#include <SegmentSequenceProfileMover.hh>

Inheritance diagram for protocols::indexed_structure_store::movers::SegmentSequenceProfileMover:

Public Member Functions
	SegmentSequenceProfileMover ()=default

void	structure_store_path (std::string path)

std::string	structure_store_path ()

core::select::residue_selector::ResidueSelectorCOP	selector ()

void	selector (core::select::residue_selector::ResidueSelectorCOP new_selector)

SegmentSequenceProfileConfig	profile_config ()

void	profile_config (SegmentSequenceProfileConfig new_profile_config)

std::string	output_lookup_count ()

void	output_lookup_count (std::string new_output_lookup_count)

std::string	output_pssm_filename ()

void	output_pssm_filename (std::string new_output_pssm_filename)

std::string	output_pssm_inline ()

void	output_pssm_inline (std::string const &new_output_pssm_inline)

bool	apply_profile ()

void	apply_profile (bool new_apply_profile)

std::string	scaling ()

void	scaling (std::string new_scaling)

core::Real	weight ()

void	weight (core::Real new_weight)

indexed_structure_store::StructureStoreOP	structure_store ()

search::StructureDatabaseOP	structure_database ()

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

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

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

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...

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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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...

Static Public Attributes
static std::string	pssm_output_order

Private Member Functions
void	init_structure_store ()

core::sequence::SequenceProfile	to_sequence_profile (SegmentSequenceProfileResult::ArrayXaa profile)

void	write_profile (core::sequence::SequenceProfile profile, std::ostream &outstream)

Private Attributes
std::string	structure_store_path_

core::select::residue_selector::ResidueSelectorCOP	selector_

SegmentSequenceProfileConfig	profile_config_

std::string	output_lookup_count_ = ""

std::string	output_pssm_filename_ = ""

std::string	output_pssm_inline_ = ""

bool	apply_profile_ = true

std::string	scaling_ = "prob"

core::Real	weight_ = 1

StructureStoreOP	structure_store_

search::StructureDatabaseOP	structure_database_

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...

Constructor & Destructor Documentation

protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::SegmentSequenceProfileMover ( )

default

Member Function Documentation

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::simple_moves::FavorSequenceProfile::apply(), apply_profile_, protocols::indexed_structure_store::SegmentSequenceProfile::config, protocols::jd2::current_output_name(), protocols::jd2::get_current_job(), protocols::jd2::jd2_used(), protocols::indexed_structure_store::SegmentSequenceProfileResult::log_odds, core::chemical::num_canonical_aas, core::conformation::membrane::out, output_lookup_count_, output_pssm_filename_, output_pssm_inline_, profile_config_, protocols::indexed_structure_store::SegmentSequenceProfileConfig::pseudocount, protocols::indexed_structure_store::SegmentSequenceProfileResult::query_results, protocols::indexed_structure_store::SegmentSequenceProfileConfig::rmsd_tolerance, scaling_, protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(), selector_, protocols::simple_moves::FavorSequenceProfile::set_profile(), protocols::simple_moves::FavorSequenceProfile::set_scaling(), protocols::simple_moves::FavorSequenceProfile::set_weight(), core::pose::setPoseExtraScore(), structure_database(), structure_store(), to_sequence_profile(), core::pose::Pose::total_residue(), protocols::indexed_structure_store::TR(), weight_, and write_profile().

bool protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply_profile ( )

inline

References apply_profile_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply_profile ( bool new_apply_profile )

inline

References apply_profile_.

moves::MoverOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::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.

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::init_structure_store ( )

private

References structure_database_, structure_store_, and structure_store_path().

Referenced by structure_database(), and structure_store().

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::mover_name ( )

static

Referenced by get_name(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMoverCreator::keyname(), and provide_xml_schema().

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_lookup_count ( )

inline

References output_lookup_count_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_lookup_count ( std::string new_output_lookup_count )

inline

References output_lookup_count_.

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_filename ( )

inline

References output_pssm_filename_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_filename ( std::string new_output_pssm_filename )

inline

References output_pssm_filename_.

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_inline ( )

inline

References output_pssm_inline_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_inline ( std::string const & new_output_pssm_inline )

inline

References output_pssm_inline_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::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 apply_profile_, output_lookup_count_, output_pssm_filename_, output_pssm_inline_, core::select::residue_selector::parse_residue_selector(), profile_config_, protocols::indexed_structure_store::SegmentSequenceProfileConfig::pseudocount, protocols::indexed_structure_store::SegmentSequenceProfileConfig::rmsd_tolerance, scaling_, selector_, structure_store_path(), and weight_.

SegmentSequenceProfileConfig protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::profile_config ( )

inline

References profile_config_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::profile_config ( SegmentSequenceProfileConfig new_profile_config )

inline

References profile_config_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector_when_required(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::indexed_structure_store::movers::SegmentSequenceProfileMoverCreator::provide_xml_schema().

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::scaling ( )

inline

References scaling_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::scaling ( std::string new_scaling )

inline

References scaling_.

core::select::residue_selector::ResidueSelectorCOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::selector ( )

inline

References selector_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::selector ( core::select::residue_selector::ResidueSelectorCOP new_selector )

inline

References selector_.

search::StructureDatabaseOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_database ( )

References init_structure_store(), and structure_database_.

Referenced by apply().

StructureStoreOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store ( )

References init_structure_store(), and structure_store_.

Referenced by apply().

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_path ( std::string path )

References protocols::hybridization::path, structure_database_, structure_store_, and structure_store_path_.

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_path ( )

References structure_store_path_.

Referenced by init_structure_store(), and parse_my_tag().

core::sequence::SequenceProfile protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::to_sequence_profile ( SegmentSequenceProfileResult::ArrayXaa profile )

private

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::sequence::SequenceProfile::alphabet(), core::chemical::first_l_aa, core::sequence::SequenceProfile::profile(), pssm_output_order, and core::sequence::Sequence::sequence().

Referenced by apply().

core::Real protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::weight ( )

inline

References weight_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::weight ( core::Real new_weight )

inline

References weight_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::write_profile	(	core::sequence::SequenceProfile	profile,
		std::ostream &	outstream
	)

private

References core::sequence::SequenceProfile::alphabet(), core::sequence::Sequence::length(), core::conformation::membrane::out, core::sequence::SequenceProfile::prof_row(), core::sequence::Sequence::sequence(), and core::sequence::SequenceProfile::width().

Referenced by apply().

Member Data Documentation

bool protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply_profile_ = true

private

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

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_lookup_count_ = ""

private

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

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_filename_ = ""

private

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

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_inline_ = ""

private

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

SegmentSequenceProfileConfig protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::profile_config_

private

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

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::pssm_output_order

static

Initial value:

= {

'A','R','N','D','C','Q','E','G','H','I','L','K','M','F','P','S','T','W','Y','V'}

Referenced by to_sequence_profile().

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::scaling_ = "prob"

private

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

core::select::residue_selector::ResidueSelectorCOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::selector_

private

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

search::StructureDatabaseOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_database_

private

Referenced by init_structure_store(), structure_database(), and structure_store_path().

StructureStoreOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_

private

Referenced by init_structure_store(), structure_store(), and structure_store_path().

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_path_

private

Referenced by structure_store_path().

core::Real protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::weight_ = 1

private

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

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

src/protocols/indexed_structure_store/movers/SegmentSequenceProfileMover.hh
src/protocols/indexed_structure_store/movers/SegmentSequenceProfileMover.cc

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation