Classes
class	CreateGlycanSequonMover
	Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation as well as other positions that have been shown to influence the glycosylation chemistry. More...

class	CreateGlycanSequonMoverCreator

class	GlycanSampler
	Main mover for Glycan Relax, which optimizes glycans in a pose. Each round optimizes either one residue for BB sampling, linkage, or multiple for minimization. Currently uses a random sampler with a set of weights to each mover for sampling. More...

class	GlycanSamplerCreator

class	GlycanTreeMinMover
	A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector. More...

class	GlycanTreeMinMoverCreator

class	GlycanTreeModeler
	A protocol for optimizing glycan trees using the GlycanSampler from the base of the tree out to the leaves. More...

class	GlycanTreeModelerCreator

class	IdealizeAnomericHydrogens
	This code sets all the anomeric hydrogen positions based on the input structure. More...

class	IdealizeAnomericHydrogensCreator

class	LinkageConformerMover
	This code changes all of the dihedrals of a particular glycosidic linkage based on database info, esentially sampling carbohydrate dihedral conformers of two residues. Randomly samples on any set selector at each apply or (default) samples a linkage conformer for each residue set. More...

class	LinkageConformerMoverCreator

class	RingPlaneFlipMover
	A Mover class for flipping the plane of a carbohydrate pyranose ring 180 degrees about its anomeric bond. More...

class	RingPlaneFlipMoverCreator
	MoverCreator allowing the MoverFactory to create a RingConformationMover. More...

class	SimpleGlycosylateMover
	A mover for glycosylation of biological glycosylations. Currently glysolylation is done based on string, not from PDB. Use the GlycanSampler to model the resulting glycosylation!. More...

class	SimpleGlycosylateMoverCreator

class	TautomerizeAnomerMover
	A Mover class for tautomerizing from one anomer to another at a reducing end. More...

class	TautomerizeAnomerMoverCreator
	MoverCreator allowing the MoverFactory to create a TautomerizeAnomerMover. More...

Typedefs
typedef utility::pointer::shared_ptr< CreateGlycanSequonMover >	CreateGlycanSequonMoverOP

typedef utility::pointer::shared_ptr< CreateGlycanSequonMover const >	CreateGlycanSequonMoverCOP

typedef utility::pointer::shared_ptr< GlycanSampler >	GlycanSamplerOP

typedef utility::pointer::shared_ptr< GlycanSampler const >	GlycanSamplerCOP

typedef utility::pointer::shared_ptr< GlycanTreeMinMover >	GlycanTreeMinMoverOP

typedef utility::pointer::shared_ptr< GlycanTreeMinMover const >	GlycanTreeMinMoverCOP

typedef utility::pointer::shared_ptr< GlycanTreeModeler >	GlycanTreeModelerOP

typedef utility::pointer::shared_ptr< GlycanTreeModeler const >	GlycanTreeModelerCOP

typedef utility::pointer::shared_ptr< IdealizeAnomericHydrogensMover >	IdealizeAnomericHydrogensMoverOP

typedef utility::pointer::shared_ptr< IdealizeAnomericHydrogensMover const >	IdealizeAnomericHydrogensMoverCOP

typedef utility::pointer::shared_ptr< LinkageConformerMover >	LinkageConformerMoverOP

typedef utility::pointer::shared_ptr< LinkageConformerMover const >	LinkageConformerMoverCOP

typedef utility::pointer::shared_ptr< RingPlaneFlipMover >	RingPlaneFlipMoverOP

typedef utility::pointer::shared_ptr< RingPlaneFlipMover const >	RingPlaneFlipMoverCOP

typedef utility::pointer::shared_ptr< SimpleGlycosylateMover >	SimpleGlycosylateMoverOP

typedef utility::pointer::shared_ptr< SimpleGlycosylateMover const >	SimpleGlycosylateMoverCOP

typedef utility::pointer::shared_ptr< TautomerizeAnomerMover >	TautomerizeAnomerMoverOP

typedef utility::pointer::shared_ptr< TautomerizeAnomerMover const >	TautomerizeAnomerMoverCOP

Enumerations
enum	GlycanSequon { n_linked_typical = 1 , n_linked_basic_enhanced , n_linked_best_enhanced , c_linked_NxC , c_linked_WxxW , c_linked_WSTxC }

enum	QuenchDirection { forward = 1 , backward }

Functions
std::map< GlycanSequon, std::string >	create_sequons ()
	Create a map of the name and full sequon. More...

std::ostream &	operator<< (std::ostream &os, CreateGlycanSequonMover const &mover)
	private methods /// More...

std::ostream &	operator<< (std::ostream &os, GlycanSampler const &mover)

std::ostream &	operator<< (std::ostream &os, GlycanTreeModeler const &mover)
	private methods /// More...

