#include <StructProfileMover.hh>

Inheritance diagram for protocols::simple_moves::StructProfileMover:

[legend]

Public Member Functions
	StructProfileMover ()

	StructProfileMover (core::Real rmsThreshold, core::Real burialThreshold, core::Size consider_topN_frags, core::Real burialWt, bool only_loops, bool censorByBurial, core::Real allowed_deviation, core::Real allowed_deviation_loops, bool eliminate_background, bool psiblast_style_pssm, bool outputProfile, bool add_csts_to_pose, bool ignore_terminal_res, std::string fragment_store_path="", std::string fragment_store_format="", std::string fragment_store_compression="")

core::Size	ss_type_convert (char ss_type)

void	read_P_AA_SS_cen6 ()

utility::vector1< std::string >	get_closest_sequence_at_res (core::pose::Pose const &pose, core::Size res, utility::vector1< core::Real > cenList)

utility::vector1< utility::vector1< std::string > >	get_closest_sequences (core::pose::Pose const &pose, utility::vector1< core::Real > cenList, core::select::residue_selector::ResidueSubset const &subset)

utility::vector1< utility::vector1< core::Size > >	generate_counts (utility::vector1< utility::vector1< std::string > > top_frag_sequences, core::pose::Pose const &pose)

utility::vector1< utility::vector1< core::Real > >	generate_profile_score (utility::vector1< utility::vector1< core::Size > > res_per_pos, core::pose::Pose const &pose)

utility::vector1< utility::vector1< core::Real > >	generate_profile_score_wo_background (utility::vector1< utility::vector1< core::Size > > res_per_pos, utility::vector1< core::Real > cenList, core::pose::Pose const &pose)

void	save_MSAcst_file (utility::vector1< utility::vector1< core::Real > > profile_score, core::pose::Pose const &pose)

void	add_MSAcst_to_pose (utility::vector1< utility::vector1< core::Real > > profile_score, core::pose::Pose &pose)

core::Real	get_cen_deviation (std::vector< core::Real > cenListFrag, utility::vector1< core::Real > cenListModel)

std::string	censorFragByBurial (std::vector< core::Real > cenListFrag, utility::vector1< core::Real > cenListModel, std::string cenListFragSeq)

void	set_profile_save_name (std::string const &name)

utility::vector1< core::Real >	calc_cenlist (core::pose::Pose const &pose)

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

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

void	set_residue_selector (core::select::residue_selector::ResidueSelector const &selector)

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...

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 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::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Types
typedef utility::vector1< utility::vector1< utility::vector1< Probability > > >	Probability_AA_n_n

Private Attributes
core::Real	rmsThreshold_

core::Real	burialThreshold_

std::string	aa_order_

core::Size	consider_topN_frags_

core::Real	burialWt_

bool	psiblast_style_pssm_

bool	outputProfile_

bool	add_csts_to_pose_

core::Size	cenType_

protocols::indexed_structure_store::SSHashedFragmentStoreOP	SSHashedFragmentStoreOP_

Probability_AA_n_n	P_AA_SS_burial_

core::Real	allowed_deviation_

core::Real	allowed_deviation_loops_

bool	only_loops_

bool	censorByBurial_

bool	eliminate_background_

bool	ignore_terminal_res_

core::select::residue_selector::ResidueSelectorCOP	residue_selector_

std::string	profile_save_filename_

std::string	fragment_store_path_

std::string	fragment_store_format_

std::string	fragment_store_compression_

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...

Member Typedef Documentation

◆ Probability_AA_n_n

typedef utility::vector1< utility::vector1< utility::vector1< Probability > > > protocols::simple_moves::StructProfileMover::Probability_AA_n_n

private

Constructor & Destructor Documentation

◆ StructProfileMover() [1/2]

protocols::simple_moves::StructProfileMover::StructProfileMover ( )

References aa_order_, and read_P_AA_SS_cen6().

◆ StructProfileMover() [2/2]

protocols::simple_moves::StructProfileMover::StructProfileMover	(	core::Real	rmsThreshold,
		core::Real	burialThreshold,
		core::Size	consider_topN_frags,
		core::Real	burialWt,
		bool	only_loops,
		bool	censorByBurial,
		core::Real	allowed_deviation,
		core::Real	allowed_deviation_loops,
		bool	eliminate_background,
		bool	psiblast_style_pssm,
		bool	outputProfile,
		bool	add_csts_to_pose,
		bool	ignore_terminal_res,
		std::string	fragment_store_path = `""`,
		std::string	fragment_store_format = `""`,
		std::string	fragment_store_compression = `""`
	)

Member Function Documentation

◆ add_MSAcst_to_pose()

void protocols::simple_moves::StructProfileMover::add_MSAcst_to_pose	(	utility::vector1< utility::vector1< core::Real > >	profile_score,
		core::pose::Pose &	pose
	)

References protocols::cluster::calibur::aa, aa_order_, core::pose::Pose::add_constraint(), core::sequence::end, core::pose::symmetry::is_symmetric(), core::pose::Pose::sequence(), core::pose::Pose::size(), and core::pose::symmetry::symmetry_info().

Referenced by apply().

