RunSimpleMetrics

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RunSimpleMetrics

Reference

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design Jared Adolf-Bryfogle, J. W Labonte, J. C Kraft, M. Shapavolov, S. Raemisch, T. Lutteke, F. Dimaio, C. D Bahl, J. Pallesen, N. P King, J. J Gray, D. W Kulp, W. R Schief bioRxiv 2021.09.27.462000; https://doi.org/10.1101/2021.09.27.462000

Run a set of SimpleMetrics and add the data to the pose for output into the scorefile/scoretable. Set prefix/suffix to output the set with a particular tag. It is recommended to use JSON scorefile output for easy analysis in python, especially with pandas -scorefile_format json

Use the prefix/suffix options to group metrics or to run metrics at different points in a protocol. Each SimpleMetric also has a custom_type option, which can be used to have multiple configurations of a single type of SimpleMetric run during RunSimpleMetrics. Any set prefix, suffix, and custom_type options are added to the data tag in the score file.

See Effective Use of SimpleMetrics for more.

Autogenerated Tag Syntax Documentation:

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) Run a set of SimpleMetrics on the pose, with a particular prefix and suffix. (prefix + custom_type + _ + metric_name + suffix)

References and author information for the RunSimpleMetrics mover:

RunSimpleMetrics Mover's author(s): Jared Adolf-Bryfogle, The Scripps Research Institute, La Jolla, CA [jadolfbr@gmail.com]

<RunSimpleMetrics name="(&string;)" metrics="(&string;)" prefix="(&string;)"
        suffix="(&string;)" override="(false &bool;)"
        metric_to_bfactor="(&string;)" >
    <Simple Metric Tag ... />
</RunSimpleMetrics>

metrics: Comma-separated list of previously defined simple_metrics to be added.
prefix: Prefix tag for the values to be added to the output score file for these metrics. (prefix + custom_type + _ + metric_name + suffix)
suffix: suffix tag for the values to be added to the output score file for these metrics. (prefix + custom_type + _ + metric_name + suffix)
override: Should we override any existing data?
metric_to_bfactor: Name of a PerResidueRealMetric which values will be written to the b factor column.

"Simple Metric Tag": Any of the SimpleMetrics

Example:

Example with comparison to native through -in:file:native:

<ROSETTASCRIPTS>
	<SCOREFXNS>
	</SCOREFXNS>
	<RESIDUE_SELECTORS>
		<CDR name="L1" cdrs="L1"/>
	</RESIDUE_SELECTORS>
	<MOVE_MAP_FACTORIES>
		<MoveMapFactory name="movemap_L1" bb="0" chi="0">
			<Backbone residue_selector="L1" />
			<Chi residue_selector="L1" />
		</MoveMapFactory>
	</MOVE_MAP_FACTORIES>
	<SIMPLE_METRICS>
		<TimingProfileMetric name="timing" />
		<RMSDMetric name="rmsd" rmsd_type="rmsd_protein_bb_heavy" residue_selector="L1" use_native="1"/>
		<SasaMetric name="sasa" residue_selector="L1"/>
		<DihedralDistanceMetric name="dihedral" residue_selector="L1" use_native="1"/>
		<SelectedResiduesMetric name="selection" residue_selector="L1"/>
		<SelectedResiduesMetric name="rosetta_sele" residue_selector="L1" rosetta_numbering="1"/>
		<SelectedResiduesPyMOLMetric name="pymol_selection" residue_selector="L1" />
		<SequenceMetric name="sequence" residue_selector="L1" />
		<SecondaryStructureMetric name="ss" residue_selector="L1" />
		<TotalEnergyMetric name="total_energy" residue_selector="L1" />
		<CompositeEnergyMetric name="composite_energy" residue_selector="L1" use_native="1"/>
	</SIMPLE_METRICS>
	<MOVERS>
		<MinMover name="min_mover" movemap_factory="movemap_L1" tolerance=".1" /> 
		<RunSimpleMetrics name="run_metrics1" metrics="sasa,pymol_selection,sequence,ss,total_energy,rosetta_sele" prefix="m1_" />
		<RunSimpleMetrics name="run_metrics2" metrics="sasa,selection,pymol_selection,sequence,ss,total_energy,rmsd,dihedral,composite_energy" prefix="m2_" />
	</MOVERS>
	<PROTOCOLS>
		<Add mover_name="run_metrics1"/>
		<Add mover_name="min_mover" />
		<Add mover_name="run_metrics2" />
	</PROTOCOLS>
</ROSETTASCRIPTS>

RunSimpleMetrics