SEQUENCE: D[DASP]X[DORN]DX[DORN]DX[ORN]DX[ORN] teststruct_0001 +NONCANONICAL_CONNECTION: 8 C 1 N +LezeTCj5dUCkvdOWvoEoTCj7p+C0yS0wPaUwSC7qnfDEJ69hvl31SCTm8CEU5OqfP2rFVCXrCNDkfuPwPu7/VCLbAxCECO76PXYmVC3SVlCkFNyBQ/ZFXC3ZinCU8002Pni2TCTZYPCEgBt3v+8TTCHWp8CES/v8PYycVCXvfMDEQkNwvOZKVCDN8tDUOC81P teststruct_0001 +L5i6RCvZhQD0yyk4vlF+QCT+SsD00YH+vy8hPCPC8fDUj6j7vT2pOCDCb7DUKQ06vCLNRCvLtqDEIXGFwsapSCbv3yDEcAyGwXUxSCPNW2DkFmaKwbJMUCHBT1DUvuTLwHl7RCby/wCERCW6vsNIRCL7dGEEOFU7vjg6QCbsYLD0hHoGwg9kQCz2PBEUKEEHwV+/SCH0RIE0cL+EwzyRTC7fvYD0SdYFwnLPSC/32bDkYqWLwNmUSC/dIKEkNiFLw6nOUCfNs3DUolUNwIRsUCDGBHEUgseKwITnUCnxdZD0/vuKw teststruct_0001 +LQzSPCjKc2CERFP6vve+NCHwmmC0iZb2vVLCNC3jxlC0QXZAwtysMCPLrDCUdhdCweUFOCftdzBEYahpvUKwMCrZESBUkblmP4h4LCDMmCCUFehvPRknMCnMxFAkuivrPG8CQCDOVhCU7mW7vztjNCPqB8CkmxlhvPUzOCfpJ0BkrtWwPlOdOCnmEHB0mUa4v teststruct_0001 +Lr8mMCL1jLDEfFJCwnTuLCDuTPD0ADwGwNsdMC75yCDEjp5JwSzdNCbUjWDUpunKwwHLLCzdz8DEYMQHwH7LKCnVgBEkTa6Jw/FpJCf4OYEkMo9JwfqrICfekbE05tMMwIA6MCn2YmD0/bOAwWIzKC77/7CULsOGwp/qKCTu3CEkw8iDwB6/LCDyjJE0lN2HwGsrKCzIZ8Dks3zLwUyWJCz+usDkvvrJwZjIJCz0nbEUyGFIwv3dKC3YfjEkZKMKwGHWICHmzqE08aKMwuWJJCH/vYEk7Y9NwGy5HC3MbREkPp/Lw teststruct_0001 +LN2AMC/+shCUM5WLw/QtMC7QxTCkoWxNwiAxNC/IJlB0NgGNw64aOCjLcCB0ak4OwA+tLCzVRBCU5SzPw2quKCb4YiCkK4aQwv0/KC7Z1HD0CISQwLytJCvD7VC08r8Qw4YLLCXnFSCU+uxKwyJINCjT1vC0qazOw+PKLCnZUOBESd4OwoCRMCjXBoBUm1vQw teststruct_0001 +L147NCv8eTBkdkhKwwn7OCD9yVAkronJwE6LQCDzoCBEdGnIwzcJQCrC4wBkNAPFwhhWOCDaG5+juc2GwvLLNCL6kW8zaHUIwc8qMCHXdU67BhFEwLWGMC/mpD8z5uQ/vt9WNCf0fxBEyDKJwfaNPCr2ua/jZdTLwWQBOC/ODEA00pgDwqQIPCPXjH9zlkWFwpyeNCvVnD1rRi+JwxOXMCnzod+jJY/IwCqfNCPm4j9LG7hCw2l5LCbEf29LcglFwotxLCnpeU3LwWa5v8qULCTCAI+jFWABwMwzMCvquQ+jyhT8v teststruct_0001 +LyETRCzXx0AUwAAKwawiSCrOIhB0zJYJwIZBTC3XyLB0oBIFwW4xTC/qU8BUePtCw+QoTCzGvJBEvCaLwjF7UCjfR7BEf2+KwTb5UCX5IkCkFlMLw6M7VCDuoTBEtncKwB+RRCXCcKAE0rhLw3AZSCvXQTCEnZmJwpBRTCn/YWBEzKbNwoH2TCXVeFAELfRLw teststruct_0001 +LQ59SCXZd2/zqLpDwBXYTCL2r/+Trxo8vF5MSCrI89+zRj1xv3ulRCfSAi7zTJOsvkyBUCXQhn3jqIH9vkdVVCLOiA2jEHrBwe26VCf+wr+rmetBwh1MXCD/F0+73nuEwo7oSCzg9d+jE/RGwfuHUCHgFNAUWRo5vphVTCHeuX8rjjZAwKnOUCbbZ057ksByvAmDWCLyd+8Dg6t/vmKKVC7byC7TuDyFwbTNVCf23BAMPFjDwIiGWCPcWV/7mhO7vagjXCbclWAM7CqEwQA4XC/weJ9L+cBDwxvCXCTrBQ+L3yRIw teststruct_0001 + +[END 1: teststruct_0001] +[BEGIN 2: teststruct_0010] +SEQUENCE: TXDXDXDD +SCORE: score fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref chainbreak rama_prepro description +REMARK BINARY SILENTFILE +ANNOTATED_SEQUENCE: T[DTHR]X[DORN]DX[DORN]DX[ORN]DD teststruct_0010 +NONCANONICAL_CONNECTION: 8 C 1 N +LTtNTCv1FVCU8nZhPRZETCrUm5C0NZW4Pi5ISC/2ObDEfncuPXgmRCTJN2DUk+W5P62bUCD59ND0DK36PPaCVCH67cD00aNhP60WVCDwhtCUWxEAQ3AfTCDzNaCUwfA1vO/oSCDsWuC0lh3/Pq9SUCL4FpDUXSHAQDhfUCrpGzDEjYKnvAUUWC/Kf8CExy7AQfB6UCHxWiC0ApyDQ6cgVCH+dSC0riy6P teststruct_0010 +LiA9RCLMdZD0rp01vt2CRCHQo2Dkg0Y8v6BnPC7QOmDEQZA8vuJrOCX2w+D0HcM6vb6eRCHTI9DEa6/DwWB1SCTYsJEUpqoEw5qJTCn4sNEUm6PJwDycUCLDAZEE40lJwaDdSCj3TDDEmFO7vDxERCLNqKEE7GQ4vJ4iRCnPMeDUP+/FwkDvQCP+DIEEcqGGw9zzSC/t9YEkhohCwkKnTCjmj/DkXU5CwAsMTCX678DUazTKwWRXSC/zZXEk9LJKwwFoUCD1WbEUPvjLwdcaUCX8RnEE2VpIwRTMVCTWDQEE/SzIw teststruct_0010 +LSacPCj9m8CkH1u9vp+HOCzJ1oCUBWf9v7LXNCHvWxCE/e6Dw9WJNCjdVUCUNBIHwupPOCPCGxBEmuq7vuK5MC7/UEBU1IM7vQo6LCDciuBkMpE5vpe2MCz7uw/jzi88vhKQQCz4NqCUVKQ/v71jNCvFn2CUfvv1vSnxOCvEMlBUUAZwvmP1OC3hrUBkUQDBw teststruct_0010 +LbO9MCPsXZDkTFsEwrnOMCXw5lDEAsvIwgeHNC7k8gDkkhLLwgEJOCD6Y2DU8FbLwKbuLCLo/JEkOjhIwe3sKCrpmNEUAcoEwPcOKCjQukEUsyhEwGWOJCrJhoEkIpOAwQIKNCnHsvDUaK4BwkKSLCrUfTD0MF+IwNXkMC3aqUEUT+JIwXVRLCX+yOEEnbaKwV71JCDsJDEEslRFwtUJLCDIsJEkznxAwB/ELCn9SvEkhx3Dw5dxJCrpvoE0UqLIwjz7ICnBA4EU64SAwq7aICnlAfE0jI1AwKtoJCL6HlEUl1R5v