Classes
class	GlycopeptideDockingFlags
	Holds flags, options, and pose variables for the Glycosylation Protocol. More...

class	GlycopeptideDockingHighResRefinement
	High resolution refinement of glycosyltransferase substrate. More...

class	GlycopeptideDockingLowResRefinement
	Low resolution refinement of substrate. More...

class	GlycopeptideDockingProtocol
	A protocol to predict glycosylation and elongation of glycans. More...

class	GlycopeptideDockingProtocolCreator

Typedefs
typedef utility::pointer::shared_ptr< GlycopeptideDockingFlags >	GlycopeptideDockingFlagsOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingFlags const >	GlycopeptideDockingFlagsCOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingHighResRefinement >	GlycopeptideDockingHighResRefinementOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingHighResRefinement const >	GlycopeptideDockingHighResRefinementCOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingLowResRefinement >	GlycopeptideDockingLowResRefinementOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingLowResRefinement const >	GlycopeptideDockingLowResRefinementCOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingProtocol >	GlycopeptideDockingProtocolOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingProtocol const >	GlycopeptideDockingProtocolCOP

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

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

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

core::Real	calculate_sampled_distance (core::pose::Pose const &pose, core::Size const glycosylation_residue, core::Size const donor_residue)
	Calculate distance between donor and substrate. More...

std::map< std::string, core::Real >	calculate_additional_glycosylation_metrics (core::pose::Pose const &pose, core::Size glycosylation_residue, core::Size const donor_residue)
	Calculate additional distance metrics for glycosylation. More...

void	write_debug_pdb (core::pose::Pose const &pose, core::Size const nstruct_max, core::Size const nstruct_index, std::string name)
	Write pdbs with output string with specified name and prefix, suffix and decoy number to match the fianl decoy. More...

void	glycosylate_residues (core::pose::Pose &pose, utility::vector1< core::Size > const &sugar_residues, utility::vector1< std::string > &sugar_names)
	Glycosylate residues (sugar_residues) with sugars specified in sugar_names. This feature is experimental. More...

void	setup_glycosylation_foldtree (core::pose::Pose &pose, protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags, core::kinematics::FoldTreeOP ft_docking)

void	record_pose_metrics (core::pose::Pose &pose, protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags, utility::vector1< int > const jumps, core::pose::PoseOP ref_pose)
	Record metrics such as important distances, rmsds and interaction energies (to match publication) More...

Typedef Documentation

◆ GlycopeptideDockingFlagsCOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingFlags const > protocols::glycopeptide_docking::GlycopeptideDockingFlagsCOP

◆ GlycopeptideDockingFlagsOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingFlags > protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP

◆ GlycopeptideDockingHighResRefinementCOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingHighResRefinement const > protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinementCOP

◆ GlycopeptideDockingHighResRefinementOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingHighResRefinement > protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinementOP

◆ GlycopeptideDockingLowResRefinementCOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingLowResRefinement const > protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinementCOP

◆ GlycopeptideDockingLowResRefinementOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingLowResRefinement > protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinementOP

◆ GlycopeptideDockingProtocolCOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingProtocol const > protocols::glycopeptide_docking::GlycopeptideDockingProtocolCOP

◆ GlycopeptideDockingProtocolOP

typedef utility::pointer::shared_ptr< GlycopeptideDockingProtocol > protocols::glycopeptide_docking::GlycopeptideDockingProtocolOP

Function Documentation

◆ calculate_additional_glycosylation_metrics()

std::map< std::string, core::Real > protocols::glycopeptide_docking::calculate_additional_glycosylation_metrics	(	core::pose::Pose const &	pose,
		core::Size const	glycosylation_residue,
		core::Size const	donor_residue
	)

Calculate additional distance metrics for glycosylation.

For specific glycosylation cases when the sugar is donated from a UDP to a substrate This function will be updated as more cases are added for sugar donors For example, pdb_HWU is encountered in O-glycosylating enzymes GalNAcTs (20 enzymes) TODO: Create a dictionary of possible donors and how to treat them.

TODO: generalize

References calculate_sampled_distance(), core::conformation::Residue::name(), core::pose::Pose::residue(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by record_pose_metrics().

◆ calculate_sampled_distance()

core::Real protocols::glycopeptide_docking::calculate_sampled_distance	(	core::pose::Pose const &	pose,
		core::Size const	glycosylation_residue,
		core::Size const	donor_residue
	)

Calculate distance between donor and substrate.

Tracks distance between donor and acceptor. If the distance exceeds a specified distance, the protocol terminates sampling early.

References core::kinematics::distance(), core::conformation::Residue::name(), core::pose::Pose::residue(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::apply(), protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::apply(), and calculate_additional_glycosylation_metrics().

◆ glycosylate_residues()

void protocols::glycopeptide_docking::glycosylate_residues	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	sugar_residues,
		utility::vector1< std::string > &	sugar_names
	)

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

Calls simpleglycosylate mover to generate pre-glycosylated peptides for sampling.

References protocols::carbohydrates::SimpleGlycosylateMover::apply(), protocols::carbohydrates::SimpleGlycosylateMover::set_glycosylations(), protocols::carbohydrates::SimpleGlycosylateMover::set_residue_selector(), and protocols::TR().

◆ operator<<() [1/3]

std::ostream & protocols::glycopeptide_docking::operator<<	(	std::ostream &	os,
		GlycopeptideDockingHighResRefinement const &	mover
	)

References protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::show().

◆ operator<<() [2/3]

std::ostream & protocols::glycopeptide_docking::operator<<	(	std::ostream &	os,
		GlycopeptideDockingLowResRefinement const &	mover
	)

References protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::show().

◆ operator<<() [3/3]

std::ostream & protocols::glycopeptide_docking::operator<<	(	std::ostream &	os,
		GlycopeptideDockingProtocol const &	mover
	)

References protocols::glycopeptide_docking::GlycopeptideDockingProtocol::show().

◆ record_pose_metrics()

void protocols::glycopeptide_docking::record_pose_metrics	(	core::pose::Pose &	pose,
		protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP	flags,
		utility::vector1< int > const	jumps,
		core::pose::PoseOP	ref_pose
	)

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

Record a collection of decoy metrics. Includes distances, rmsds and interaction energies.

References core::scoring::atom_pair_constraint, core::scoring::CA_rmsd(), protocols::docking::calc_Fnat(), protocols::docking::calc_interaction_energy(), calculate_additional_glycosylation_metrics(), core::scoring::get_score_function(), core::scoring::is_protein_CA(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::scoring::rmsd_no_super_subset(), core::pose::setPoseExtraScore(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::glycopeptide_docking::GlycopeptideDockingProtocol::apply().

◆ setup_glycosylation_foldtree()

void protocols::glycopeptide_docking::setup_glycosylation_foldtree	(	core::pose::Pose &	pose,
		protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP	flags,
		core::kinematics::FoldTreeOP	ft_docking
	)

setup specialized foldtree.

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.

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_chemical_edges(), core::kinematics::FoldTree::get_jump_edges(), protocols::docking::setup_foldtree(), protocols::loops::start, protocols::loops::stop, and protocols::TR().

Referenced by protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::apply(), protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::apply(), and protocols::glycopeptide_docking::GlycopeptideDockingProtocol::apply().

◆ write_debug_pdb()

void protocols::glycopeptide_docking::write_debug_pdb	(	core::pose::Pose const &	pose,
		core::Size const	nstruct_max,
		core::Size const	nstruct_index,
		std::string	name
	)

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

Write additional pdb files during low resolution and high resolution sampling. Useful for debugging and making movies.

References core::pose::Pose::dump_pdb(), and protocols::TR().