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Rosetta
2021.07
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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_residue_selector (core::select::residue_selector::ResidueSelector const &selector) |
std::string | name () const override |
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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 | |
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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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private |
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overridevirtual |
Apply the SSShapeComplementarityFilter. Overloaded apply function from filter base class.
Implements protocols::filters::Filter.
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virtual |
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_rejection_thresh(), set_residue_selector(), and verbose_.
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static |
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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().
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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 |
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().
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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().
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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().
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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().
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should we calculate SC from each helix to the rest of the protein?
Referenced by compute_from_ss_info(), and parse_my_tag().
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should we calculate SC from each loop to the rest of the protein?
Referenced by compute_from_ss_info(), and parse_my_tag().
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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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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().
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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(), and parse_my_tag().