teststruct_0010 +LwcxMCH7uEDkOdFNwzhlNCH1E/CEMvePwsBpOCjFzcCUzYCPw8QbPCbMATCkxqaQwOjtMCHBGzCU2G8QwkvwLCff0WDUYeWRwymKMCPuP7DEknURw8BpKCX1VNDEvNsRwQ17LCDaCzC0HL3Mw1lBOCHCCeDUs5BQwh+HMCnOuWCUmtsQw6NWNCnQIrC0OiyRw teststruct_0010 +LtSqOCj/iKC0fzoMwpprPCbA2WBEnf5LwTzyQCLZQACkplRKw+giQCXVSUCkAxNIwV+DPCXr8MAUUjUKw+p/NCvmU2+jbl1LwJEZNC7Uon6Tr6GKwbJnMCnG3h9zQJqHwDu8NCLiZSC0QqSLwpmHQCXx18AEVHuNweAnOCvhmlA0AjfIwb+1PC/wCA/TbJvJwA5bOCbOH59DUcnNwIANNCL+qGA0JwdMwVEMOCn1Yb6LMOUJwvtuMC3fGV6rhgULwdpOMC3N1+3DPAeFwc82LCvkS6+jkZiIwO5NNCnm24+D5YVFw teststruct_0010 +L6xBSCrL62BUStNLwiELTCje9PCkrN8JwSEUTCT43BCk2yEGwTFoTCDlqbCExjkCwoddUCjUtFCUJ8dLwxpjUCn6HdCkhbIOw3R0TCLdB7CEGshOw9rXVC7v4QC0ZvvPwrTLSCLxRSB0Zg2MwjtDTCL06yCkufEKwS/gUCXrwGBkY01LwuoUVCfEYOCUC1PKw teststruct_0010 +LheFTCT89uAUyqPFwtNQTCbNlIAkmR8/vU//RCL20TA0BAK5vSWKRC7hs0+D4Mh4vyklTCTgRl8TqbeAw4L3TCT7bCy7DxZ0v9zpTCftde8j6mzmPn1RUCjgJT+LCrS0vOyxSCfs6JA0RLKIwtGFUCjyooA00t57v4sdUCLmmF8jZMBDwegwSCv0MB4zroZCw teststruct_0010 + +[END 2: teststruct_0010] +[BEGIN 3: teststruct_0011] +SEQUENCE: DXDXDXDX +SCORE: score fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref chainbreak rama_prepro description +REMARK BINARY SILENTFILE +ANNOTATED_SEQUENCE: D[DASP]X[DORN]DX[DORN]DX[ORN]DX[ORN] teststruct_0011 +NONCANONICAL_CONNECTION: 8 C 1 N +Lk5PTCXlhLCUmyJpP0AETCjAnqCk1Q36PEdJSC3N9ODkebt2PVLsRC3eXoDUAj79PSUaUCHHy8C03Ud+PYvSVCfumbCU9i9BQH5wUCPta5BkFB9DQaIfWCDkehCUS+BCQF4bTCHeFWC03mZyvLnmSCDkZaCklM1AQbe8UCrJfJD0rHG3PouPUCj4PXDUFl/BQ teststruct_0011 +Lsl4RCfaQRD0DGOsv6E+QCXYLxDEPry2vvniPC7BNpDUAwluvm6wOCz2mDEUGL3ova4BRCLUWxDkL7zBwv9XSCT/3+DkVUHEwtgWSCvVm+D0dXGJw25pTCr8HGE0saQKwqAVSCnZV8CUBVF4vOxRRCLCPIEkdi3wvPZzQCLnaRDUNUUDwzSRQCP8gDE0LHYDwYmnSCPShPE070uCw5jJTC/6BpD00buCwH8HSCrCaeD0T0zJwWykRCP1HKE0w8zJwjSmTCXs0FEkBgRMwzo3TCX1IVEUnDpJw8dYUCbPH4D0kCpJw teststruct_0011 +Lc1MPCbolADkToUov434NCLmx0CkZkLoPBE2MCz+V0CUq3q1vAkYMCfIZSCU3+L6vRc8NC/Q1ICEM032PMBnMCnDz2B0OmP8P5ezLC3t6WCEf5Y+PTIaMC3kgrA0CWu9Pfi3PCDvTpCkMhLvvXulNC7nZMD06x/3PfcsOCn7PJC0h9w9PrBQOCDgmhBkpk1kP teststruct_0011 +LNdeMC/WTaDEO/m6vcNgLCXxWeDkEhnBw/oDMC7swKDUFwsGwrVGNC7vPYDEhcWIwTjILCbHoGEklfjCwHfEKC71GKEEF80GwlGtJCnuphEkszUHwApqICjwUlE0dovJw1U4MCvID1DkGk12vuohKCLR4PDEdNhAwbJxKCH2mNEUU3q9vmeBMCrbiPE0kFvDwQRcKCrPaEEUYjVJwSQLJC3BCBE0ZUzFwq8UJCrIenEUP5fDwX9lKCTD2qEEX9LIwJ+cICDdG1EUDP2JwFrAJCrLQgEkeRiLwRH1HCHgHdEEl/QJw teststruct_0011 +LBQZLCraTqCUpigIwm12LCX/cXC0bwALw558MCnjjtB0sffKw5pjNCnF6LBEaHXMwMosKC3kPCCU2dgMwVlpJCXpMiC0/FdNwvt+JC34FHDEk4vNwb5hICP8ZVC0mB4NwJ1jKC/+oeCEKVRHwIsLMCbeExCkWCYMwGvNKCn9xVBUmNNLwaUFLCfxCiB0lWPOw teststruct_0011 +LpSNNCzxmbB0fC5HwSaQOCPilfAkDJXGwwplPCDZMNBks4lFwpUtPC3ZXDCkFiQCw8n3NC/ozf/Dx3PBwSzoMCDo9c9TnzyBwxvUMC76xW4DKTJ5vWV3LCPwiL+jJ8NbvmQqMC/DN4B0kRAFwh7XOCjifh/zNsxIwrWrNCDU8dA0L4H8vCysOCfsPP+Tdy7/vnszMCvOb23jDj6EwR+xLCLCk8+zBs7Cwy5NNCTNc867I3l0vltiLCLq0X878Jg6visqLCTKyT8j5OK0PYtBLCTa7H/joyvsv5klMCza2i/DSC5bP teststruct_0011 +L7nlQCjIPzA0USWIwPM3RC7pjgBEhcbIwmGfSCvEXmBk/zTDwBh8SCbmMVCk+LpBwKT1SCLoC0A0mCWKwwHeSCH1TBBExfRNwpVrRCnj14B0VI1Nwua/SCrBzTAkhO7OwJkdQCPxk9/jAHgJwHGtRCP4aQCUHURJwCG2SCT3Gf/DpZ7JwA51TCrhNMBEmtAKw teststruct_0011 +LJBTSC/aImAUo7CAwEd2SCjsglAE+amyv1a9RCLY0WBEqQupPw6IRCLWPxAECxE4PFoCTC/0MT+zlm/iv7KwTCbMLE+TVzW5PSvNVCfME4+zgFd4PcB3VCXSJJ/jLJkBQADxRCn6Km/TIxUBwf80TCv5hEB0qn+yvghnTCv8aW8TOeg2v6ZESCvFaq8jKQAavwjsTCDBCUsD2mL8P4uQTCP1cW/D4dM/PjdSVCbpLZAk+ekwPpcwVCbZCw8DkVavPg40WCftkr/zh6FBQwE0VCfY6v8zIygDQ1LYVCPCvRAU88tDQ teststruct_0011 + +[END 3: teststruct_0011] +[BEGIN 4: teststruct_0014] +SEQUENCE: TXDXDXDX +SCORE: score fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref chainbreak rama_prepro description +REMARK BINARY SILENTFILE +ANNOTATED_SEQUENCE: T[DTHR]X[DORN]DX[DORN]DX[ORN]DX[ORN] teststruct_0014 +NONCANONICAL_CONNECTION: 8 C 1 N +LchSTCLy/PCUC7rjPvbLTCTEzzCEbK54P1iPSCjvJWD05fJxPRP1RCbXCzDESFa6PpxjUC/RiHDEt6O7PfCIVCL2xXDEIgGkP5mfVC3zLmCEwM//PpojTCTawVC0iLZ0vudxSC785nCUFtNAQlocUCTY5hDEt3bAQNyiUCvdLtDE2hgjvYtdWC3Qt0CU/7yAQ2jEVCfQCaCkxstDQ2enVC/t4LCUEpW6P teststruct_0014 +LVM6RC7V1SD0NLYzvmm+QCvRmwDk/Kt6vYJjPCXijoDUTv71vGmwOCzcNDEUffrzvA2DRCzXMtDEOocDwgWZSCLeA7D0MozFwcRYSCfSo4D0VT8JwsaqTCH6tDEUnWILwe4TSCrME7CEhvH6vhWQRCHydIE0NaT4v/M4QCv/LMDUfOqEwV/RQC7pcAEUL4PFwkRnSCnw5NEE9FmEwC9LTCj5SmDEF0SEwS1MSCXOrXD0QRkKwOpkRCvUSGEU+rtKw/FnTCPFsCE0kOJNwAP1TCPnETEkpGmKwdwaUCv720DU5bdKw teststruct_0014 +LIUOPCL1CAD03LIyvZf5NCnuI0CUM27hvJA5MCbMEzCk0gY6v2TcMCDV4QCEOhs9vZP8NC3ZdICUhElwPVZlMC3pD1B0RVl4P2FvLC3GhVCEy475P+MaMCX9EqAk4Ae6PFY6PCzb6oC0Kdm0vKhkNCbE+LDke3HxPKkpOCLfiJC0Ll66PA9SOCncsgBEqMuiv teststruct_0014 +LediMCnsvYDEgKb+v7ZmLCfbLcDkXypDwg6LMCH1ZHDUxPTIwGHQNC7T/TDkv1PJwwEQLC79eFE01EyEwKHOKC7vqIEkWRmIwuF4JCLgNgE0wy8IwD73ICbjmjEkP6GLwim7MC/vtzDUOqQ7vJEnKC7fMODkoOoCwaQ3KCHj5MEkevJBwb2JMCrOJOEk0w6Fw6UnKCrIeCEE2oeKw8AUJCPyv/DEcrGIwQTeJC35gmEEYeKGwi3xKCnWIpEEIucJwYGrICrtYzEUdzRLwJgPJCTDFeEEC92MwBkBICnhpbE0k5pKw teststruct_0014 +L9thLC/94mCEqddJwUtBMCTdtSCkXL5Lw64GNCjQYkBEuNPLwLGwNCzMcBBkJ+BNw744KCLzw5BEQ6aNwNB4JCv6gcCU9qiOw9DPKCvZyADk669Ow6DwICvdGQCEmi9OwSwqKCnuHcCUEzoIwMNYMCf1krCEBSSNwxsXKCfJZNBUKGGMwFTTLC3DhUBkidEPw teststruct_0014 +LTwTNC7QJUBEFRqIwv1VOCzOzYAkGLiHwpLqPCbU/GBET1iGwQbuPCHCeBCUkxWDwoQ5NC/qSU/jXfdCw90pMCDPKL9D3aKDw8WRMCPAJX3TAa67vldzLCPnrJ+Tv1yuvftuMCLfmxB0IakGwiDgOCH6kS/TTAVJw18rNCHfwYAUiap+vE7sOCbNNC+zSvCBwv81MCnqwP0DqGNGwxk0LCzJC1+zwGfEw/lINC/7sd77ubw4vrReLCvq3c87JIb9vG3jLCLNkU8D52RsPDk/KCv11I/z2O80vXniMCroXe/z/mcov teststruct_0014 +LHQtQCvszqAUphpIwLW/RCPvMXB0qplIwMthSCHaydBE9QfDwKVLTCzwSOC0BXDCwioATCPALpA0HEXKwZXvSC7/M1AEgYVNwoq9RCrpVsBUduAOwUCUTCTiJHAkHk5OwDPnQC3Vkq/zUAxJwHt3RCXxmLC0VWeJwz6/SCjcyJ/zBW6JwVsAUCvM6ABUAl6Jw teststruct_0014 +L3fPSCXhheA0nSNAwaUvSC7CvcA05w5yvu1uRC7zEEBE7HCpPc+8QCnmmWAEzkr2PiJETCrQ/B+jp0RovdZNUC7YYA7T4ER4v3FgUCH1uD+72mcwvQ0nVCbMSV/bT5K6v69qRCLJOb/zRRiBw8EqTCLpQCBkN+JyvopLSCD7BH7DA1Zsvh5UTCbuq/9Dery0PY3GVCzaR89DEO02v9y8TCPR0m6jzIXAwWFnTCTiDT/LjCPyvc4wUCjTA99bK5dwPhMyVCfHCmAshOg2vvXdWCvuJO+LKlS5vLqYVCP6Dd/rsSABw teststruct_0014 + +[END 4: teststruct_0014] +[BEGIN 5: teststruct_0003] +SEQUENCE: DAXDXDDX +SCORE: score fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref chainbreak rama_prepro description +REMARK BINARY SILENTFILE +ANNOTATED_SEQUENCE: D[DASP]A[DALA]X[ORN]D[DASP]X[ORN]DDX[ORN] teststruct_0003 +NONCANONICAL_CONNECTION: 8 C 1 N +LGtBTCrIiaCkdTHjPGOxSCrBW9C0Xf44PtNyRCHdidDkdXdwPXGhRC/70+D0XnC5P7tEUC/ZDUDk0H27PodDVCvBD3CUBg2AQO4nUCHvCfCE2aOEQ+WOWCrML5CUB7X/PThQTCrJlhC0MTj0vrmVSC3K3vCkG8EAQ4bjUC7iCgDk9IOxPIn2TC/vjvDkOSdAQ teststruct_0003 +Lb1PRCvLaTD0nKVyv9bSQCjIYvDkvpe6vyXDPCbxc2DUtmOuvLEdOCrabMEEPC3uv7E5PCPn3cDkPFpCw4pgRCLNn3CEyUt4vH6wQC3JLHEU05u7vIPLPCPTHyD0UBlEwuwxQCL1uZDE1zJFw3EcPCbSh9CE4eECw teststruct_0003 +LjQrOC7zqVD0J1AqPR6jNCH2GZDkff95PBhPMC/stNDkWLHxPElqLC7U9rCUL7R1PhlyNC7eS8CkYv1BQqwCPCrN3GD0DrCFQbmIPC3OsrCklfCJQqjIPCfIO6BER7aIQ+KLPCnwp5CEqmZnPYDgNC37F6DEkbw8PtY3NCLxEbCknciAQy27MCfck+Cko4hEQ6vBPCvWkoDk4ALGQBN7PCX8GBDEoflCQQUSOCjjuyC0eqVKQ5VDQCTzazC0UGHKQ4hMPCPZeYB067IKQFP7PCreHsBUfXfGQv5ROCbMvqBUZh6GQ teststruct_0003 +LrVxLCHEIqDESSlpvOvfKCHM4jDEWup3viAqKCjtvDD088ZAwBBMLC7RDOD0J3pEwNn9JCLoGHEU4YR8v4YlICrm7EEkTpqAwH2GICHUgmDEIyFBwfZBICjC+UEU1oJCwS2TMCT8XCE0yf1vvaosJC/w9ZDUZ1novHE6JCbM4SEExBtzvJ4pKCXxQNEEzrIBw teststruct_0003 +LoaNKCzPnbCkpDa/vOzYKCP9E2BEyi0DwaWkLCXCp8A0nsfCwXS9LCTkQGAkh5sFwGfHJCfTiABEgOdEwaI2HCnhz0BUIHOFwjv6HCzAiVC0KfIJw7KtGCnumwC0hfeJwGbvJCzIuTC0Iuh4vykfKC3KpKC0cwvHwV2+ICjoWYA02p7AwRNOJCTFNWA01c5Hw43sHCf3WPCkF7xBwIX/GC7C5JBEubgFwhFBIC78uACEJ63KwGryICvcUqCEOYCJwKvyGC/uECDEVuKLwiKnGCDRcEDEqGyHwz44FCzutdCE9omJw teststruct_0003 +LE9IMCLTxIB0FFh7vHISNCz4/VAEwdC4v+7lOCLEj9Ak9tz7vhw9OC74vBCEkBY4v53SNCXvaNAU2YUwPPTaOCPiLn+jetN4P5/NPCHEmj9zUxxmPSecOCHwVF+jya0AQsZxLCTwR2BkMnL1v3yMNCDfrs+zBch7vEvVMC/1Qn/jStt1PwXaNCXTgMBEAZi3P teststruct_0003 +LGeSPCfUbQA0yocBwVmdQCXcxzAE4SHEwjFfRC7FzTBUQTEAwBSMSCHfKJCkvwDBw/zGRCP5Ph/zCKwHwHfSQCvgh9+T2lYKwJyZPC7c7PA0L29KwKujQC73hA8jjYsLwx0/OC/APo+jHRUCwpeJQCHT7nBUjoyGwAtORCTVtT9TAKjFwyWGSCDJOGAk6UeIw teststruct_0003 +LSlbRCHq3hAk15L1vbxUSCrxnzAECtapPuJpRCXTkrBU27t6PXfHRCfyiLB0heVBQVkzSCjFSA/zhM62PT2yTC3FFY/zvOTAQ0+HVCD4qOA0NTl8P5p/VCbtOsAknOwCQEguQCzr9n/jFVmzvtfMTCDg9VBEI+tavaKSTC7Vmh9TtpHjPjx8RCPPpy9jDOi6Pbu9TCnmB78zYnRCQ2XYTC3ZlYAkp3NDQrg8UCHmWEBkybY2P1mpVCTtf5+DWOL4P3X3WC/UpCBUAeQBQKtLWCj2h1/jQwPFQpvhVCHkWbB0umyEQ teststruct_0003 + +[END 5: teststruct_0003] +[BEGIN 6: teststruct_0009] +SEQUENCE: DXDXDXDX +SCORE: score fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref chainbreak rama_prepro description +REMARK BINARY SILENTFILE +ANNOTATED_SEQUENCE: D[DASP]X[DORN]DX[DORN]DX[ORN]DX[ORN] teststruct_0009 +NONCANONICAL_CONNECTION: 8 C 1 N +LdNPTCvE7NCUqjLoP05DTCzAhuCUjpR6PK9NSCDRpTDEMRW0Ptj4RCb99wDUcnL8PFyaUCL9K/CkGyG+PIiPVCfSJdCE9A6BQu3qUCP6/DC0MlxEQD+bWCXQocCESMMBQbtcTC/hGXCUTECzvnDjSCnyCgCEBWiAQFQ/UCfY+KDEY8j2PUHRUCDzAaDUIgxBQ teststruct_0009 +LOI4RCLhMSDUN4Mwvm2/QCvwKyDE0B34vFtjPCPnNsDEtMSyvIDzOCXBhFEEN4vwvEhERCHHIwDEFSiCwmsbSCTUi7D0J02EwHObSC3O44DkO2dJw21vTCznHCE0ngoKwuFPSCrOU6CE3Zu4vsMVRCHw0IEEDBc0vAU0QC7K7PDEK+3Dw/eVQCna+CE0R6PEwA6sSCTY/NEkbVqDwU0LTCf2llDEgLTDwMxKSC3saYDEFRFKw0LrRCjUXHEk9yQKwX2sTCHPDBEEVZpMwBW/TCbRPREUHxGKwZ2cUC/s3vDEUI8Jw teststruct_0009 +LWJMPCvpZED0baarvP72NCbTm6CExVlhPi41MC7lP4CkZ6u3v5XWMCnjzVCEppj6vOn3NCv1SQCUJRv2PKXhMCnesFCUvlY8PyfxLC7W0iCk5Mi+PaLQMC7qKBBE5BB+PRX2PCLUUsCEYhzvvuljNCPSDUDU2JT1PUonOCzGwRC0x9r9PDmJOCvbqsBkPF8nP teststruct_0009 +LQDiMC3cHdDUv3i8vAHjLCLDffDE7LkCwzNGMCbFeKDkIRkHwgfHNCf3HYDUkS3IwKWKLCvr9GEEpFuDwQLdKCbZOSEkzoO+vFgFKCbdFpE0o0lAwEcZJCjLV0E0dBQ4vGX/MCbpN4DUGpF6v7/kKCPnDRD0tAXBwMmDMCT1IQEU2tsEwTLgKCLxhHEEbQMHwjEjJC3JfJEUnGK8vdAHLCrWfSEEfzg2v0S/KCHh9xE0M/nBwpMbJCDp9oEEcrDEwh0KJC71ZDFE7ph6vzIjICDoasEUhhs0vWYAKCXQ00EkoCdmv teststruct_0009 +LOHdLCvqjoC0sW0Iwkm7LCXJkTCkYjPLwVZ/MCv3ukBEjBlKwt5jNC/Dq8A0qbXMwWcxKCvUo8BkgRvMwW4xJCXkfeC0a13NwQnKKCXdXCD0ShVOwDOpIC/A5SC0x3QOw9CoKCzPSdCkM0zHwD8SMCf15rCU9GqMwJePKCL6mRBU17YLw8mKLCzaGWBUcMYOw teststruct_0009 +LXXQNCHRHZBEKAAIw60SOCXVMeA0toNGwNeoPC3jsLBUyPnFwzvvPC37RFCUQOrCw3V5NCXsbo/Dt66AwsxpMCrzow9TMsPBw7IVMCHztf6DGza3v9B7LCjwSq+TLIrSPRQuMCv335BU6uPFwZCaOC7gEY/zhhmIwcptNCztmlA04t27vN8tOC7vRZ+zPw8+vEC0MCr82W4j7BLEwodzLCbzYF/jNZiCwvSNNCnOXe5r8XbxvhKhLCfakP7rrwp4vU5tLC3w2f9z2it2PtVGLCDmgo/ThsIpvUFrMCrsD//DAtKjP teststruct_0009 +L/OpQCDHprAUEVNIwCH8RCzQbWBkRFVIwmliSCH31gBUUPGDw3vFTC3eCSCUSpxBwI/5SCj6VkAU+QHKwLHlSCHofsA0a9ENwnU0RCfHNkBkiexNwzJGTCLN41/zxfnOwM3gQCXweo/DryNJw0W0RCP5iKC0YdTJwNW4SCXdoB/zjRkJwdF7TCjuJ7A0bHyJw teststruct_0009 +L9cSSCvKwjA09CN/vF0zSC3g3mAUkeowvZ16RCXgGdBkMNjrPGMERCXek7AkHHn4PAg8SCLhBZ+zQjcQP2slTCHLSR+jb3S7PiKEVC7Oy/+TXty6PjZpVCjCjZ/zrL0CQwauRCzDfi/jCCvAwDOzTCjw9DBU2bCxvg1iTC/KrV8jjYSyvla9RCPxL88T8RQdPuQfTC3lYC4j+Ki+PGMFTCXLEq/DVxUAQMJMVCbytaA0KeZ0PNXnVCTXez8jEel1Pa/nWCbJE4/jDbeCQ7ajVCTJRZ9DZq9EQ2GKVCfItcA0mPsEQ teststruct_0009 + +[END 6: teststruct_0009] +End full poses at pareto front +``` + +### Named values produced + +The ParetoFront ensemble metric does not produce any named values. + +##See Also + +* [[SimpleMetrics]]: Available SimpleMetrics. +* [[EnsembleMetrics]]: Available EnsembleMetrics. +* [[CentralTendency ensemble metric|CentralTendency]]: An ensemble metric that computes the mean, median, mode, standard deviation, etc. for a simple metric over an ensemble of poses. +* [[I want to do x]]: Guide to choosing a tool in Rosetta. \ No newline at end of file diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/_Sidebar.md b/scripting_documentation/RosettaScripts/FeaturesReporter/_Sidebar.md index de27f22ed..4d334d69b 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/_Sidebar.md @@ -20,6 +20,8 @@ * [[Simple Metrics | SimpleMetrics]] + * [[Ensemble Metrics|EnsembleMetrics]] + * [[Filters|Filters-RosettaScripts]] * [[FeaturesReporters|Features-reporter-overview]] diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/_Sidebar.md b/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/_Sidebar.md index 4faf9cccc..209569d19 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/_Sidebar.md +++ b/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]] diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/_Sidebar.md b/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/_Sidebar.md index 94af5a392..3800286b4 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/_Sidebar.md +++ b/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]] diff --git a/scripting_documentation/RosettaScripts/Filters/Filters-RosettaScripts.md b/scripting_documentation/RosettaScripts/Filters/Filters-RosettaScripts.md index 5beb4a849..8518db1fe 100644 --- a/scripting_documentation/RosettaScripts/Filters/Filters-RosettaScripts.md +++ b/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. diff --git a/scripting_documentation/RosettaScripts/Filters/_Sidebar.md b/scripting_documentation/RosettaScripts/Filters/_Sidebar.md index b37eb316e..3752c97cf 100644 --- a/scripting_documentation/RosettaScripts/Filters/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/Filters/_Sidebar.md @@ -20,6 +20,8 @@ * [[Simple Metrics | SimpleMetrics]] + * [[Ensemble Metrics | EnsembleMetrics]] + * [[Filters|Filters-RosettaScripts]] * [[FeaturesReporters|Features-reporter-overview]] diff --git a/scripting_documentation/RosettaScripts/Filters/AlignmentAAFinderFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/AlignmentAAFinderFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/AlignmentAAFinderFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/AlignmentAAFinderFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/AlignmentGapInserterFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/AlignmentGapInserterFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/AlignmentGapInserterFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/AlignmentGapInserterFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/ChainBreakFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/ChainBreakFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/ChainBreakFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/ChainBreakFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/filter_pages/EnsembleFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/EnsembleFilter.md new file mode 100644 index 000000000..7dfbda089 --- /dev/null +++ b/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 (vmulligan@flatironinstitute.org) 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +``` + +### 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. \ No newline at end of file diff --git a/scripting_documentation/RosettaScripts/Filters/FragQualFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/FragQualFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/FragQualFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/FragQualFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/FragmentScoreFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/FragmentScoreFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/FragmentScoreFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/FragmentScoreFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/HelixHelixAngleFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/HelixHelixAngleFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/HelixHelixAngleFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/HelixHelixAngleFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/HolesFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/HolesFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/HolesFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/HolesFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/LongestContinuousApolarSegmentFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/LongestContinuousApolarSegmentFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/LongestContinuousApolarSegmentFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/LongestContinuousApolarSegmentFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/MPSpanAngleFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/MPSpanAngleFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/MPSpanAngleFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/MPSpanAngleFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/SequenceDistanceFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/SequenceDistanceFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/SequenceDistanceFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/SequenceDistanceFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/SpanTopologyMatchPoseFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/SpanTopologyMatchPoseFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/SpanTopologyMatchPoseFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/SpanTopologyMatchPoseFilter.md diff --git a/scripting_documentation/RosettaScripts/Filters/TMsAACompFilter.md b/scripting_documentation/RosettaScripts/Filters/filter_pages/TMsAACompFilter.md similarity index 100% rename from scripting_documentation/RosettaScripts/Filters/TMsAACompFilter.md rename to scripting_documentation/RosettaScripts/Filters/filter_pages/TMsAACompFilter.md diff --git a/scripting_documentation/RosettaScripts/Movers/_Sidebar.md b/scripting_documentation/RosettaScripts/Movers/_Sidebar.md index b37eb316e..dd495fff9 100644 --- a/scripting_documentation/RosettaScripts/Movers/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/Movers/_Sidebar.md @@ -20,6 +20,8 @@ * [[Simple Metrics | SimpleMetrics]] + * [[Ensemble Metrics|EnsembleMetrics]] + * [[Filters|Filters-RosettaScripts]] * [[FeaturesReporters|Features-reporter-overview]] diff --git a/scripting_documentation/RosettaScripts/RosettaScripts.md b/scripting_documentation/RosettaScripts/RosettaScripts.md index 8162b50ea..87c20cb24 