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

#include <GlycopeptideDockingProtocol.hh>

Inheritance diagram for protocols::glycopeptide_docking::GlycopeptideDockingProtocol:

[legend]

Public Member Functions
	GlycopeptideDockingProtocol ()
	Constructors ///. More...

	GlycopeptideDockingProtocol (GlycopeptideDockingFlags &flags)
	Constructor with flags. More...

	GlycopeptideDockingProtocol (GlycopeptideDockingProtocol const &object_to_copy)
	Copy constructor (not needed unless you need deep copies) More...

GlycopeptideDockingProtocol &	operator= (GlycopeptideDockingProtocol const &object_to_copy)
	Assignment operator. More...

	~GlycopeptideDockingProtocol () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	show (std::ostream &output=std::cout) const override
	Show mover information. More...

void	set_ref_pose_from_filename (std::string const &filename)
	Set reference pose (native) from file name. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Rosetta Scripts Support ///. More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	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). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	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. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	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. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	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. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
void	copy_data (GlycopeptideDockingProtocol &object_to_copy_to, GlycopeptideDockingProtocol const &object_to_copy_from)
	Copy protocol data. More...

void	prepare_score_function ()
	Prepare scorefunction. Currently the scorefunction is fixed by design. Benchmarking has not been done with other scorefunctions. More...

Private Attributes
protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP	flags_

core::scoring::ScoreFunctionOP	sf_

protocols::moves::MonteCarloOP	mc_

protocols::constraint_movers::ConstraintSetMoverOP	constraint_setter_

core::pose::PoseOP	ref_pose_ =nullptr

core::kinematics::FoldTreeOP	ft_docking_ =nullptr

core::kinematics::FoldTreeOP	ft_substrate_ =nullptr

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

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

Constructor & Destructor Documentation

◆ GlycopeptideDockingProtocol() [1/3]

protocols::glycopeptide_docking::GlycopeptideDockingProtocol::GlycopeptideDockingProtocol ( )

Constructors ///.

Default constructor

References constraint_setter_, flags_, prepare_score_function(), and protocols::moves::Mover::type().

◆ GlycopeptideDockingProtocol() [2/3]

protocols::glycopeptide_docking::GlycopeptideDockingProtocol::GlycopeptideDockingProtocol ( GlycopeptideDockingFlags & flags )

Constructor with flags.

Constructor with flags object as argument.

References constraint_setter_, flags_, prepare_score_function(), and protocols::moves::Mover::type().

◆ GlycopeptideDockingProtocol() [3/3]

protocols::glycopeptide_docking::GlycopeptideDockingProtocol::GlycopeptideDockingProtocol ( GlycopeptideDockingProtocol const & object_to_copy )

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References copy_data().

◆ ~GlycopeptideDockingProtocol()

protocols::glycopeptide_docking::GlycopeptideDockingProtocol::~GlycopeptideDockingProtocol ( )

override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

◆ apply()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover

Apply 1. Setups sampling options that require pose, including setting up glycosylation fold tree, substrate and enzyme chains. If user specifies residues to be preglycosylated before sampling, apply does it. 2. Randomizes peptide backbone torsions if requested.

Runs low-resolution sampling of peptide/glycopeptide-enzyme if enabled. 4. Runs high-resolution of peptide/glycopeptide-enzyme of enabled. 5. Records metrics.

Implements protocols::moves::Mover.

References protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::apply(), protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::apply(), constraint_setter_, flags_, core::pose::Pose::fold_tree(), ft_docking_, ft_substrate_, protocols::jd2::JobDistributor::get_instance(), protocols::glycopeptide_docking::record_pose_metrics(), ref_pose_, core::scoring::rg, core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::glycopeptide_docking::setup_glycosylation_foldtree(), sf_, protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::show(), protocols::TR(), and protocols::glycopeptide_docking::write_debug_pdb().

