#include <MatcherMover.hh>

Inheritance diagram for protocols::match::MatcherMover:

Public Types
typedef core::Real	Real

typedef core::Size	Size

typedef protocols::moves::MoverOP	MoverOP

typedef utility::tag::TagCOP	TagCOP

typedef protocols::filters::Filters_map	Filters_map

typedef basic::datacache::DataMap	DataMap

typedef protocols::moves::Movers_map	Movers_map

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Public Member Functions
	MatcherMover (bool incorporate_matches_into_pose=true)
	Construction and Destruction. More...

	~MatcherMover () override

	MatcherMover (MatcherMover const &rval)
	copy constructor More...

MoverOP	clone () const override
	clone this object More...

MoverOP	fresh_instance () const override
	create this type of object More...

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

void	apply (core::pose::Pose &pose) override

void	set_ligres (core::conformation::ResidueCOP ligres)

void	set_match_positions (utility::vector1< core::Size > const &match_positions)

void	set_return_single_random_match (bool const single_random)
	if set to true, a single random match will be returned. More...

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

Public Member Functions inherited from protocols::rosetta_scripts::MultiplePoseMover
	MultiplePoseMover ()
	No-argument constructor. More...

	~MultiplePoseMover () override=default
	Virtual destructor. 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...

void	apply (core::pose::Pose &pose) override
	Process input pose. More...

core::pose::PoseOP	get_additional_output () override
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override
	Parse settings in tag. More...

void	set_previous_mover (protocols::moves::MoverOP const m)
	Used by RosettaScripts to set the previous mover to pull poses from. More...

void	set_rosetta_scripts_tag (utility::tag::TagCOP tag)
	sets rosettascripts tag More...

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

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

	~Mover () override

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 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...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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	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 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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Protected Member Functions
bool	process_pose (core::pose::Pose &, utility::vector1< core::pose::PoseOP > &) override
	Process a single input pose by the RosettaScripts mover. More...

void	setup_seqpos_from_selectors (protocols::match::MatcherTask &mtask, core::pose::Pose const &pose) const

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
bool	incorporate_matches_into_pose_

bool	return_single_random_match_

core::conformation::ResidueCOP	ligres_

utility::vector1< core::Size >	match_positions_

utility::vector1 < core::select::residue_selector::ResidueSelectorCOP >	selectors_

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::match::MatcherMover::DataMap

typedef protocols::filters::Filters_map protocols::match::MatcherMover::Filters_map

typedef protocols::moves::MoverOP protocols::match::MatcherMover::MoverOP

typedef protocols::moves::Movers_map protocols::match::MatcherMover::Movers_map

typedef core::Real protocols::match::MatcherMover::Real

typedef core::Size protocols::match::MatcherMover::Size

typedef utility::tag::TagCOP protocols::match::MatcherMover::TagCOP

Constructor & Destructor Documentation

protocols::match::MatcherMover::MatcherMover ( bool incorporate_matches_into_pose = true )

Construction and Destruction.

Referenced by clone(), and fresh_instance().

protocols::match::MatcherMover::~MatcherMover ( )

overridedefault

protocols::match::MatcherMover::MatcherMover ( MatcherMover const & rval )

default

copy constructor

Member Function Documentation

void protocols::match::MatcherMover::apply ( core::pose::Pose & pose )

overridevirtual

Implements protocols::moves::Mover.

References protocols::rosetta_scripts::MultiplePoseMover::apply(), and core::pose::Pose::pdb_info().

MatcherMover::MoverOP protocols::match::MatcherMover::clone ( ) const

overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

References MatcherMover().

MatcherMover::MoverOP protocols::match::MatcherMover::fresh_instance ( ) const

overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

References MatcherMover().

std::string protocols::match::MatcherMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::match::MatcherMover::mover_name ( )

static

Referenced by get_name(), protocols::match::MatcherMoverCreator::keyname(), and provide_xml_schema().

void protocols::match::MatcherMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Filters_map const &	filters,
		Movers_map const &	movers,
		Pose const &	pose
	)

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 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.

References incorporate_matches_into_pose_, selectors_, and protocols::match::tr().

bool protocols::match::MatcherMover::process_pose	(	core::pose::Pose &	pose,
		utility::vector1< core::pose::PoseOP > &	additional_poses
	)

overrideprotectedvirtual

Process a single input pose by the RosettaScripts mover.

Reimplemented from protocols::rosetta_scripts::MultiplePoseMover.

References core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clone(), core::pose::Pose::conformation(), protocols::match::output::ProcessorFactory::create_processor(), core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::delete_residue_slow(), protocols::moves::FAIL_DO_NOT_RETRY, core::chemical::FULL_ATOM_t, core::scoring::get_score_function(), incorporate_matches_into_pose_, ligres_, match_positions_, protocols::moves::MS_SUCCESS, core::chemical::ResidueType::name3(), protocols::sic_dock::scores::nbr1(), protocols::sic_dock::scores::nbr2(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), return_single_random_match_, selectors_, protocols::moves::Mover::set_last_move_status(), protocols::match::set_ligpose_rotamer(), setup_seqpos_from_selectors(), core::pose::Pose::size(), and protocols::match::tr().

void protocols::match::MatcherMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::match::MatcherMoverCreator::provide_xml_schema().

void protocols::match::MatcherMover::set_ligres ( core::conformation::ResidueCOP ligres )

References ligres_.

void protocols::match::MatcherMover::set_match_positions ( utility::vector1< core::Size > const & match_positions )

References match_positions_.

void protocols::match::MatcherMover::set_return_single_random_match ( bool const single_random )

if set to true, a single random match will be returned.

The default behavior is to use the MultiplePoseMover framework to return all matches

References return_single_random_match_.

void protocols::match::MatcherMover::setup_seqpos_from_selectors	(	protocols::match::MatcherTask &	mtask,
		core::pose::Pose const &	pose
	)		const

protected

References selectors_, protocols::match::MatcherTask::set_ignore_cmdline_for_build_points(), protocols::match::MatcherTask::set_original_scaffold_build_points_for_geometric_constraint(), protocols::match::tr(), and protocols::match::MatcherTask::use_different_build_points_for_each_geometric_constraint().

Referenced by process_pose().

Member Data Documentation

bool protocols::match::MatcherMover::incorporate_matches_into_pose_

private

Referenced by parse_my_tag(), and process_pose().

core::conformation::ResidueCOP protocols::match::MatcherMover::ligres_

private

Referenced by process_pose(), and set_ligres().

utility::vector1< core::Size > protocols::match::MatcherMover::match_positions_

private

Referenced by process_pose(), and set_match_positions().

bool protocols::match::MatcherMover::return_single_random_match_

private

Referenced by process_pose(), and set_return_single_random_match().

utility::vector1< core::select::residue_selector::ResidueSelectorCOP > protocols::match::MatcherMover::selectors_

private

Referenced by parse_my_tag(), process_pose(), and setup_seqpos_from_selectors().

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

src/protocols/match/MatcherMover.hh
src/protocols/match/MatcherMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation