#include <SSShapeComplementarityFilter.hh>

Inheritance diagram for protocols::denovo_design::filters::SSShapeComplementarityFilter:

Public Member Functions
	SSShapeComplementarityFilter ()
	Initialize SSShapeComplementarityFilter. More...

	~SSShapeComplementarityFilter () override
	virtual constructor to allow derivation More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Parses the SSShapeComplementarityFilter tags. More...

virtual std::string	get_name () const
	Return the name of this mover. More...

protocols::filters::FilterOP	clone () const override
	return a fresh instance of this class in an owning pointer More...

protocols::filters::FilterOP	fresh_instance () const override
	Apply the SSShapeComplementarityFilter. Overloaded apply function from filter base class. More...

void	report (std::ostream &out, core::pose::Pose const &pose) const override

core::Real	report_sm (core::pose::Pose const &pose) const override
	used to report filter internals through a score or silent file More...

bool	apply (core::pose::Pose const &pose) const override
	Does the SSShapeComplementarity Filtering. More...

core::Real	compute (core::pose::Pose const &pose) const

void	set_rejection_thresh (core::Real const &val)
	Set the threshold below which structures are rejected. More...

core::Real	rejection_thresh () const
	Get the threshold below which structures are rejected. More...

void	set_secstruct (std::string const &secstruct)
	Set the secondary structure to be used for the pose. If unspecified, dssp will be used. More...

void	set_verbose (bool const verbose)
	Sets the verbosity; if true, shape complementarity information will be printed out to the tracer when the filter is run. Not sure why the code can't just use the Tracer system to do this, but that is how the code works right now. More...

void	set_calc_loops (bool const calc_loops)
	Sets whether or not to include loops in the calculations. More...

void	set_calc_helices (bool const calc_helices)
	Sets whether or not to include helices in the calculations. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelector const &selector)
	Sets the residue selector to be used; clones the residue selector. More...

std::string	name () const override

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	~Filter () override

virtual std::string	get_type () const

std::string	get_user_defined_name () const

void	set_user_defined_name (std::string const &name)

virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...

virtual core::Real	score (core::pose::Pose &pose)

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	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
void	setup_sc (core::pose::Pose const &pose, protocols::fldsgn::topology::SS_BaseCOP const ss) const
	sets up the underlying filter to work based on a helix More...

void	setup_sc_hss (core::pose::Pose const &pose, protocols::fldsgn::topology::SS_Info2 const &ss_info, protocols::fldsgn::topology::HSSTripletCOP hss_triplet) const
	sets up the underlying shapecomplementarity filter to work based on secondary structure elements More...

void	setup_sc_hh (core::pose::Pose const &pose, protocols::fldsgn::topology::SS_Info2 const &ss_info, protocols::fldsgn::topology::HelixPairingCOP helix_pair) const
	sets up the underlying shapecomplementarity filter to work based on secondary structure elements More...

core::Real	compute_from_selector (core::pose::Pose const &pose) const
	computes sc score for selectoed residues vs the rest of the pose Residue selector MUST be set to call this More...

core::Real	compute_from_ss_info (core::pose::Pose const &pose) const

core::scoring::sc::RESULTS const &	get_sc_and_area () const
	Runs the SC calculator to obtain an SC score and an interaction area. Returns a result in the format core::scoring::sc::RESULTS. Assumes the SC calculator has been initialized and has the correct residues added. More...

Private Attributes
bool	verbose_
	controls outputtting verbose information about SC More...

bool	calc_loops_
	should we calculate SC from each loop to the rest of the protein? More...

bool	calc_helices_
	should we calculate SC from each helix to the rest of the protein? More...

core::Real	rejection_thresh_
	Threshold below which structures are rejected. Default 0.0 (no filtration). More...

std::string	secstruct_
	If set, this will be used as the secondary structure for the pose, instead of DSSP. More...

core::select::residue_selector::ResidueSelectorCOP	selector_
	residue selector More...

core::scoring::sc::ShapeComplementarityCalculatorOP	scc_
	the shape complementarity calculator More...

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Constructor & Destructor Documentation

◆ SSShapeComplementarityFilter()

protocols::denovo_design::filters::SSShapeComplementarityFilter::SSShapeComplementarityFilter ( )

Initialize SSShapeComplementarityFilter.

SSShapeComplementarityFilter main code:

◆ ~SSShapeComplementarityFilter()

protocols::denovo_design::filters::SSShapeComplementarityFilter::~SSShapeComplementarityFilter ( )

overridedefault

virtual constructor to allow derivation

destructor - this class has no dynamic allocation, so / nothing needs to be cleaned. C++ will take care of that for us.

Member Function Documentation

◆ apply()

bool protocols::denovo_design::filters::SSShapeComplementarityFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

Does the SSShapeComplementarity Filtering.

Implements protocols::filters::Filter.

References rejection_thresh(), report_sm(), and protocols::TR().

