High resolution refinement of glycosyltransferase substrate. More...

#include <GlycopeptideDockingHighResRefinement.hh>

Inheritance diagram for protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement:

[legend]

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

	GlycopeptideDockingHighResRefinement (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...

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

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

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

void	setup ()
	Mover Methods ///. More...

void	apply (core::pose::Pose &pose) override
	Apply the mover. More...

void	show (std::ostream &output=std::cout) const override
	show mover details 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
	get 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 ()

void	set_target_attractive_weight (core::Real w)

core::Real	get_target_attractive_weight ()

void	set_target_repulsive_weight (core::Real w)

core::Real	get_target_repulsive_weight ()

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 ()
	get mover name More...

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	ramp_score_weight (core::scoring::ScoreType const method, core::Real const target, core::Real const fraction_completion)
	Ramps up weight for repulsive term and ramps down attractive LJ term. More...

Private Attributes
protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP	flags_

core::Real	kt_
	Boltmann sampling temperature. More...

core::Real	target_atr_
	Final weight of the attractive force term. More...

core::Real	target_rep_
	Final weight of the repulsive force term. More...

core::Real	starting_ramp_down_factor_
	Fractional factor by which the attractive weight is ramped down. More...

core::Real	starting_ramp_up_factor_
	Fractional factor by which the repulsive weight is ramped up. More...

core::scoring::ScoreFunctionOP	sf_

core::kinematics::FoldTreeOP	ft_docking_

core::kinematics::FoldTreeOP	ft_substrate_

protocols::moves::MonteCarloOP	mc_

protocols::rigid::RigidBodyPerturbMoverOP	perturber_

protocols::minimization_packing::MinMoverOP	jump_minimizer_

protocols::minimization_packing::MinMoverOP	torsion_minimizer_

protocols::simple_moves::SmallMoverOP	small_mover_

protocols::simple_moves::ShearMoverOP	shear_mover_

protocols::minimization_packing::PackRotamersMoverOP	packer_substrate_

protocols::minimization_packing::PackRotamersMoverOP	packer_interface_

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

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:

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)
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)

Constructor & Destructor Documentation

◆ GlycopeptideDockingHighResRefinement() [1/4]

protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::GlycopeptideDockingHighResRefinement ( )

Constructors ///.

Default constructor

Default constructors does not setup anything. Various getters and setters are provided to setup all options.

Default constructor

◆ GlycopeptideDockingHighResRefinement() [2/4]

protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::GlycopeptideDockingHighResRefinement	(	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.

Constructor with arguments.

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().

◆ GlycopeptideDockingHighResRefinement() [3/4]

protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::GlycopeptideDockingHighResRefinement	(	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().

◆ GlycopeptideDockingHighResRefinement() [4/4]

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~GlycopeptideDockingHighResRefinement()

protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::~GlycopeptideDockingHighResRefinement ( )

override

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

Member Function Documentation

◆ apply()

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

overridevirtual

Apply the mover.

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:

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)
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) TODO: add sugar bbsampler to sample torsions for higher glycans. Protocol currently tested for monosaccharides. TODO: Test sampling of "donor residue" in the torsional space.

Implements protocols::moves::Mover.

References protocols::glycopeptide_docking::calculate_sampled_distance(), core::scoring::fa_atr, core::scoring::fa_rep, flags_, core::pose::Pose::fold_tree(), ft_docking_, protocols::jd2::JobDistributor::get_instance(), jump_minimizer_, kt_, mc_, packer_interface_, packer_substrate_, perturber_, ramp_score_weight(), protocols::glycopeptide_docking::setup_glycosylation_foldtree(), sf_, shear_mover_, show(), small_mover_, starting_ramp_down_factor_, starting_ramp_up_factor_, target_atr_, target_rep_, 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::GlycopeptideDockingHighResRefinement::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::GlycopeptideDockingHighResRefinement::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::GlycopeptideDockingHighResRefinement::get_docking_foldtree ( )

inline

References ft_docking_.

◆ get_name()

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

overridevirtual

get name

Implements protocols::moves::Mover.

References mover_name().

◆ get_options()

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_options ( )

inline

References flags_.

◆ get_scorefunction()

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

inline

References sf_.

◆ get_substrate_foldtree()

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

inline

References ft_substrate_.

◆ get_target_attractive_weight()

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_target_attractive_weight ( )

inline

References target_atr_.

◆ get_target_repulsive_weight()

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_target_repulsive_weight ( )

inline

References target_rep_.

◆ mover_name()

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

static

get mover name

Referenced by get_name().

◆ ramp_score_weight()

void protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::ramp_score_weight	(	core::scoring::ScoreType const	method,
		core::Real const	target,
		core::Real const	fraction_completion
	)

private

Ramps up weight for repulsive term and ramps down attractive LJ term.

Function to ramp up and ramp down score weights. fa_atr is ramped down from an upweighted weight. fa_rep is ramped up from an downweighted weight. The refinement protocol currently uses it to ramp down attractive terms and ramp up repulsive terms.

References sf_, starting_ramp_down_factor_, and starting_ramp_up_factor_.

