Rosetta
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#include <SSShapeComplementarityFilter.hh>
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 |
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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 | |
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std::string | scorename_ |
protocols::denovo_design::filters::SSShapeComplementarityFilter::SSShapeComplementarityFilter | ( | ) |
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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.
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overridevirtual |
Does the SSShapeComplementarity Filtering.
Implements protocols::filters::Filter.
References rejection_thresh(), report_sm(), and protocols::TR().
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static |
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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().
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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().
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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().
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overridevirtual |
Apply the SSShapeComplementarityFilter. Overloaded apply function from filter base class.
Implements protocols::filters::Filter.
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Return the name of this mover.
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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().
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overridevirtual |
Reimplemented from protocols::filters::Filter.
References class_name().
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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_.
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inline |
Get the threshold below which structures are rejected.
References rejection_thresh_.
Referenced by apply().
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overridevirtual |
Reimplemented from protocols::filters::Filter.
References compute(), and core::conformation::membrane::out.
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overridevirtual |
used to report filter internals through a score or silent file
Reimplemented from protocols::filters::Filter.
References compute().
Referenced by apply().
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inline |
Sets whether or not to include helices in the calculations.
References calc_helices_.
Referenced by parse_my_tag().
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Sets whether or not to include loops in the calculations.
References calc_loops_.
Referenced by parse_my_tag().
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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().
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Set the secondary structure to be used for the pose. If unspecified, dssp will be used.
References secstruct_.
Referenced by parse_my_tag().
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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().
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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().
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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().
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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().
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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().
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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().
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Threshold below which structures are rejected. Default 0.0 (no filtration).
Referenced by rejection_thresh(), and set_rejection_thresh().
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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().
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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().
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residue selector
Referenced by compute(), compute_from_selector(), and set_residue_selector().
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controls outputtting verbose information about SC
Referenced by get_sc_and_area(), parse_my_tag(), and set_verbose().