Low resolution refinement of substrate. More...

#include <GlycopeptideDockingLowResRefinement.hh>

Inheritance diagram for protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement:

[legend]

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

	GlycopeptideDockingLowResRefinement (protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags, core::scoring::ScoreFunctionOP sf, core::kinematics::FoldTreeOP ft_docking, core::kinematics::FoldTreeOP ft_substrate)
	Constructor requiring flags, scorefunction sf and folding trees. More...

	GlycopeptideDockingLowResRefinement (protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags, core::scoring::ScoreFunctionOP sf)
	Constructor that only requires the GlycopeptideDockingFlagsOP flags and scorefunction sf. More...

	GlycopeptideDockingLowResRefinement (GlycopeptideDockingLowResRefinement const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~GlycopeptideDockingLowResRefinement () 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 the contents of the Mover. 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...

void	set_options (protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags)
	Getters and setters for sf, foldtrees, flags. More...

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP	get_options ()

void	set_scorefunction (core::scoring::ScoreFunctionOP sf)

core::scoring::ScoreFunctionOP	get_scorefunction ()

void	set_docking_foldtree (core::kinematics::FoldTreeOP ft_docking)

core::kinematics::FoldTreeCOP	get_docking_foldtree ()

void	set_substrate_foldtree (core::kinematics::FoldTreeOP ft_substrate)

core::kinematics::FoldTreeCOP	get_substrate_foldtree ()

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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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 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	setup_backbone_and_jump_movemap ()

void	sample_torsions (core::pose::Pose &pose, core::Size cycles, core::Real &acceptance_rate, core::kinematics::MoveMapOP mm)
	private methods /// More...

Private Attributes
protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP	flags_
	Flags object with options specifying glycopeptide_docking options. More...

core::scoring::ScoreFunctionOP	sf_
	Scorefunction. More...

core::kinematics::FoldTreeOP	ft_docking_ =nullptr
	Foldtree for peptide-enzyme docking. More...

core::kinematics::FoldTreeOP	ft_substrate_ =nullptr
	Foldtree for sampling peptide degrees of freedon. More...

protocols::moves::MonteCarloOP	mc_
	Monte Carlo object for sampling. More...

protocols::minimization_packing::MinMoverOP	torsion_minimizer_
	Min mover for minimizing torsional dofs. More...

protocols::minimization_packing::MinMoverOP	jump_minimizer_
	Min mover for minmizing peptide-enzyme jump. More...

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

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:

rigidbody perturber mover
minimization across the jump
Samples torsions of the peptide with small and shear mover
Minimizes peptide

Constructor & Destructor Documentation

◆ GlycopeptideDockingLowResRefinement() [1/4]

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::GlycopeptideDockingLowResRefinement ( )

Constructors ///.

Default constructor

◆ GlycopeptideDockingLowResRefinement() [2/4]

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::GlycopeptideDockingLowResRefinement	(	protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP	flags,
		core::scoring::ScoreFunctionOP	sf,
		core::kinematics::FoldTreeOP	ft_docking,
		core::kinematics::FoldTreeOP	ft_substrate
	)

Constructor requiring flags, scorefunction sf and folding trees.

Sets up movemap for torsion sampling. Sets jumps. Torsions are sampled for backbone and chi angle for the peptide substrate only (along with glycans that branch out). Sets up minimizers for peptide torsion sampling and for enzyme-peptide interface jump.

Constructor initialized with the GlycopeptideDockingFlagsOP flags
(all options for setting up glycopeptide_docking), scorefunction sf and fold trees for peptide-enzyme docking and sampling the substrate. Currently, the use of ft_substrate is disabled as it worsened predictions.

References setup_backbone_and_jump_movemap().

◆ GlycopeptideDockingLowResRefinement() [3/4]

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::GlycopeptideDockingLowResRefinement	(	protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP	flags,
		core::scoring::ScoreFunctionOP	sf
	)

Constructor that only requires the GlycopeptideDockingFlagsOP flags and scorefunction sf.

The foldtree is automatically setup with a util function based on options
in the flags.

References setup_backbone_and_jump_movemap().

◆ GlycopeptideDockingLowResRefinement() [4/4]

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::GlycopeptideDockingLowResRefinement ( GlycopeptideDockingLowResRefinement const & src )

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~GlycopeptideDockingLowResRefinement()

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::~GlycopeptideDockingLowResRefinement ( )

override

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

Member Function Documentation

◆ apply()

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

overridevirtual

Mover Methods ///.

Apply the mover

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:

rigidbody perturber mover
minimization across the jump
Samples torsions of the peptide with small and shear mover
Minimizes peptide

Implements protocols::moves::Mover.

