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InteractionEnergyMetric

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

Autogenerated Tag Syntax Documentation:

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) A metric for measuring the short and long range interaction energy between residues using two sets of residue selectors. Will use the current energies of the pose, unless force_rescore option is set.

References and author information for the InteractionEnergyMetric simple metric:

InteractionEnergyMetric SimpleMetric's author(s): Jared Adolf-Bryfogle, Scripps Research Institute jadolfbr@gmail.com John Karanicolas, Department of Molecular Biosciences, University of Kansas johnk@ku.edu Roland A. Pache, Department of Bioengineering and Therapeutic Sciences, University of California San Francisco johnk@ku.edu

<InteractionEnergyMetric name="(&string;)" custom_type="(&string;)"
        scoretypes_only="(&string;)" scoretypes_skip="(&string;)"
        include_rama_prepro_and_proclose="(false &bool;)"
        force_rescore="(false &bool;)" residue_selector="(&string;)"
        residue_selector2="(&string;)" scorefxn="(&string;)" />
  • 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.
  • scoretypes_only: Include only this list of ScoreTypes
  • scoretypes_skip: Always skip these score types
  • include_rama_prepro_and_proclose: Include rama_prepro energy term AND pro_close? (Which are two-body backbone score terms)
  • force_rescore: Should we rescore the pose, even if it has an energies object? This will force a pose copy and rescore and will not be as efficent as having a scored pose
  • residue_selector: Selector specifying first set of residues. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.
  • residue_selector2: Selector specifying second set of residues. Default is TrueResidueSelector. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.
  • scorefxn: Name of score function to use

See Also