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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_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 (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 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

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_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().

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().

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)

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().

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().

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().

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(), parse_my_tag(), and set_calc_helices().

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().

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(), parse_my_tag(), and set_secstruct().

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(), parse_my_tag(), and set_verbose().


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