#include <EnzdesMovers.hh>

Inheritance diagram for protocols::enzdes::PredesignPerturbMover:

Collaboration diagram for protocols::enzdes::PredesignPerturbMover:

Public Member Functions
	PredesignPerturbMover ()

	~PredesignPerturbMover ()

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)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. 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::TagPtr const tag, protocols::moves::DataMap &datamap, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). 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 > 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 &)

virtual	~RigidBodyPerturbMover ()

void	rot_magnitude (core::Real const magnitude)

void	trans_magnitude (core::Real const magnitude)

core::Size	get_trans_mag () const

core::Size	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)

virtual	~RigidBodyMover ()

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

virtual bool	preserve_detailed_balance () const
	get whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...

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

virtual utility::vector1 < core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose)
	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 ()

virtual	~ThermodynamicMover ()

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 More...

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

virtual core::Real	last_proposal_density_ratio ()
	callback for proposal density ratio of 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 More...

virtual bool	is_multi_trial ()
	determine whether the move performs multiple trials on a single apply More...

virtual core::Real	last_inner_score_temperature_delta ()
	get change in internal score/temperature for last apply method of multiple trial movers More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	get the MetropolisHastingsMover for multiple trial movers More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	set the MetropolisHastingsMover for multiple trial movers More...

virtual utility::vector1 < core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)
	get the DOF_IDs perturbed by the mover during moves (not including those returned by torsion_id_ranges(), along with their ranges More...

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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...

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

jobdist::BasicJobCOP	get_current_job () const

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

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

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_
	perturbation magnitudes (rotational and translational) More...

core::Real	trans_mag_

utility::vector1< core::Real >	rb_delta_

Detailed Description

Definition at line 122 of file EnzdesMovers.hh.

Constructor & Destructor Documentation

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

Definition at line 215 of file EnzdesMovers.cc.

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

Referenced by clone().

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

Definition at line 223 of file EnzdesMovers.cc.

Member Function Documentation

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

virtual

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

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 364 of file EnzdesMovers.cc.

References PredesignPerturbMover().

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

Definition at line 254 of file EnzdesMovers.cc.

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

Referenced by apply().

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

Definition at line 278 of file EnzdesMovers.cc.

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

Referenced by find_rotation_center().

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

Definition at line 262 of file EnzdesMovers.cc.

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().

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

virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

Definition at line 370 of file EnzdesMovers.cc.

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.

Definition at line 166 of file EnzdesMovers.hh.

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

std::string protocols::enzdes::PredesignPerturbMover::get_name ( ) const

virtual

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

Reimplemented from protocols::rigid::RigidBodyPerturbMover.

Definition at line 376 of file EnzdesMovers.cc.

void protocols::enzdes::PredesignPerturbMover::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

Definition at line 347 of file EnzdesMovers.cc.

References constraint_reporter_, dock_trials_, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), protocols::enzdes::EnzdesConstraintReporter::ligand_resno(), core::pose::Pose::num_jump(), protocols::rosetta_scripts::parse_task_operations(), protocols::rigid::RigidBodyPerturbMover::rot_magnitude(), task_factory_, and protocols::rigid::RigidBodyPerturbMover::trans_magnitude().