Referenced by apply().

◆ set_docking_foldtree()

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

inline

References ft_docking_.

◆ set_options()

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

inline

Getters and setters for sf, foldtrees, flags.

References flags_.

◆ set_scorefunction()

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

inline

References sf_.

◆ set_substrate_foldtree()

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

inline

References ft_substrate_.

◆ set_target_attractive_weight()

void protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_target_attractive_weight ( core::Real w )

inline

References target_atr_.

◆ set_target_repulsive_weight()

void protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_target_repulsive_weight ( core::Real w )

inline

References target_rep_.

◆ setup()

void protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::setup ( )

Mover Methods ///.

setup default for the mover

References core::scoring::fa_atr, core::scoring::fa_rep, flags_, jump_minimizer_, kt_, packer_interface_, packer_substrate_, perturber_, sf_, shear_mover_, small_mover_, starting_ramp_down_factor_, starting_ramp_up_factor_, target_atr_, target_rep_, and torsion_minimizer_.

Referenced by GlycopeptideDockingHighResRefinement().

◆ show()

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

overridevirtual

show mover details

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

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

Referenced by apply(), protocols::glycopeptide_docking::GlycopeptideDockingProtocol::apply(), and protocols::glycopeptide_docking::operator<<().

Member Data Documentation

◆ flags_

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::flags_

private

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

◆ ft_docking_

core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::ft_docking_

private

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

◆ ft_substrate_

core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::ft_substrate_

private

Referenced by get_substrate_foldtree(), and set_substrate_foldtree().

◆ jump_minimizer_

protocols::minimization_packing::MinMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::jump_minimizer_

private

Referenced by apply(), and setup().

◆ kt_

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::kt_

private

Boltmann sampling temperature.

Referenced by apply(), and setup().

◆ mc_

protocols::moves::MonteCarloOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::mc_

private

Referenced by apply().

◆ packer_interface_

protocols::minimization_packing::PackRotamersMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::packer_interface_

private

Referenced by apply(), and setup().

◆ packer_substrate_

protocols::minimization_packing::PackRotamersMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::packer_substrate_

private

Referenced by apply(), and setup().

◆ perturber_

protocols::rigid::RigidBodyPerturbMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::perturber_

private

Referenced by apply(), and setup().

◆ sf_

core::scoring::ScoreFunctionOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::sf_

private

Referenced by apply(), get_scorefunction(), ramp_score_weight(), set_scorefunction(), and setup().

◆ shear_mover_

protocols::simple_moves::ShearMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::shear_mover_

private

Referenced by apply(), and setup().

◆ small_mover_

protocols::simple_moves::SmallMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::small_mover_

private

Referenced by apply(), and setup().

◆ starting_ramp_down_factor_

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::starting_ramp_down_factor_

private

Fractional factor by which the attractive weight is ramped down.

Referenced by apply(), ramp_score_weight(), and setup().

◆ starting_ramp_up_factor_

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::starting_ramp_up_factor_

private

Fractional factor by which the repulsive weight is ramped up.

Referenced by apply(), ramp_score_weight(), and setup().

◆ target_atr_

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::target_atr_

private

Final weight of the attractive force term.

Set to be the same as ref2015 weight

Referenced by apply(), get_target_attractive_weight(), set_target_attractive_weight(), and setup().

◆ target_rep_

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::target_rep_

private

Final weight of the repulsive force term.

Set to be the same as ref2015 weight

Referenced by apply(), get_target_repulsive_weight(), set_target_repulsive_weight(), and setup().

◆ torsion_minimizer_

protocols::minimization_packing::MinMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::torsion_minimizer_

private

Referenced by apply(), and setup().

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

src/protocols/glycopeptide_docking/GlycopeptideDockingHighResRefinement.hh
src/protocols/glycopeptide_docking/GlycopeptideDockingHighResRefinement.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ GlycopeptideDockingHighResRefinement() [1/4]

◆ GlycopeptideDockingHighResRefinement() [2/4]

◆ GlycopeptideDockingHighResRefinement() [3/4]

◆ GlycopeptideDockingHighResRefinement() [4/4]

◆ ~GlycopeptideDockingHighResRefinement()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_docking_foldtree()

◆ get_name()

◆ get_options()

◆ get_scorefunction()

◆ get_substrate_foldtree()

◆ get_target_attractive_weight()

◆ get_target_repulsive_weight()

◆ mover_name()

◆ ramp_score_weight()

◆ set_docking_foldtree()

◆ set_options()

◆ set_scorefunction()

◆ set_substrate_foldtree()

◆ set_target_attractive_weight()

◆ set_target_repulsive_weight()

◆ setup()

◆ show()

Member Data Documentation

◆ flags_

◆ ft_docking_

◆ ft_substrate_

◆ jump_minimizer_

◆ kt_

◆ mc_

◆ packer_interface_

◆ packer_substrate_

◆ perturber_

◆ sf_

◆ shear_mover_

◆ small_mover_

◆ starting_ramp_down_factor_

◆ starting_ramp_up_factor_

◆ target_atr_

◆ target_rep_

◆ torsion_minimizer_