#include <EnzdesMovers.hh>

Inheritance diagram for protocols::enzdes::PredesignPerturbMover:

[legend]

Public Member Functions
	PredesignPerturbMover ()

	~PredesignPerturbMover () override

void	set_docking_pose (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task)

void	reinstate_pose (core::pose::Pose &pose, core::pose::Pose const &old_Pose)

void	find_constraints_to_ligand (core::pose::Pose const &pose)

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	set_ligand (core::Size res_no)

utility::vector1< core::Size > const &	get_constrained_lig_atoms () const
	Allow an outside interpretter to the set of atoms for which there are AtomPair constraints to the ligand. More...

core::Vector	find_rotation_center (core::pose::Pose const &pose)

core::Vector	find_geometric_center_for_constrained_lig_atoms (core::pose::Pose const &pose)

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

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

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

Public Member Functions inherited from protocols::rigid::RigidBodyPerturbMover
	RigidBodyPerturbMover ()

	RigidBodyPerturbMover (int const rb_jump_in, core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in=partner_downstream, bool interface_in=false)

	RigidBodyPerturbMover (int const rb_jump_in, core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in, utility::vector1< bool > const &ok_for_centroid_calculation)

	RigidBodyPerturbMover (core::pose::Pose const &pose_in, core::kinematics::MoveMap const &mm, core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in=partner_downstream, bool interface_in=false)

	RigidBodyPerturbMover (core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in=partner_downstream, bool interface_in=false)

	RigidBodyPerturbMover (RigidBodyPerturbMover const &)

	~RigidBodyPerturbMover () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

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

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

void	rot_magnitude (core::Real const magnitude)

void	trans_magnitude (core::Real const magnitude)

core::Distance	get_trans_mag () const

core::Angle	get_rot_mag () const

void	rot_center (core::Vector const &)
	Manual override of rotation center. More...

Public Member Functions inherited from protocols::rigid::RigidBodyMover
	RigidBodyMover ()

	RigidBodyMover (int const rb_jump_in, Direction dir_in=n2c)

	RigidBodyMover (RigidBodyMover const &src)

	~RigidBodyMover () override

void	rot_center (core::Vector const &rot_center_in)
	Manual override of rotation center. More...

bool	preserve_detailed_balance () const override
	Return true if detailed balance is being preserved (i.e. no branch angle optimization). More...

void	set_preserve_detailed_balance (bool) override
	set whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...

utility::vector1< core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose) override
	get the TorsionIDs perturbed by the mover during moves, along with their ranges More...

int	rb_jump () const

void	rb_jump (int jump_id)

void	unfreeze ()

void	freeze ()

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
	ThermodynamicMover ()
	Default constructor. More...

	~ThermodynamicMover () override
	Default destructor. More...

virtual void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
	Callback executed before any Monte Carlo trials are attempted. More...

virtual void	observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after the Metropolis criterion is evaluated. More...

core::Real	last_proposal_density_ratio () override
	Return the proposal density ratio for last apply method. More...

virtual void	finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after all Monte Carlo trials are completed. More...

virtual bool	is_multi_trial ()
	Return true if the move performs multiple trials on each apply. More...

virtual core::Real	last_inner_score_delta_over_temperature ()
	If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. More...

virtual utility::vector1< core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)
	Return a list specifying which degrees of freedom may be perturbed by apply(), and the in what range each perturbation may be. 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 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 Attributes
EnzdesConstraintReporter	constraint_reporter_

utility::vector1< core::Size >	positions_to_replace_

core::Size	dock_trials_

core::pack::task::TaskFactoryOP	task_factory_

Additional Inherited Members
Public Types inherited from protocols::rigid::RigidBodyPerturbMover
typedef RigidBodyMover	parent

Public Types inherited from protocols::rigid::RigidBodyMover
typedef ThermodynamicMover	parent

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...

