#include <BackboneSampler.hh>

Inheritance diagram for protocols::enzdes::BackboneSampler:

Public Types
typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::pose::Pose	Pose

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

Public Member Functions
	BackboneSampler ()

	BackboneSampler (ScoreFunctionCOP scorefxn, core::Size const bb_moves, core::Real const mc_kt)

void	apply (Pose &pose) override
	Main Method. 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...

	~BackboneSampler () override

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

Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
	LigandBaseProtocol ()

	~LigandBaseProtocol () override

LigandBaseProtocolOP	shared_from_this ()

core::scoring::ScoreFunctionOP	get_scorefxn ()

core::scoring::ScoreFunctionCOP	get_scorefxn () const

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	restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func) const

void	reorder_foldtree_around_mobile_regions (core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const
	reorders a fold tree such that movement in the mobile regions will More...

void	get_non_bb_clashing_rotamers (core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const

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	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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::ligand_docking::LigandBaseProtocol
static core::Size	get_ligand_jump_id (core::pose::Pose const &pose)

static core::Size	get_ligand_id (core::pose::Pose const &pose)
	Return the residue sequence number for our ligand. More...

static core::Size	get_ligand_id (core::pose::Pose const &pose, core::Size jump_id)
	Return the residue sequence number for our ligand. 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...

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

Protected Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
core::scoring::ScoreFunctionOP	make_tweaked_scorefxn (std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight)

core::Vector	choose_desired_centroid (core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >)

void	move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts)

void	move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid)

core::kinematics::MoveMapOP	make_movemap (core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const

core::pack::task::PackerTaskOP	make_packer_task (core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const
	Shared machinery for the next two. More...

core::pack::task::PackerTaskOP	make_packer_task (core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const
	Receptor (interface?) plus ligand. More...

core::pack::task::PackerTaskOP	make_packer_task_ligand_only (core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const
	Just ligand, not the receptor. More...

void	find_interface_rsds (core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const

void	find_interface_backbone (core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const

core::scoring::constraints::ConstraintOP	restrain_ligand_nbr_atom (core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const

void	setup_bbmin_foldtree (core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms)

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...

Private Attributes
core::Size	bb_moves_

core::Real	mc_kt_

core::scoring::ScoreFunctionOP	scorefxn_repack_

Additional Inherited Members
Protected Attributes inherited from protocols::ligand_docking::LigandBaseProtocol
bool	use_soft_rep_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	hard_scorefxn_

core::scoring::ScoreFunctionOP	soft_scorefxn_

core::Real	sc_interface_padding_

core::Real	bb_interface_cutoff_

core::pack::rotamer_set::UnboundRotamersOperationOP	unboundrot_

Member Typedef Documentation

typedef core::pose::Pose protocols::enzdes::BackboneSampler::Pose

typedef core::scoring::ScoreFunctionCOP protocols::enzdes::BackboneSampler::ScoreFunctionCOP

typedef core::scoring::ScoreFunctionOP protocols::enzdes::BackboneSampler::ScoreFunctionOP

Constructor & Destructor Documentation

protocols::enzdes::BackboneSampler::BackboneSampler ( )

protocols::enzdes::BackboneSampler::BackboneSampler	(	ScoreFunctionCOP	scorefxn,
		core::Size const	bb_moves,
		core::Real const	mc_kt
	)

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

protocols::enzdes::BackboneSampler::~BackboneSampler ( )

overridedefault

Member Function Documentation

void protocols::enzdes::BackboneSampler::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::loops::add_cutpoint_variants(), protocols::enzdes::DetectProteinLigandInterface::add_observer_cache_segments_to_set(), protocols::simple_moves::BBGaussianMover::apply(), protocols::moves::MonteCarlo::boltzmann(), protocols::simple_moves::BBGaussianMover::factorA(), protocols::simple_moves::BBGaussianMover::factorB(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_protein(), protocols::moves::MonteCarlo::lowest_score_pose(), protocols::simple_moves::BBGaussianMover::movemap(), protocols::loops::remove_cutpoint_variants(), protocols::moves::MonteCarlo::reset(), core::pose::Pose::residue(), protocols::moves::MonteCarlo::show_counters(), core::pose::Pose::size(), protocols::enzdes::TR(), and protocols::moves::Mover::type().

protocols::moves::MoverOP protocols::enzdes::BackboneSampler::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.

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

inlineoverridevirtual

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.

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

overridevirtual

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

Implements protocols::moves::Mover.

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

static

Referenced by protocols::enzdes::BackboneSamplerCreator::keyname().

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

overrideprotectedvirtual

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 core::scoring::parse_score_function().

void protocols::enzdes::BackboneSampler::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::enzdes::BackboneSamplerCreator::provide_xml_schema().