PackRotamersMoverPartGreedy

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PackRotamersMoverPartGreedy

Autogenerated Tag Syntax Documentation:

Greedily optimizes around a set of target residues, then repacks sidechains with user-supplied options, including TaskOperations. Given a task and a set of target residues, this mover will first greedily choose the neighbors of these residues, and then perform the usual simulated annealing on the rest (while maintaining the identity of the greedily chosen sidechains). The greedy choices are made one by one, i.e. first convert every neighbor of a given target sidechain to Ala, choose the lowest energy neighbor rotamer and minimize, then look at the rest of the neighbors and choose the best for interacting with the two chosen so far, and so on, until you're out of neighbor positions. If more than one target residues are specified, a random permutation of this list is used in each run of the mover.

<PackRotamersMoverPartGreedy name="(&string;)"
        task_operations="(&task_operation_comma_separated_list;)"
        task_factory="(&string;)" packer_palette="(&named_packer_palette;)"
        scorefxn_repack="(&string;)" scorefxn_repack_greedy="(&string;)"
        scorefxn_minimize="(&string;)" target_residues="(&string;)"
        target_cstids="(&string;)" distance_threshold="(8.0 &real;)"
        choose_best_n="(&non_negative_integer;)" />

task_operations: A comma-separated list of TaskOperations to use.
task_factory: A TaskFactory specification to use.
packer_palette: A previously-defined PackerPalette to use, which specifies the set of residue types with which to design (to be pruned with TaskOperations).
scorefxn_repack: Name of score function to use
scorefxn_repack_greedy: Name of score function to use
scorefxn_minimize: Name of score function to use
target_residues: comma-separated list of target residues
target_cstids: comma-separated list of target cstids (e.g. 1B,2B,3B etc)
distance_threshold: distance between residues to be considered neighbors (of target residue)
choose_best_n: number of lowest scoring residues on a protein-ligand interface to use as targets

PackRotamersMoverPartGreedy

PackRotamersMoverPartGreedy

See Also