◆ class_name()

std::string protocols::denovo_design::filters::SSShapeComplementarityFilter::class_name ( )

static

Referenced by protocols::denovo_design::filters::SSShapeComplementarityFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::denovo_design::filters::SSShapeComplementarityFilter::clone ( ) const

overridevirtual

return a fresh instance of this class in an owning pointer

Return a copy of ourselves.

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::denovo_design::filters::SSShapeComplementarityFilter::compute ( core::pose::Pose const & pose ) const

References compute_from_selector(), compute_from_ss_info(), scc_, selector_, and protocols::TR().

Referenced by report(), and report_sm().

◆ compute_from_selector()

core::Real protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_selector ( core::pose::Pose const & pose ) const

private

computes sc score for selectoed residues vs the rest of the pose Residue selector MUST be set to call this

References core::scoring::sc::_RESULTS::area, get_sc_and_area(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::scoring::sc::_RESULTS::sc, scc_, protocols::filters::Filter::score(), selector_, core::simple_metrics::metrics::sum, protocols::TR(), and core::scoring::sc::_RESULTS::valid.

Referenced by compute().

◆ compute_from_ss_info()

core::Real protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_ss_info ( core::pose::Pose const & pose ) const

private

References core::scoring::sc::_RESULTS::area, calc_helices_, calc_loops_, protocols::simple_filters::dssp(), get_sc_and_area(), core::scoring::sc::_RESULTS::sc, scc_, secstruct_, setup_sc(), core::simple_metrics::metrics::sum, protocols::TR(), and core::scoring::sc::_RESULTS::valid.

Referenced by compute().

◆ fresh_instance()

protocols::filters::FilterOP protocols::denovo_design::filters::SSShapeComplementarityFilter::fresh_instance ( ) const

overridevirtual

Apply the SSShapeComplementarityFilter. Overloaded apply function from filter base class.

Implements protocols::filters::Filter.

◆ get_name()

std::string protocols::denovo_design::filters::SSShapeComplementarityFilter::get_name ( ) const

virtual

Return the name of this mover.

◆ get_sc_and_area()

core::scoring::sc::RESULTS const & protocols::denovo_design::filters::SSShapeComplementarityFilter::get_sc_and_area ( ) const

private

Runs the SC calculator to obtain an SC score and an interaction area. Returns a result in the format core::scoring::sc::RESULTS. Assumes the SC calculator has been initialized and has the correct residues added.

References core::scoring::sc::_RESULTS::d_mean, core::scoring::sc::_RESULTS::d_median, core::scoring::sc::_RESULTS::nAllDots, core::scoring::sc::_RESULTS::nAtoms, core::scoring::sc::_RESULTS::nBlockedAtoms, core::scoring::sc::_RESULTS::nBuriedAtoms, core::scoring::sc::_RESULTS::nTrimmedDots, core::scoring::sc::_RESULTS::s_mean, core::scoring::sc::_RESULTS::s_median, scc_, core::scoring::sc::_RESULTS::surface, protocols::TR(), core::scoring::sc::_RESULTS::trimmedArea, and verbose_.

Referenced by compute_from_selector(), and compute_from_ss_info().

◆ name()

std::string protocols::denovo_design::filters::SSShapeComplementarityFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

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

overridevirtual

Parses the SSShapeComplementarityFilter tags.

Reimplemented from protocols::filters::Filter.

References calc_helices_, calc_loops_, core::select::residue_selector::parse_residue_selector(), protocols::parser::BluePrint::secstruct(), secstruct_, set_calc_helices(), set_calc_loops(), set_rejection_thresh(), set_residue_selector(), set_secstruct(), set_verbose(), and verbose_.

◆ provide_xml_schema()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::denovo_design::filters::SSShapeComplementarityFilterCreator::provide_xml_schema().

◆ rejection_thresh()

core::Real protocols::denovo_design::filters::SSShapeComplementarityFilter::rejection_thresh ( ) const

inline

Get the threshold below which structures are rejected.

References rejection_thresh_.

Referenced by apply().

◆ report()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

◆ report_sm()

core::Real protocols::denovo_design::filters::SSShapeComplementarityFilter::report_sm ( core::pose::Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

Referenced by apply().

◆ set_calc_helices()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::set_calc_helices ( bool const calc_helices )

inline

Sets whether or not to include helices in the calculations.

References calc_helices_.

Referenced by parse_my_tag().

◆ set_calc_loops()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::set_calc_loops ( bool const calc_loops )

inline

Sets whether or not to include loops in the calculations.

References calc_loops_.

Referenced by parse_my_tag().

◆ set_rejection_thresh()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::set_rejection_thresh ( core::Real const & val )

inline

Set the threshold below which structures are rejected.

References rejection_thresh_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_residue_selector()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::set_residue_selector ( core::select::residue_selector::ResidueSelector const & selector )

Sets the residue selector to be used; clones the residue selector.

