Creates a bridge connection between two chains using remodel. More...

#include <BridgeChainsMover.hh>

Inheritance diagram for protocols::denovo_design::movers::BridgeChainsMover:

Public Member Functions
	BridgeChainsMover ()

	BridgeChainsMover (std::string const &class_name)
	subclasses should call this constructor More...

	~BridgeChainsMover () override

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) 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...

connection::ConnectionArchitect const &	architect () const

void	set_id (std::string const &my_id)

void	set_segment1_ids (std::string const &segments)

void	set_segment2_ids (std::string const &segments)

void	set_motifs (std::string const &motifs_str, std::string const &cut_resis_str)

core::Size	overlap () const

void	set_overlap (core::Size const overlap_val)

void	set_iterations (core::Size const iterations)

core::scoring::ScoreFunction const &	scorefxn () const

void	set_scorefxn (core::scoring::ScoreFunction const &sfxn)

bool	dry_run () const

void	set_dry_run (bool const dry_run)

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 ()

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 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 void	setup_attlist_for_derived_classes (utility::tag::AttributeList &attlist)

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
connection::ConnectionArchitectOP	architect_

core::scoring::ScoreFunctionOP	scorefxn_

core::Size	overlap_

core::Size	iterations_

bool	dry_run_

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

Creates a bridge connection between two chains using remodel.

Constructor & Destructor Documentation

protocols::denovo_design::movers::BridgeChainsMover::BridgeChainsMover ( )

protocols::denovo_design::movers::BridgeChainsMover::BridgeChainsMover ( std::string const & class_name )

subclasses should call this constructor

protocols::denovo_design::movers::BridgeChainsMover::~BridgeChainsMover ( )

overridedefault

Member Function Documentation

void protocols::denovo_design::movers::BridgeChainsMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

connection::ConnectionArchitect const & protocols::denovo_design::movers::BridgeChainsMover::architect ( ) const

References architect_.

Referenced by apply(), and scorefxn().

protocols::moves::MoverOP protocols::denovo_design::movers::BridgeChainsMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

bool protocols::denovo_design::movers::BridgeChainsMover::dry_run ( ) const

References dry_run_.

Referenced by apply(), and set_dry_run().

protocols::moves::MoverOP protocols::denovo_design::movers::BridgeChainsMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::denovo_design::movers::BridgeChainsMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::denovo_design::movers::BridgeChainsMover::mover_name ( )

static

Referenced by get_name(), protocols::denovo_design::movers::BridgeChainsMoverCreator::keyname(), and provide_xml_schema().

core::Size protocols::denovo_design::movers::BridgeChainsMover::overlap ( ) const

References overlap_.

Referenced by apply().

void protocols::denovo_design::movers::BridgeChainsMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References architect_, dry_run_, iterations_, overlap_, core::scoring::parse_score_function(), set_dry_run(), set_iterations(), set_overlap(), and set_scorefxn().

void protocols::denovo_design::movers::BridgeChainsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::denovo_design::movers::BridgeChainsMoverCreator::provide_xml_schema(), and protocols::denovo_design::movers::BridgeChainsCreator::provide_xml_schema().

core::scoring::ScoreFunction const & protocols::denovo_design::movers::BridgeChainsMover::scorefxn ( ) const

References architect(), protocols::denovo_design::architects::StructureArchitect::id(), and scorefxn_.

Referenced by apply().

void protocols::denovo_design::movers::BridgeChainsMover::set_dry_run ( bool const dry_run )

References dry_run(), and dry_run_.

Referenced by parse_my_tag().

void protocols::denovo_design::movers::BridgeChainsMover::set_id ( std::string const & my_id )

References architect_.

void protocols::denovo_design::movers::BridgeChainsMover::set_iterations ( core::Size const iterations )

inline

References iterations_.

Referenced by parse_my_tag().

void protocols::denovo_design::movers::BridgeChainsMover::set_motifs	(	std::string const &	motifs_str,
		std::string const &	cut_resis_str
	)

References architect_.

void protocols::denovo_design::movers::BridgeChainsMover::set_overlap ( core::Size const overlap_val )

References overlap_.

Referenced by parse_my_tag().

void protocols::denovo_design::movers::BridgeChainsMover::set_scorefxn ( core::scoring::ScoreFunction const & sfxn )

References core::scoring::ScoreFunction::clone(), and scorefxn_.

Referenced by parse_my_tag().

void protocols::denovo_design::movers::BridgeChainsMover::set_segment1_ids ( std::string const & segments )

References architect_.

void protocols::denovo_design::movers::BridgeChainsMover::set_segment2_ids ( std::string const & segments )

References architect_.

void protocols::denovo_design::movers::BridgeChainsMover::setup_attlist_for_derived_classes ( utility::tag::AttributeList & attlist )

static

References protocols::denovo_design::connection::ConnectionArchitect::attributes_for_parse_my_tag(), and core::scoring::attributes_for_parse_score_function().

Referenced by provide_xml_schema().

void protocols::denovo_design::movers::BridgeChainsMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

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

Referenced by protocols::denovo_design::movers::operator<<().

Member Data Documentation

connection::ConnectionArchitectOP protocols::denovo_design::movers::BridgeChainsMover::architect_

private

Referenced by architect(), parse_my_tag(), set_id(), set_motifs(), set_segment1_ids(), and set_segment2_ids().

bool protocols::denovo_design::movers::BridgeChainsMover::dry_run_

private

Referenced by dry_run(), parse_my_tag(), and set_dry_run().

core::Size protocols::denovo_design::movers::BridgeChainsMover::iterations_

private

Referenced by apply(), parse_my_tag(), and set_iterations().

core::Size protocols::denovo_design::movers::BridgeChainsMover::overlap_

private

Referenced by overlap(), parse_my_tag(), and set_overlap().

core::scoring::ScoreFunctionOP protocols::denovo_design::movers::BridgeChainsMover::scorefxn_

private

Referenced by apply(), scorefxn(), and set_scorefxn().

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

src/protocols/denovo_design/movers/BridgeChainsMover.hh
src/protocols/denovo_design/movers/BridgeChainsMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation