scripting_documentation/RosettaScripts/xsd/mover_LinkageConformerMover

Autogenerated Tag Syntax Documentation:

Authors: Jared Adolf-Bryfogle (jadolfbr@gmail.com) and Jason W. Labonte (JWLabonte@jhu.edu) Mover to sample glycan linkages using conformers generated from the PDB using adaptive kernal density estimates.

References and author information for the LinkageConformerMover mover:

LinkageConformerMover Mover's citation(s): Labonte JW, Adolf-Bryfogle J, Schief WR, and Gray JJ. (2017). Residue-centric modeling and design of saccharide and glycoconjugate structures. J Comput Chem 38(5):276–87. doi: 10.1002/jcc.24679.

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

<LinkageConformerMover name="(&string;)" upper_resnum="(&non_negative_integer;)"
        use_sugar_bb_if_needed="(true &bool;)"
        idealize_torsions="(false &bool;)" gaussian_sampling="(false &bool;)"
        sample_protein_linkage="(true &bool;)"
        use_conformer_population_stats="(true &bool;)"
        root_populations_only="(false &bool;)" residue_selector="(&string;)" />

upper_resnum: (REQUIRED) XRW TO DO
use_sugar_bb_if_needed: Use sugar backbone data if needed?
idealize_torsions: Use the Mean values of each torsion angle making up a conformer instead of sampling using the SD either uniformly or through a gaussian.
gaussian_sampling: Use standard deviation and means to sample on the gaussian of each torsion angle that make up a conformer
sample_protein_linkage: Also sample linkage between glycan and protein
use_conformer_population_stats: Use statistics about conformer populations for sampling
root_populations_only: Use population-based sampling for only the linkage between the amino acid and glycan residue
residue_selector: . 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.

scripting_documentation/RosettaScripts/xsd/mover_LinkageConformerMover_type