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protocols::denovo_design::filters::SSShapeComplementarityFilter Class Reference

#include <SSShapeComplementarityFilter.hh>

Inheritance diagram for protocols::denovo_design::filters::SSShapeComplementarityFilter:
Inheritance graph
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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 ( )
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
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
core::Real protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_selector ( core::pose::Pose const &  pose) const
private
core::Real protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_ss_info ( core::pose::Pose const &  pose) const
private
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
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
void protocols::denovo_design::filters::SSShapeComplementarityFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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)
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

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
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: