glycopeptide_docking¶

Bindings for protocols::glycopeptide_docking namespace

class pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags¶

Bases: pybind11_object

Holds flags, options, and pose variables for the Glycosylation Protocol.

additional_metrics(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → bool¶

Get whether to output additional distance metrics to scorefile

Get the same output as publication Mahajan et. al. 2020 Biorxiv

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::additional_metrics() –> bool

anchor_residue_substrate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get index (internal numbering) of the: fold tree anchor (fold tree goes out in all direction from this residue). Only important when fold tree is specified as ‘outward’.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::anchor_residue_substrate() const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, : pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::operator=(const class protocols::glycopeptide_docking::GlycopeptideDockingFlags &) –> class protocols::glycopeptide_docking::GlycopeptideDockingFlags &

clone(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::clone() const –> class std::shared_ptr<class protocols::glycopeptide_docking::GlycopeptideDockingFlags>

debug_pdbs(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → bool¶

Get whether to output interim debug pdbs during low and high resolution: cycles.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::debug_pdbs() –> bool

enable_additional_metrics(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: bool) → None¶

Enable writing of additional metrics to scorefile

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::enable_additional_metrics(bool) –> void

enable_backbone_moves_substrate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → bool¶

Get whether to sample substrate backbone: TODO: Add similar option for enzyme

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::enable_backbone_moves_substrate() –> bool

first_residue_enzyme(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get first residue of the enzyme

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::first_residue_enzyme() const –> unsigned long

first_residue_substrate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get index (internal numbering) of the first residue of the substrate

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::first_residue_substrate() const –> unsigned long

get_allow_glycan_torsion_moves(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → bool¶

Get whether to sample glycan torsional dofs with glycan sampler

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_allow_glycan_torsion_moves() –> bool

get_anchor_residue(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get anchor residue with internal numbering

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_anchor_residue() –> unsigned long

get_backbone_moves(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get cycles for backbone moves in high resolution

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_backbone_moves() –> unsigned long

get_constraints_file(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → str¶

Get name of constraints file

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_constraints_file() –> std::string

get_downstream_chain(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → str¶

Get downstream chain for ‘outward’ fold tree

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_downstream_chain() –> std::string

get_glycosylation_residue(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get glycosylation residue with internal numbering

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_glycosylation_residue() –> unsigned long

get_interface_distance(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → float¶

Get interface distance

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_interface_distance() –> double

get_interface_moves(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get how frequently the interface is sampled

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_interface_moves() –> unsigned long

get_residues_to_preglycosylate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Get residue indices (int numbering) to pre-glycosylate before starting sampling

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_residues_to_preglycosylate() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_sugar_donor(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get residue index of sugar donor

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_sugar_donor() –> unsigned long

get_sugars_to_preglycosylate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → pyrosetta.rosetta.utility.vector1_std_string¶

Get names of sugars for pre-glycosylate before starting sampling: #sugar names must match #residue indices for preglycosylation.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_sugars_to_preglycosylate() –> class utility::vector1<std::string, class std::allocator<std::string > >

get_upstream_chain(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → str¶

Get upstream chain for ‘outward’ fold tree

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::get_upstream_chain() –> std::string

glycosylation_residue_substrate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get index (internal numbering) of the site of glycosylation: under investigation. (There may be other glycosylated residues on the peptide)

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::glycosylation_residue_substrate() const –> unsigned long

high_res_outer_cycles(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get how many outer MC cycles to run for high-res refinement

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::high_res_outer_cycles() –> unsigned long

high_res_refinement(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → bool¶

Get whether high refinement is on

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::high_res_refinement() –> bool

jump_num_substrate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get jump number of the substrate

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::jump_num_substrate() const –> unsigned long

last_residue_enzyme(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get last residue of the enzyme

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::last_residue_enzyme() const –> unsigned long

last_residue_substrate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get index (internal numbering) of the last residue of the substrate

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::last_residue_substrate() const –> unsigned long

low_res_inner_cycles(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get how many inner MC cycles to run for low-res refinement

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::low_res_inner_cycles() –> unsigned long

low_res_outer_cycles(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → int¶

Get how many outer MC cycles to run for low-res refinement

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::low_res_outer_cycles() –> unsigned long

low_res_refinement(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → bool¶

Get whether low refinement is on

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::low_res_refinement() –> bool

pack_anchor(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → bool¶

Get whether anchor repacking on or off

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::pack_anchor() –> bool

randomize_substrate_torsions(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → bool¶

Get whether to randomize initial torsions

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::randomize_substrate_torsions() –> bool

score_only(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → bool¶

Get whether to run in sampling or score-only mode.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::score_only() –> bool

set_allow_glycan_torsion_moves(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: bool) → None¶

Set whether to sample glycan torsional dofs with glycan sampler

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_allow_glycan_torsion_moves(bool) –> void

set_anchor_repacking(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: bool) → None¶

On anchor residue sidechain repacking on or off

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_anchor_repacking(bool) –> void

set_anchor_residue(*args, **kwargs)¶

Overloaded function.

set_anchor_residue(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose, special_residue: str) -> None

Set anchor residue. Residue from which the foldtree: emnates outwards when fold tree type is set as “outward”

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_anchor_residue(const class core::pose::Pose &, const std::string &) –> void

set_anchor_residue(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: int) -> None

Set anchor residue with internal numbering

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_anchor_residue(unsigned long) –> void

set_backbone_moves(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, n: int) → None¶

Set cycles for backbone moves in high resolution

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_backbone_moves(unsigned long) –> void

set_backbone_moves_substrate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: bool) → None¶

Set whether to sample substrate backbone

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_backbone_moves_substrate(bool) –> void

set_constraints_file(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, filename: str) → None¶

Set name of constraints file: Useful for setting constraints to preserve any catalytic motifs

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_constraints_file(const std::string &) –> void

set_debug_pdbs(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: bool) → None¶

Set whether to output interim debug pdbs during low and high resolution: cycles.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_debug_pdbs(bool) –> void

set_downstream_chain(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, chain: str) → None¶

Set downstream chain for ‘outward’ fold tree

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_downstream_chain(const std::string &) –> void

set_enzyme_chain(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Set enzyme chain.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_enzyme_chain(const class core::pose::Pose &) –> void

set_fold_tree_type(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: str) → None¶

Set fold tree type: outward OR docking

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_fold_tree_type(const std::string &) –> void

set_glycosylation_refinement(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, low: bool, high: bool) → None¶

Set low and high res refinement options

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_glycosylation_refinement(bool, bool) –> void

set_glycosylation_residue(*args, **kwargs)¶

Overloaded function.

set_glycosylation_residue(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose, special_residue: str) -> None

Set glycosylation residue from pose and pdb numbering

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_glycosylation_residue(const class core::pose::Pose &, const std::string &) –> void

set_glycosylation_residue(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: int) -> None

Set glycosylation residue with internal numbering

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_glycosylation_residue(unsigned long) –> void

set_interface_distance(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, distance: float) → None¶

Set interface distance

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_interface_distance(double) –> void

set_interface_moves(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, n: int) → None¶

Set how frequently the interface must be sampled:: Eg. every 3rd cycle

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_interface_moves(unsigned long) –> void

set_randomize_substrate_torsions(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: bool) → None¶

Set whether to randomize initial torsions

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_randomize_substrate_torsions(bool) –> void

set_residues_to_preglycosylate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Set residue indices (int numbering) to pre-glycosylate before starting sampling

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_residues_to_preglycosylate(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

set_score_only(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: bool) → None¶

Set whether to run in score_only mode. Protocol is not run.: Only score is evaluated with distance, rmsd and interaction energy metrics.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_score_only(bool) –> void

set_substrate_chain(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Set substrate chain.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_chain(const class core::pose::Pose &) –> void

set_substrate_type(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: str) → None¶

Set substrate type: Only ‘peptide’ type is supported for now: TODO: lipids - if there are interesting applications

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_type(const std::string &) –> void

set_sugar_donor(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: int) → None¶

Set residue index of sugar donor

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_sugar_donor(unsigned long) –> void

set_sugars_to_preglycosylate(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, in: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Set names of sugars for pre-glycosylate before starting sampling: #sugar names must match #residue indices for preglycosylation.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_sugars_to_preglycosylate(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

set_upstream_chain(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, chain: str) → None¶

Set upstream chain for ‘outward’ fold tree

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_upstream_chain(const std::string &) –> void

setup_from_options(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → None¶

Set variables from specified command line options.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::setup_from_options() –> void

show(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → None¶

Show set options.

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::show() const –> void

substrate_type(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → str¶

Get substrate type: Only ‘peptide’ type is supported for now

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::substrate_type() –> std::string

tree_type(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → str¶

Get fold tree type

C++: protocols::glycopeptide_docking::GlycopeptideDockingFlags::tree_type() –> std::string

class pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement¶

Bases: Mover

High resolution refinement of glycosyltransferase substrate.