std::ostream &	operator<< (std::ostream &os, LinkageConformerMover const &mover)

std::ostream &	operator<< (std::ostream &output, RingPlaneFlipMover const &object_to_output)

std::ostream &	operator<< (std::ostream &os, SimpleGlycosylateMover const &mover)

std::ostream &	operator<< (std::ostream &output, TautomerizeAnomerMover const &object_to_output)

core::pack::task::TaskFactoryOP	get_all_glycans_and_neighbor_res_task_factory (utility::vector1< bool > const &subset, core::Real pack_distance=6.0, bool read_resfile=true)
	Get a TaskFactory of all residues in the subset and neighboring residues. More...

void	run_shear_min_pack (protocols::minimization_packing::MinMover &min_mover, protocols::minimization_packing::PackRotamersMover &packer, protocols::simple_moves::ShearMover &shear, protocols::moves::MonteCarlo &mc, core::Size n_glycan_residues, core::pose::Pose &pose, bool use_shear=true)
	Run a shear/min/pack on all residues set to move. More...

core::Size	get_total_rounds_for_overlap_one_layer_two (core::pose::Pose const &pose, utility::vector1< bool > const &residue_subset, core::Size sampler_rounds)
	Used for benchmarking to test even sampling of different kinematic protocols Get the total number of sampling rounds for the GlycanTreeModeler protocol with previous default settings. More...

Typedef Documentation

◆ CreateGlycanSequonMoverCOP

typedef utility::pointer::shared_ptr< CreateGlycanSequonMover const > protocols::carbohydrates::CreateGlycanSequonMoverCOP

◆ CreateGlycanSequonMoverOP

typedef utility::pointer::shared_ptr< CreateGlycanSequonMover > protocols::carbohydrates::CreateGlycanSequonMoverOP

◆ GlycanSamplerCOP

typedef utility::pointer::shared_ptr< GlycanSampler const > protocols::carbohydrates::GlycanSamplerCOP

◆ GlycanSamplerOP

typedef utility::pointer::shared_ptr< GlycanSampler > protocols::carbohydrates::GlycanSamplerOP

◆ GlycanTreeMinMoverCOP

typedef utility::pointer::shared_ptr< GlycanTreeMinMover const > protocols::carbohydrates::GlycanTreeMinMoverCOP

◆ GlycanTreeMinMoverOP

typedef utility::pointer::shared_ptr< GlycanTreeMinMover > protocols::carbohydrates::GlycanTreeMinMoverOP

◆ GlycanTreeModelerCOP

typedef utility::pointer::shared_ptr< GlycanTreeModeler const > protocols::carbohydrates::GlycanTreeModelerCOP

◆ GlycanTreeModelerOP

typedef utility::pointer::shared_ptr< GlycanTreeModeler > protocols::carbohydrates::GlycanTreeModelerOP

◆ IdealizeAnomericHydrogensMoverCOP

typedef utility::pointer::shared_ptr< IdealizeAnomericHydrogensMover const > protocols::carbohydrates::IdealizeAnomericHydrogensMoverCOP

◆ IdealizeAnomericHydrogensMoverOP

typedef utility::pointer::shared_ptr< IdealizeAnomericHydrogensMover > protocols::carbohydrates::IdealizeAnomericHydrogensMoverOP

◆ LinkageConformerMoverCOP

typedef utility::pointer::shared_ptr< LinkageConformerMover const > protocols::carbohydrates::LinkageConformerMoverCOP

◆ LinkageConformerMoverOP

typedef utility::pointer::shared_ptr< LinkageConformerMover > protocols::carbohydrates::LinkageConformerMoverOP

◆ RingPlaneFlipMoverCOP

typedef utility::pointer::shared_ptr< RingPlaneFlipMover const > protocols::carbohydrates::RingPlaneFlipMoverCOP

◆ RingPlaneFlipMoverOP

typedef utility::pointer::shared_ptr< RingPlaneFlipMover > protocols::carbohydrates::RingPlaneFlipMoverOP

◆ SimpleGlycosylateMoverCOP

typedef utility::pointer::shared_ptr< SimpleGlycosylateMover const > protocols::carbohydrates::SimpleGlycosylateMoverCOP

◆ SimpleGlycosylateMoverOP

typedef utility::pointer::shared_ptr< SimpleGlycosylateMover > protocols::carbohydrates::SimpleGlycosylateMoverOP

◆ TautomerizeAnomerMoverCOP

typedef utility::pointer::shared_ptr< TautomerizeAnomerMover const > protocols::carbohydrates::TautomerizeAnomerMoverCOP

◆ TautomerizeAnomerMoverOP

typedef utility::pointer::shared_ptr< TautomerizeAnomerMover > protocols::carbohydrates::TautomerizeAnomerMoverOP

Enumeration Type Documentation

◆ GlycanSequon

enum protocols::carbohydrates::GlycanSequon

Enumerator
n_linked_typical
n_linked_basic_enhanced
n_linked_best_enhanced
c_linked_NxC
c_linked_WxxW
c_linked_WSTxC

◆ QuenchDirection

enum protocols::carbohydrates::QuenchDirection

Enumerator
forward
backward

Function Documentation

◆ create_sequons()

std::map< GlycanSequon, std::string > protocols::carbohydrates::create_sequons ( )

Create a map of the name and full sequon.

References c_linked_NxC, c_linked_WSTxC, c_linked_WxxW, n_linked_basic_enhanced, n_linked_typical, and protocols::TR().

Referenced by protocols::carbohydrates::CreateGlycanSequonMover::CreateGlycanSequonMover().

◆ get_all_glycans_and_neighbor_res_task_factory()

core::pack::task::TaskFactoryOP protocols::carbohydrates::get_all_glycans_and_neighbor_res_task_factory	(	utility::vector1< bool > const &	subset,
		core::Real	pack_distance = `6.0`,
		bool	read_resfile = `true`
	)

Get a TaskFactory of all residues in the subset and neighboring residues.

Operations: InitializeFromCommandline ReadResFile? If option given on cmd-line, returns TF up to this. NeighborhoodResidueSelector/OperateOnResidueSubset RestrictRepacking/PreventRepacking

References core::chemical::VIRTUAL_RESIDUE.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::carbohydrates::GlycanSampler::setup_default_task_factory(), and protocols::carbohydrates::GlycanSampler::setup_packer().

◆ get_total_rounds_for_overlap_one_layer_two()

core::Size protocols::carbohydrates::get_total_rounds_for_overlap_one_layer_two	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	residue_subset,
		core::Size	sampler_rounds
	)

Used for benchmarking to test even sampling of different kinematic protocols Get the total number of sampling rounds for the GlycanTreeModeler protocol with previous default settings.

References core::select::residue_selector::AND_combine(), core::select::residue_selector::GlycanLayerSelector::apply(), core::select::residue_selector::count_selected(), core::pose::Pose::glycan_tree_set(), core::chemical::element::N, protocols::pose_metric_calculators::residue_subset(), and core::select::residue_selector::GlycanLayerSelector::set_layer().

Referenced by protocols::carbohydrates::GlycanSampler::apply(), and protocols::carbohydrates::GlycanTreeModeler::apply().

◆ operator<<() [1/7]

std::ostream & protocols::carbohydrates::operator<<	(	std::ostream &	os,
		CreateGlycanSequonMover const &	mover
	)

private methods ///

References protocols::carbohydrates::CreateGlycanSequonMover::show().

◆ operator<<() [2/7]

std::ostream & protocols::carbohydrates::operator<<	(	std::ostream &	os,
		GlycanSampler const &	mover
	)

References protocols::carbohydrates::GlycanSampler::show().

◆ operator<<() [3/7]

std::ostream & protocols::carbohydrates::operator<<	(	std::ostream &	os,
		GlycanTreeModeler const &	mover
	)

private methods ///

References protocols::carbohydrates::GlycanTreeModeler::show().

◆ operator<<() [4/7]

std::ostream & protocols::carbohydrates::operator<<	(	std::ostream &	os,
		LinkageConformerMover const &	mover
	)

References protocols::carbohydrates::LinkageConformerMover::show().

◆ operator<<() [5/7]

std::ostream & protocols::carbohydrates::operator<<	(	std::ostream &	os,
		SimpleGlycosylateMover const &	mover
	)

References protocols::carbohydrates::SimpleGlycosylateMover::show().

◆ operator<<() [6/7]

std::ostream & protocols::carbohydrates::operator<<	(	std::ostream &	output,
		RingPlaneFlipMover const &	object_to_output
	)

References protocols::carbohydrates::RingPlaneFlipMover::show().

◆ operator<<() [7/7]

std::ostream & protocols::carbohydrates::operator<<	(	std::ostream &	output,
		TautomerizeAnomerMover const &	object_to_output
	)

References protocols::carbohydrates::TautomerizeAnomerMover::show().

◆ run_shear_min_pack()

void protocols::carbohydrates::run_shear_min_pack	(	minimization_packing::MinMover &	min_mover,
		minimization_packing::PackRotamersMover &	packer,
		simple_moves::ShearMover &	shear,
		moves::MonteCarlo &	mc,
		core::Size	n_glycan_residues,
		core::pose::Pose &	pose,
		bool	use_shear
	)

Run a shear/min/pack on all residues set to move.

References protocols::simple_moves::BackboneMover::apply(), protocols::minimization_packing::MinMover::apply(), protocols::minimization_packing::PackRotamersMover::apply(), protocols::moves::MonteCarlo::boltzmann(), and protocols::TR().