◆ apply()

void protocols::simple_moves::StructProfileMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References add_csts_to_pose_, add_MSAcst_to_pose(), calc_cenlist(), eliminate_background_, generate_counts(), generate_profile_score(), generate_profile_score_wo_background(), get_closest_sequences(), core::scoring::dssp::Dssp::insert_ss_into_pose(), outputProfile_, residue_selector_, save_MSAcst_file(), and core::pose::Pose::size().

◆ calc_cenlist()

vector1< Real > protocols::simple_moves::StructProfileMover::calc_cenlist ( core::pose::Pose const & pose )

References core::scoring::EnvPairPotential::cenlist_from_pose(), core::chemical::CENTROID, cenType_, core::pose::Pose::clone(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::CenListInfo::fcen10(), core::scoring::CenListInfo::fcen12(), core::scoring::CenListInfo::fcen6(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), core::util::switch_to_residue_type_set(), and core::pose::symmetry::symmetry_info().

Referenced by apply().

◆ censorFragByBurial()

std::string protocols::simple_moves::StructProfileMover::censorFragByBurial	(	std::vector< core::Real >	cenListFrag,
		utility::vector1< core::Real >	cenListModel,
		std::string	cenListFragSeq
	)

References burialThreshold_.

Referenced by get_closest_sequence_at_res().

◆ clone()

moves::MoverOP protocols::simple_moves::StructProfileMover::clone ( ) const

inlineoverridevirtual

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.

◆ generate_counts()

vector1< vector1< core::Size > > protocols::simple_moves::StructProfileMover::generate_counts	(	utility::vector1< utility::vector1< std::string > >	top_frag_sequences,
		core::pose::Pose const &	pose
	)

References aa_order_, core::pose::symmetry::is_symmetric(), core::pose::Pose::size(), and core::pose::symmetry::symmetry_info().

Referenced by apply().

◆ generate_profile_score()

vector1< vector1< Real > > protocols::simple_moves::StructProfileMover::generate_profile_score	(	utility::vector1< utility::vector1< core::Size > >	res_per_pos,
		core::pose::Pose const &	pose
	)

References only_loops_, psiblast_style_pssm_, and core::pose::Pose::secstruct().

Referenced by apply().

◆ generate_profile_score_wo_background()

vector1< vector1< Real > > protocols::simple_moves::StructProfileMover::generate_profile_score_wo_background	(	utility::vector1< utility::vector1< core::Size > >	res_per_pos,
		utility::vector1< core::Real >	cenList,
		core::pose::Pose const &	pose
	)

References allowed_deviation_, allowed_deviation_loops_, ignore_terminal_res_, core::pose::symmetry::is_symmetric(), only_loops_, P_AA_SS_burial_, protocols::noesy_assign::round(), core::pose::Pose::secstruct(), core::pose::Pose::size(), ss_type_convert(), and core::pose::symmetry::symmetry_info().

Referenced by apply().

◆ get_cen_deviation()

Real protocols::simple_moves::StructProfileMover::get_cen_deviation	(	std::vector< core::Real >	cenListFrag,
		utility::vector1< core::Real >	cenListModel
	)

Referenced by get_closest_sequence_at_res().

◆ get_closest_sequence_at_res()

vector1< std::string > protocols::simple_moves::StructProfileMover::get_closest_sequence_at_res	(	core::pose::Pose const &	pose,
		core::Size	res,
		utility::vector1< core::Real >	cenList
	)

References protocols::cluster::calibur::aa, burialWt_, protocols::simple_moves::Hit::cend, censorByBurial_, censorFragByBurial(), consider_topN_frags_, get_cen_deviation(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), rmsThreshold_, and SSHashedFragmentStoreOP_.

Referenced by get_closest_sequences().

◆ get_closest_sequences()

vector1< vector1< std::string > > protocols::simple_moves::StructProfileMover::get_closest_sequences	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real >	cenList,
		core::select::residue_selector::ResidueSubset const &	subset
	)

References get_closest_sequence_at_res(), core::pose::symmetry::is_symmetric(), core::pose::Pose::size(), SSHashedFragmentStoreOP_, and core::pose::symmetry::symmetry_info().

Referenced by apply().

◆ get_name()

std::string protocols::simple_moves::StructProfileMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::simple_moves::StructProfileMover::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::StructProfileMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::simple_moves::StructProfileMover::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 add_csts_to_pose_, allowed_deviation_, allowed_deviation_loops_, burialThreshold_, burialWt_, censorByBurial_, cenType_, consider_topN_frags_, eliminate_background_, fragment_store_compression_, fragment_store_format_, fragment_store_path_, ignore_terminal_res_, only_loops_, outputProfile_, core::select::residue_selector::parse_residue_selector(), profile_save_filename_, psiblast_style_pssm_, rmsThreshold_, set_profile_save_name(), set_residue_selector(), and SSHashedFragmentStoreOP_.

◆ provide_xml_schema()

void protocols::simple_moves::StructProfileMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::simple_moves::StructProfileMoverCreator::provide_xml_schema().

◆ read_P_AA_SS_cen6()

void protocols::simple_moves::StructProfileMover::read_P_AA_SS_cen6 ( )

References aa_order_, P_AA_SS_burial_, and ss_type_convert().

Referenced by StructProfileMover().

◆ save_MSAcst_file()

void protocols::simple_moves::StructProfileMover::save_MSAcst_file	(	utility::vector1< utility::vector1< core::Real > >	profile_score,
		core::pose::Pose const &	pose
	)