Applies a set of samplers to the pose in high resolution mode. At the beginning, the fa_atr term is upweighted and the fa_rep term is downweighted. The terms are ramped down and up respectively to their score function weights over n_cycles_. For each cycles, the pose is subjected to: 1. N cycles of rigid body moves 1.1. Rigid body perturbation 1.2 Sidechain packing of substrate 1.3 Sidechain packing of interface 1.4 Minimization across the substrate-enzyme jump 1.5 Metropolis criterion (MCM with 1.4) 2. N cycles of torsion moves “induced fit” 2.1 Apply small or shear mover 2.2 Sidechain packing of substrate 2.3 Sidechain packing of interface 2.4 Minimize and apply Metropolis criterion (MCM)

apply(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement, : pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::operator=(const class protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement &) –> class protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_docking_foldtree(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → pyrosetta.rosetta.core.kinematics.FoldTree¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_docking_foldtree() –> class std::shared_ptr<const class core::kinematics::FoldTree>

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → str¶

get name

C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_options(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_options() –> class std::shared_ptr<class protocols::glycopeptide_docking::GlycopeptideDockingFlags>

get_scorefunction(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_scorefunction() –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_substrate_foldtree(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → pyrosetta.rosetta.core.kinematics.FoldTree¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_substrate_foldtree() –> class std::shared_ptr<const class core::kinematics::FoldTree>

get_target_attractive_weight(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → float¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_target_attractive_weight() –> double

get_target_repulsive_weight(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → float¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_target_repulsive_weight() –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶

get mover name

C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_docking_foldtree(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement, ft_docking: pyrosetta.rosetta.core.kinematics.FoldTree) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_docking_foldtree(class std::shared_ptr<class core::kinematics::FoldTree>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_options(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement, flags: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → None¶

Getters and setters for sf, foldtrees, flags

C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_options(class std::shared_ptr<class protocols::glycopeptide_docking::GlycopeptideDockingFlags>) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_substrate_foldtree(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement, ft_substrate: pyrosetta.rosetta.core.kinematics.FoldTree) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_substrate_foldtree(class std::shared_ptr<class core::kinematics::FoldTree>) –> void

set_target_attractive_weight(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement, w: float) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_target_attractive_weight(double) –> void

set_target_repulsive_weight(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement, w: float) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_target_repulsive_weight(double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

setup(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) → None¶

setup default for the mover

C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::setup() –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement) -> None
show(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement, output: pyrosetta.rosetta.std.ostream) -> None

show mover details

C++: protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement¶

Bases: Mover

Low resolution refinement of substrate

Low resolution refinement primarly for sampling peptide conformational space. We use simulated annealing varying mc temperature from 2.0 to 0.6 (final) temperature. The protocol applies the following steps over 30 cycles of simulated annealing: 1. rigidbody perturber mover 2. minimization across the jump 3. Samples torsions of the peptide with small and shear mover 4. Minimizes peptide

apply(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement, : pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement) → pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::operator=(const class protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement &) –> class protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_docking_foldtree(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement) → pyrosetta.rosetta.core.kinematics.FoldTree¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_docking_foldtree() –> class std::shared_ptr<const class core::kinematics::FoldTree>

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement) → str¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_options(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement) → pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_options() –> class std::shared_ptr<class protocols::glycopeptide_docking::GlycopeptideDockingFlags>

get_scorefunction(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_scorefunction() –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_substrate_foldtree(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement) → pyrosetta.rosetta.core.kinematics.FoldTree¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_substrate_foldtree() –> class std::shared_ptr<const class core::kinematics::FoldTree>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_docking_foldtree(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement, ft_docking: pyrosetta.rosetta.core.kinematics.FoldTree) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_docking_foldtree(class std::shared_ptr<class core::kinematics::FoldTree>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_options(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement, flags: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags) → None¶

Getters and setters for sf, foldtrees, flags

C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_options(class std::shared_ptr<class protocols::glycopeptide_docking::GlycopeptideDockingFlags>) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_substrate_foldtree(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement, ft_substrate: pyrosetta.rosetta.core.kinematics.FoldTree) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_substrate_foldtree(class std::shared_ptr<class core::kinematics::FoldTree>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement) -> None
show(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol¶

Bases: Mover

A protocol to predict glycosylation and elongation of glycans.