◆ clone()

protocols::moves::MoverOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ copy_data()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::copy_data	(	GlycopeptideDockingProtocol &	object_to_copy_to,
		GlycopeptideDockingProtocol const &	object_to_copy_from
	)

private

Copy protocol data.

private methods ///

Copy private data, called by copy constructor

References constraint_setter_, flags_, mc_, ref_pose_, and sf_.

Referenced by GlycopeptideDockingProtocol(), and operator=().

◆ fresh_instance()

protocols::moves::MoverOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::glycopeptide_docking::GlycopeptideDockingProtocol::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::glycopeptide_docking::GlycopeptideDockingProtocol::mover_name ( )

static

Referenced by get_name(), protocols::glycopeptide_docking::GlycopeptideDockingProtocolCreator::keyname(), and provide_xml_schema().

◆ operator=()

GlycopeptideDockingProtocol & protocols::glycopeptide_docking::GlycopeptideDockingProtocol::operator= ( GlycopeptideDockingProtocol const & object_to_copy )

Assignment operator.

References copy_data().

◆ parse_my_tag()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Rosetta Scripts Support ///.

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

Reimplemented from protocols::moves::Mover.

References flags_.

◆ prepare_score_function()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::prepare_score_function ( )

private

Prepare scorefunction. Currently the scorefunction is fixed by design. Benchmarking has not been done with other scorefunctions.

Prepares the score function used by the refinement and abinitio protocols.

References core::scoring::atom_pair_constraint, core::scoring::fa_elec, core::scoring::fa_sol, core::scoring::get_score_function(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, sf_, and core::scoring::sugar_bb.

Referenced by GlycopeptideDockingProtocol().

◆ provide_xml_schema()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::glycopeptide_docking::GlycopeptideDockingProtocolCreator::provide_xml_schema().

◆ set_ref_pose_from_filename()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::set_ref_pose_from_filename ( std::string const & filename )

Set reference pose (native) from file name.

References protocols::abinitio::filename(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and ref_pose_.

◆ show()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::show ( std::ostream & output = std::cout ) const

overridevirtual

Show mover information.

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::glycopeptide_docking::operator<<().

Member Data Documentation

◆ constraint_setter_

protocols::constraint_movers::ConstraintSetMoverOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::constraint_setter_

private

Referenced by apply(), copy_data(), and GlycopeptideDockingProtocol().

◆ flags_

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::flags_

private

Referenced by apply(), copy_data(), GlycopeptideDockingProtocol(), and parse_my_tag().

◆ ft_docking_

core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::ft_docking_ =nullptr

private

Referenced by apply().

◆ ft_substrate_

core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::ft_substrate_ =nullptr

private

Referenced by apply().

◆ mc_

protocols::moves::MonteCarloOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::mc_

private

Referenced by copy_data().

◆ ref_pose_

core::pose::PoseOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::ref_pose_ =nullptr

private

Referenced by apply(), copy_data(), and set_ref_pose_from_filename().

◆ sf_

core::scoring::ScoreFunctionOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::sf_

private

Referenced by apply(), copy_data(), and prepare_score_function().

The documentation for this class was generated from the following files:

src/protocols/glycopeptide_docking/GlycopeptideDockingProtocol.hh
src/protocols/glycopeptide_docking/GlycopeptideDockingProtocol.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ GlycopeptideDockingProtocol() [1/3]

◆ GlycopeptideDockingProtocol() [2/3]

◆ GlycopeptideDockingProtocol() [3/3]

◆ ~GlycopeptideDockingProtocol()

Member Function Documentation

◆ apply()

◆ clone()

◆ copy_data()

◆ fresh_instance()

◆ get_name()

◆ mover_name()

◆ operator=()

◆ parse_my_tag()

◆ prepare_score_function()

◆ provide_xml_schema()

◆ set_ref_pose_from_filename()

◆ show()

Member Data Documentation

◆ constraint_setter_

◆ flags_

◆ ft_docking_

◆ ft_substrate_

◆ mc_

◆ ref_pose_

◆ sf_