100644 --- a/scripting_documentation/RosettaScripts/RosettaScripts.md +++ b/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]] --------------------- diff --git a/scripting_documentation/RosettaScripts/SimpleMetrics/_Sidebar.md b/scripting_documentation/RosettaScripts/SimpleMetrics/_Sidebar.md index 19e142d78..e5e662775 100644 --- a/scripting_documentation/RosettaScripts/SimpleMetrics/_Sidebar.md +++ b/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]] diff --git a/scripting_documentation/RosettaScripts/TaskOperations/_Sidebar.md b/scripting_documentation/RosettaScripts/TaskOperations/_Sidebar.md index f41e9d5c9..d2c0e52c8 100644 --- a/scripting_documentation/RosettaScripts/TaskOperations/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/TaskOperations/_Sidebar.md @@ -19,6 +19,8 @@ * [[Task Operations|TaskOperations-RosettaScripts]] * [[Simple Metrics | SimpleMetrics]] + + * [[Ensemble Metrics|EnsembleMetrics]] * [[Filters|Filters-RosettaScripts]] diff --git a/scripting_documentation/RosettaScripts/_Sidebar.md b/scripting_documentation/RosettaScripts/_Sidebar.md index b217aad09..003412fb8 100644 --- a/scripting_documentation/RosettaScripts/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/_Sidebar.md @@ -22,6 +22,8 @@ * [[Simple Metrics | SimpleMetrics]] + * [[Ensemble Metrics|EnsembleMetrics]] + * [[Filters|Filters-RosettaScripts]] * [[FeaturesReporters|Features-reporter-overview]] diff --git a/scripting_documentation/RosettaScripts/composite_protocols/_Sidebar.md b/scripting_documentation/RosettaScripts/composite_protocols/_Sidebar.md index 33d6bcd71..35255fec7 100644 --- a/scripting_documentation/RosettaScripts/composite_protocols/_Sidebar.md +++ b/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]] diff --git a/scripting_documentation/RosettaScripts/xsd/ensemble_metric_CentralTendency_type.md b/scripting_documentation/RosettaScripts/xsd/ensemble_metric_CentralTendency_type.md new file mode 100644 index 000000000..6e5c2d553 --- /dev/null +++ b/scripting_documentation/RosettaScripts/xsd/ensemble_metric_CentralTendency_type.md @@ -0,0 +1,33 @@ + + +_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 [vmulligan@flatironinstitute.org] (Created the ensemble metric framework and wote the CentralTendency ensemble metric.) + +```xml + +``` + +- **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. + +--- diff --git a/scripting_documentation/RosettaScripts/xsd/ensemble_metric_ParetoFront_type.md b/scripting_documentation/RosettaScripts/xsd/ensemble_metric_ParetoFront_type.md new file mode 100644 index 000000000..449a24ec9 --- /dev/null +++ b/scripting_documentation/RosettaScripts/xsd/ensemble_metric_ParetoFront_type.md @@ -0,0 +1,36 @@ + + +_Autogenerated Tag Syntax Documentation:_ + +--- +An ensemble metric that takes a set of real-valued metrics as input and produces the poses at the Pareto front for the metrics as output. Given N scores for each sample, the Pareto front is the set of samples at the boundary, in N-dimensional space, of the sample cloud. Put another way, these are the samples that are optimal insofar as no sample can be found that can improve any of the scores without sacrificing some of the value of at least one of the other scores. + +References and author information for the ParetoFront ensemble metric: + +ParetoFrontEnsembleMetric SimpleMetric's author(s): +Vikram K. Mulligan, Systems Biology Group, Center for Computational Biology, Flatiron Institute [vmulligan@flatironinstitute.org] (Created the EnsembleMetrics framework and wrote the ParetoFrontEnsembleMetric.) + +```xml + +``` + +- **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_metrics**: (REQUIRED) A list of previously-defined real-valued simple metrics. These N simple metrics define the N-dimensional space in which each sample will be plotted. The Pareto front, returned by this ensemble metric, is the set of samples that lie on the boundary of the cloud of points, for which the value of any one simple metric can only be improved by sacrificing some of the value of at least one other simple metric. Required input. +- **lower_is_better**: (REQUIRED) A comma-separated vector of bools indicating, for each real-value metric provided with the real_metrics option, whether lower values are better (true) or higher values are better (false). Required input. +- **return_full_poses**: If true, full poses are returned (in the form of a binary silent string in the output log) for each structure at the Pareto front. This requires more memory. If false, only the names of those structures at the Pareto front are returned. True by default. + +--- diff --git a/scripting_documentation/RosettaScripts/xsd/filter_EnsembleFilter_type.md b/scripting_documentation/RosettaScripts/xsd/filter_EnsembleFilter_type.md new file mode 100644 index 000000000..394234913 --- /dev/null +++ b/scripting_documentation/RosettaScripts/xsd/filter_EnsembleFilter_type.md @@ -0,0 +1,26 @@ + + +_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. [vmulligan@flatironinstitute.org] (Wrote the EnsembleFilter.) + +```xml + +``` + +- **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 + +--- diff --git a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md b/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md index cf17faf3b..288cf53a7 100644 --- a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md +++ b/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;)" diff --git a/scripting_documentation/RosettaScripts/xsd/mover_ParsedProtocol_type.md b/scripting_documentation/RosettaScripts/xsd/mover_ParsedProtocol_type.md index 2a4c1874f..5284f7d94 100644 --- a/scripting_documentation/RosettaScripts/xsd/mover_ParsedProtocol_type.md +++ b/scripting_documentation/RosettaScripts/xsd/mover_ParsedProtocol_type.md @@ -11,8 +11,8 @@ This is a special mover that allows making a single compound mover and filter ve apply_probability="(ℜ)" resume_support="(false &bool;)" > + ensemble_metrics="(&string;)" apply_probability="(ℜ)" + report_at_end="(true &bool;)" never_rerun_filter="(false &bool;)" /> @@ -33,6 +33,7 @@ Subtag **Add**: The steps to be applied. - **filter**: The filter whose execution is desired - **metrics**: A comma-separated list of metrics to run at this point. - **labels**: A comma-separated list of labels to use for the provided metrics in the output. If empty/missing, use the metric names from the metrics setting. If '-', use the metric's default. +- **ensemble_metrics**: A comma-separated list of ensemble metrics to add at this point. Ensemble metrics will collect information about the pose at this point, and will later report statistics about the ensemble of poses that they have seen. - **apply_probability**: by default equal probability for all tags - **report_at_end**: Report filter value via filter re-evaluation on final pose after conclusion of protocol. Otherwise report filter value as evaluated mid-protocol. - **never_rerun_filter**: Never run this filter after the original apply-time run. Use this option to avoid expensive re-runs when reporting