This protocol is intended to “sample” glycopeptide poses/conformations in the context of the glycosyltransferase “ready” to be glycosylated. Similar to enzyme-design protocols, constraints can be specified to emulate the positioning of atoms/residues in the transition state comingsoon(3-4 months): We are currently prototyping an extension to generalize the protocol for elongation to core1, core2 and higher sugars with their respective glcyosyltransferases. We hope to automate substrate generation from peptide-sequence and glycosylation (for glycopeptide substrates), donor glycosylation (e.g. UDP->UDP-Sugar) and initial setup of the peptide-substrate in the active site. Additional options are defined in GlycopeptideDockingFlags.hh

apply(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol, object_to_copy: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol) → pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol¶

Assignment operator

C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::operator=(const class protocols::glycopeptide_docking::GlycopeptideDockingProtocol &) –> class protocols::glycopeptide_docking::GlycopeptideDockingProtocol &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol) → str¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_ref_pose_from_filename(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol, filename: str) → None¶

Set reference pose (native) from file name

C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::set_ref_pose_from_filename(const std::string &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol) -> None
show(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol, output: pyrosetta.rosetta.std.ostream) -> None

Show mover information

C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocol::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator, : pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator) → pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocolCreator::operator=(const class protocols::glycopeptide_docking::GlycopeptideDockingProtocolCreator &) –> class protocols::glycopeptide_docking::GlycopeptideDockingProtocolCreator &

create_mover(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator) → str¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocolCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::glycopeptide_docking::GlycopeptideDockingProtocolCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.glycopeptide_docking.calculate_additional_glycosylation_metrics(pose: pyrosetta.rosetta.core.pose.Pose, glycosylation_residue: int, donor_residue: int) → pyrosetta.rosetta.std.map_std_string_double¶

TODO: generalize

C++: protocols::glycopeptide_docking::calculate_additional_glycosylation_metrics(const class core::pose::Pose &, unsigned long, const unsigned long) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

pyrosetta.rosetta.protocols.glycopeptide_docking.calculate_sampled_distance(pose: pyrosetta.rosetta.core.pose.Pose, glycosylation_residue: int, donor_residue: int) → float¶

Calculate distance between donor and substrate.

C++: protocols::glycopeptide_docking::calculate_sampled_distance(const class core::pose::Pose &, const unsigned long, const unsigned long) –> double

pyrosetta.rosetta.protocols.glycopeptide_docking.glycosylate_residues(pose: pyrosetta.rosetta.core.pose.Pose, sugar_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, sugar_names: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Glycosylate residues (sugar_residues) with: sugars specified in sugar_names. This feature is experimental.

C++: protocols::glycopeptide_docking::glycosylate_residues(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

pyrosetta.rosetta.protocols.glycopeptide_docking.record_pose_metrics(pose: pyrosetta.rosetta.core.pose.Pose, flags: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, jumps: pyrosetta.rosetta.utility.vector1_int, ref_pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Record metrics such as important distances,: rmsds and interaction energies (to match publication)

C++: protocols::glycopeptide_docking::record_pose_metrics(class core::pose::Pose &, class std::shared_ptr<class protocols::glycopeptide_docking::GlycopeptideDockingFlags>, const class utility::vector1<int, class std::allocator<int> >, class std::shared_ptr<class core::pose::Pose>) –> void

pyrosetta.rosetta.protocols.glycopeptide_docking.setup_glycosylation_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, flags: pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags, ft_docking: pyrosetta.rosetta.core.kinematics.FoldTree) → None¶

The foldtree for glycosylation can be set up in two ways.: The “outward” foldtree or the “docking” foldtree. The docking foldtree is the standard docking foldtree and is setup across the enzyme-peptide or enzyme -glycopeptide interface. The outward foldtree is anchored at an “anchor residue” specified with the anchor_residue flag. In the absence of this specification the residue_to_glycosylate is also the anchor residue. This foldtree goes outwards in all directions from the anchored position. The outward foldtree is especially useful for glycopeptide glycosylation i.e. glycosylating a pre-glycosylated peptide at a new site. In such a case, if the binding site of one sugar on the peptide is known, the preglycosylated site on the peptide substrate can be specified as the anchor residue. This allows for a floppy tail type of sampling. Another useful choice for anchor residue is the site of glycosylation, especially when the user is sampling with the site of glycosylation already glycosylated. In the current implementation, a specialized foldtree is setup for a pose. User-specified foldtree is not supported.

C++: protocols::glycopeptide_docking::setup_glycosylation_foldtree(class core::pose::Pose &, class std::shared_ptr<class protocols::glycopeptide_docking::GlycopeptideDockingFlags>, class std::shared_ptr<class core::kinematics::FoldTree>) –> void

pyrosetta.rosetta.protocols.glycopeptide_docking.write_debug_pdb(pose: pyrosetta.rosetta.core.pose.Pose, nstruct_max: int, nstruct_index: int, name: str) → None¶

Write pdbs with output string with specified name and prefix, suffix and decoy number to match the fianl decoy.

C++: protocols::glycopeptide_docking::write_debug_pdb(const class core::pose::Pose &, const unsigned long, const unsigned long, std::string) –> void