Protected Attributes inherited from protocols::rigid::RigidBodyPerturbMover
core::Real	rot_mag_

core::Real	trans_mag_

utility::vector1< core::Real >	rb_delta_

Protected Attributes inherited from protocols::rigid::RigidBodyMover
int	rb_jump_

Direction	dir_
	direction of folding (n-term to c-term) More...

core::Vector	rot_center_
	center of rotation More...

bool	freeze_

Constructor & Destructor Documentation

◆ PredesignPerturbMover()

protocols::enzdes::PredesignPerturbMover::PredesignPerturbMover ( )

References dock_trials_, protocols::rigid::RigidBodyPerturbMover::rot_magnitude(), and protocols::rigid::RigidBodyPerturbMover::trans_magnitude().

◆ ~PredesignPerturbMover()

protocols::enzdes::PredesignPerturbMover::~PredesignPerturbMover ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::enzdes::PredesignPerturbMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::rigid::RigidBodyMover.

References core::pose::Pose::conformation(), constraint_reporter_, core::scoring::ScoreFunctionFactory::create_score_function(), protocols::rigid::RigidBodyMover::dir_, dock_trials_, core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::downstream_jump_stub(), find_constraints_to_ligand(), find_rotation_center(), core::pose::Pose::fold_tree(), core::kinematics::Jump::gaussian_move(), core::pose::Pose::jump(), protocols::enzdes::EnzdesConstraintReporter::ligand_resno(), protocols::enzdes::mv_tr(), core::pose::Pose::num_jump(), reinstate_pose(), protocols::rigid::RigidBodyMover::rot_center_, protocols::rigid::RigidBodyPerturbMover::rot_mag_, set_docking_pose(), core::pose::Pose::set_jump(), core::kinematics::Jump::set_rb_center(), task_factory_, and protocols::rigid::RigidBodyPerturbMover::trans_mag_.

◆ clone()

protocols::moves::MoverOP protocols::enzdes::PredesignPerturbMover::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ find_constraints_to_ligand()

void protocols::enzdes::PredesignPerturbMover::find_constraints_to_ligand ( core::pose::Pose const & pose )

References constraint_reporter_, and protocols::enzdes::EnzdesConstraintReporter::find_constraints_to_ligand().

Referenced by apply().

◆ find_geometric_center_for_constrained_lig_atoms()

core::Vector protocols::enzdes::PredesignPerturbMover::find_geometric_center_for_constrained_lig_atoms ( core::pose::Pose const & pose )

References protocols::enzdes::EnzdesConstraintReporter::constrained_lig_atoms(), constraint_reporter_, protocols::enzdes::EnzdesConstraintReporter::ligand_resno(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by find_rotation_center().

◆ find_rotation_center()

core::Vector protocols::enzdes::PredesignPerturbMover::find_rotation_center ( core::pose::Pose const & pose )

References protocols::enzdes::EnzdesConstraintReporter::constrained_lig_atoms(), constraint_reporter_, find_geometric_center_for_constrained_lig_atoms(), protocols::enzdes::EnzdesConstraintReporter::ligand_resno(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::enzdes::PredesignPerturbMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_constrained_lig_atoms()

utility::vector1< core::Size > const& protocols::enzdes::PredesignPerturbMover::get_constrained_lig_atoms ( ) const

inline

Allow an outside interpretter to the set of atoms for which there are AtomPair constraints to the ligand.

References protocols::enzdes::EnzdesConstraintReporter::constrained_lig_atoms(), and constraint_reporter_.

◆ get_name()

std::string protocols::enzdes::PredesignPerturbMover::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::enzdes::PredesignPerturbMover::mover_name ( )

static

Referenced by get_name(), protocols::enzdes::PredesignPerturbMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::enzdes::PredesignPerturbMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References dock_trials_, core::pack::task::parse_task_operations(), protocols::rigid::RigidBodyPerturbMover::rot_magnitude(), task_factory_, and protocols::rigid::RigidBodyPerturbMover::trans_magnitude().