#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_residue_selector (core::select::residue_selector::ResidueSelector const &selector)

std::string	name () const override

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

	Filter (std::string const &)

	Filter (Filter 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 bool	filter_provides_citation_info () const
	Does this filter 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	filter_is_unpublished () const
	Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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	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

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

Initialize SSShapeComplementarityFilter.

SSShapeComplementarityFilter main code:

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

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().

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

static

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

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.

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().

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().

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

private

References calc_helices_, calc_loops_, protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), get_sc_and_area(), scc_, secstruct_, setup_sc(), core::simple_metrics::metrics::sum, and protocols::TR().

Referenced by compute().

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.

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

virtual

Return the name of this mover.

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().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

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_rejection_thresh(), set_residue_selector(), and verbose_.

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().

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().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

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().

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().

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

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

Referenced by parse_my_tag().

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

Referenced by compute_from_ss_info().

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

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

Member Data Documentation

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(), and parse_my_tag().

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(), and parse_my_tag().

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().

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().

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(), and parse_my_tag().

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

private

residue selector

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

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

private

controls outputtting verbose information about SC

Referenced by get_sc_and_area(), and parse_my_tag().

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 main code:

Member Function Documentation

Member Data Documentation