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This is still an in-development, unnpublished application. If you use this in your publication, please email the authors!
GlycanSampler is the main sampling component of the GlycanTreeModeler
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Authors: Jared Adolf-Bryfogle (firstname.lastname@example.org) and Jason Labonte (WLabonte@jhu.edu) Main mover for GlycanTreeModeler, which optimizes glycans in a pose. You probably want to use that instead.Each round optimizes either one residue for BB sampling, linkage, or a [part of a ] branch for minimization and packing.Minimization and packing work by default by selecting a random glycan residue from any set movemap or all of them and then selecting the rest of the downstream branch. Those residues are then minimized or packed. Packing includes a neighbor packing shell. Currently uses a random sampler with a set of weights to each mover for sampling.
<GlycanSampler name="(&string;)" kt="(ℜ)" rounds="(100 &non_negative_integer;)" final_min="(true &bool;)" pymol_movie="(false &bool;)" refine="(false &bool;)" pack_distance="(6.0 ℜ)" cartmin="(false &bool;)" tree_based_min_pack="(true &bool;)" use_conformer_probs="(false &bool;)" use_gaussian_sampling="(true &bool;)" min_rings="(false &bool;)" shear="(true &bool;)" randomize_torsions="(true &bool;)" match_sampling_of_modeler="(false &bool;)" inner_bb_cycles="(0 &non_negative_integer;)" root_populations_only="(false &bool;)" task_operations="(&task_operation_comma_separated_list;)" packer_palette="(&named_packer_palette;)" scorefxn="(&string;)" residue_selector="(&string;)" />