References core::select::residue_selector::ResidueSelector::clone(), and selector_.

Referenced by parse_my_tag().

◆ set_secstruct()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::set_secstruct ( std::string const & secstruct )

inline

Set the secondary structure to be used for the pose. If unspecified, dssp will be used.

References secstruct_.

Referenced by parse_my_tag().

◆ set_verbose()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::set_verbose ( bool const verbose )

inline

Sets the verbosity; if true, shape complementarity information will be printed out to the tracer when the filter is run. Not sure why the code can't just use the Tracer system to do this, but that is how the code works right now.

References verbose_.

Referenced by parse_my_tag().

◆ setup_sc()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc	(	core::pose::Pose const &	pose,
		protocols::fldsgn::topology::SS_BaseCOP const	ss
	)		const

private

sets up the underlying filter to work based on a helix

References core::sequence::end, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), scc_, core::pose::Pose::size(), and protocols::TR().

Referenced by compute_from_ss_info().

◆ setup_sc_hh()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc_hh	(	core::pose::Pose const &	pose,
		protocols::fldsgn::topology::SS_Info2 const &	ss_info,
		protocols::fldsgn::topology::HelixPairingCOP	helix_pair
	)		const

private

sets up the underlying shapecomplementarity filter to work based on secondary structure elements

References core::sequence::end, protocols::fldsgn::topology::SS_Info2::helix(), protocols::loops::loop_closure::ccd::helix, core::pose::Pose::residue(), scc_, and protocols::TR().

◆ setup_sc_hss()

void protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc_hss	(	core::pose::Pose const &	pose,
		protocols::fldsgn::topology::SS_Info2 const &	ss_info,
		protocols::fldsgn::topology::HSSTripletCOP	hss_triplet
	)		const

private

sets up the underlying shapecomplementarity filter to work based on secondary structure elements

References core::sequence::end, protocols::fldsgn::topology::SS_Info2::helix(), protocols::loops::loop_closure::ccd::helix, core::pose::Pose::residue(), scc_, protocols::fldsgn::topology::SS_Info2::strand(), protocols::loops::loop_closure::ccd::strand, and protocols::TR().

Member Data Documentation

◆ calc_helices_

bool protocols::denovo_design::filters::SSShapeComplementarityFilter::calc_helices_

private

should we calculate SC from each helix to the rest of the protein?

Referenced by compute_from_ss_info(), parse_my_tag(), and set_calc_helices().

◆ calc_loops_

bool protocols::denovo_design::filters::SSShapeComplementarityFilter::calc_loops_

private

should we calculate SC from each loop to the rest of the protein?

Referenced by compute_from_ss_info(), parse_my_tag(), and set_calc_loops().

◆ rejection_thresh_

core::Real protocols::denovo_design::filters::SSShapeComplementarityFilter::rejection_thresh_

private

Threshold below which structures are rejected. Default 0.0 (no filtration).

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by rejection_thresh(), and set_rejection_thresh().

◆ scc_

core::scoring::sc::ShapeComplementarityCalculatorOP protocols::denovo_design::filters::SSShapeComplementarityFilter::scc_

private

the shape complementarity calculator

Referenced by compute(), compute_from_selector(), compute_from_ss_info(), get_sc_and_area(), setup_sc(), setup_sc_hh(), and setup_sc_hss().

◆ secstruct_

std::string protocols::denovo_design::filters::SSShapeComplementarityFilter::secstruct_

private

If set, this will be used as the secondary structure for the pose, instead of DSSP.

Referenced by compute_from_ss_info(), parse_my_tag(), and set_secstruct().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::filters::SSShapeComplementarityFilter::selector_

private

residue selector

Referenced by compute(), compute_from_selector(), and set_residue_selector().

◆ verbose_

bool protocols::denovo_design::filters::SSShapeComplementarityFilter::verbose_

private

controls outputtting verbose information about SC

Referenced by get_sc_and_area(), parse_my_tag(), and set_verbose().

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

src/protocols/denovo_design/filters/SSShapeComplementarityFilter.hh
src/protocols/denovo_design/filters/SSShapeComplementarityFilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ SSShapeComplementarityFilter()

SSShapeComplementarityFilter main code:

◆ ~SSShapeComplementarityFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ compute_from_selector()

◆ compute_from_ss_info()

◆ fresh_instance()

◆ get_name()

◆ get_sc_and_area()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ rejection_thresh()

◆ report()

◆ report_sm()

◆ set_calc_helices()

◆ set_calc_loops()

◆ set_rejection_thresh()

◆ set_residue_selector()

◆ set_secstruct()

◆ set_verbose()

◆ setup_sc()

◆ setup_sc_hh()

◆ setup_sc_hss()

Member Data Documentation

◆ calc_helices_

◆ calc_loops_

◆ rejection_thresh_

◆ scc_

◆ secstruct_

◆ selector_

◆ verbose_