References protocols::glycopeptide_docking::calculate_sampled_distance(), flags_, core::pose::Pose::fold_tree(), ft_docking_, protocols::jd2::JobDistributor::get_instance(), jump_minimizer_, mc_, sample_torsions(), protocols::glycopeptide_docking::setup_glycosylation_foldtree(), sf_, torsion_minimizer_, protocols::TR(), and protocols::glycopeptide_docking::write_debug_pdb().

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

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_docking_foldtree()

core::kinematics::FoldTreeCOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_docking_foldtree ( )

inline

References ft_docking_.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_options()

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_options ( )

inline

References flags_.

◆ get_scorefunction()

core::scoring::ScoreFunctionOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_scorefunction ( )

inline

References sf_.

◆ get_substrate_foldtree()

core::kinematics::FoldTreeCOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_substrate_foldtree ( )

inline

References ft_substrate_.

◆ mover_name()

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

static

Referenced by get_name().

◆ sample_torsions()

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::sample_torsions	(	core::pose::Pose &	pose,
		core::Size	cycles,
		core::Real &	acceptance_rate,
		core::kinematics::MoveMapOP	mm
	)

private

private methods ///

Samples torsional degrees of freedom with small and shear mover.

References protocols::moves::accept_reject, and mc_.

Referenced by apply().

◆ set_docking_foldtree()

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_docking_foldtree ( core::kinematics::FoldTreeOP ft_docking )

inline

References ft_docking_.

◆ set_options()

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_options ( protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags )

inline

Getters and setters for sf, foldtrees, flags.

References flags_.

◆ set_scorefunction()

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_scorefunction ( core::scoring::ScoreFunctionOP sf )

inline

References sf_.

◆ set_substrate_foldtree()

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_substrate_foldtree ( core::kinematics::FoldTreeOP ft_substrate )

inline

References ft_substrate_.

◆ setup_backbone_and_jump_movemap()

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::setup_backbone_and_jump_movemap ( )

private

References flags_, jump_minimizer_, sf_, and torsion_minimizer_.

Referenced by GlycopeptideDockingLowResRefinement().

◆ show()

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

overridevirtual

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

◆ flags_

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::flags_

private

Flags object with options specifying glycopeptide_docking options.

Referenced by apply(), get_options(), set_options(), and setup_backbone_and_jump_movemap().

◆ ft_docking_

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

private

Foldtree for peptide-enzyme docking.

Referenced by apply(), get_docking_foldtree(), and set_docking_foldtree().

◆ ft_substrate_

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

private

Foldtree for sampling peptide degrees of freedon.

Referenced by get_substrate_foldtree(), and set_substrate_foldtree().

◆ jump_minimizer_

protocols::minimization_packing::MinMoverOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::jump_minimizer_

private

Min mover for minmizing peptide-enzyme jump.

Referenced by apply(), and setup_backbone_and_jump_movemap().

◆ mc_

protocols::moves::MonteCarloOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::mc_

private

Monte Carlo object for sampling.

Referenced by apply(), and sample_torsions().

◆ sf_

core::scoring::ScoreFunctionOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::sf_

private

Scorefunction.

Referenced by apply(), get_scorefunction(), set_scorefunction(), and setup_backbone_and_jump_movemap().

◆ torsion_minimizer_

protocols::minimization_packing::MinMoverOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::torsion_minimizer_

private

Min mover for minimizing torsional dofs.

Referenced by apply(), and setup_backbone_and_jump_movemap().

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

src/protocols/glycopeptide_docking/GlycopeptideDockingLowResRefinement.hh
src/protocols/glycopeptide_docking/GlycopeptideDockingLowResRefinement.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ GlycopeptideDockingLowResRefinement() [1/4]

◆ GlycopeptideDockingLowResRefinement() [2/4]

◆ GlycopeptideDockingLowResRefinement() [3/4]

◆ GlycopeptideDockingLowResRefinement() [4/4]

◆ ~GlycopeptideDockingLowResRefinement()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_docking_foldtree()

◆ get_name()

◆ get_options()

◆ get_scorefunction()

◆ get_substrate_foldtree()

◆ mover_name()

◆ sample_torsions()

◆ set_docking_foldtree()

◆ set_options()

◆ set_scorefunction()

◆ set_substrate_foldtree()

◆ setup_backbone_and_jump_movemap()

◆ show()

Member Data Documentation

◆ flags_

◆ ft_docking_

◆ ft_substrate_

◆ jump_minimizer_

◆ mc_

◆ sf_

◆ torsion_minimizer_