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Rosetta
2020.50
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#include <ResidueBurialFilter.hh>
Public Member Functions | |
ResidueBurialFilter () | |
bool | apply (core::pose::Pose const &pose) const override |
Returns true if the given pose passes the filter, false otherwise. 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... | |
core::Size | compute (core::pose::Pose const &pose) const |
filters::FilterOP | clone () const override |
filters::FilterOP | fresh_instance () const override |
core::pack::task::TaskFactoryOP | task_factory () const |
void | task_factory (core::pack::task::TaskFactoryOP tf) |
~ResidueBurialFilter () override | |
void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override |
Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More... | |
core::Real | residue_fraction_buried () const |
void | residue_fraction_buried (core::Real const r) |
std::string | residue () const |
void | residue (std::string const &s) |
core::Size | neighbors () const |
void | neighbors (core::Size const n) |
core::Real | distance_threshold () const |
void | distance_threshold (core::Real const r) |
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 Attributes | |
std::string | residue_ |
core::Size | neighbors_ |
core::Real | distance_threshold_ |
core::pack::task::TaskFactoryOP | task_factory_ |
core::Real | residue_fraction_buried_ |
used to determine which residues to check for burial dynamically. All designable residues will be checked, and if any of them is buried, returns true More... | |
Additional Inherited Members | |
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std::string | scorename_ |
protocols::simple_filters::ResidueBurialFilter::ResidueBurialFilter | ( | ) |
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overridedefault |
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overridevirtual |
Returns true if the given pose passes the filter, false otherwise.
Implements protocols::filters::Filter.
References apply(), compute(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), distance_threshold(), core::conformation::Residue::name3(), neighbors(), neighbors_, core::pose::parse_resnum(), residue(), core::pose::Pose::residue(), protocols::simple_filters::residue_burial_filter_tracer(), residue_fraction_buried(), protocols::rosetta_scripts::residue_packer_states(), task_factory(), and core::id::to_string().
Referenced by apply().
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Referenced by protocols::simple_filters::ResidueBurialFilterCreator::keyname(), name(), and provide_xml_schema().
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overridevirtual |
Implements protocols::filters::Filter.
core::Size protocols::simple_filters::ResidueBurialFilter::compute | ( | core::pose::Pose const & | pose | ) | const |
counts the number of residues to target_residue_ across all chains in the pose, other than the one containing target_residue_
References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), core::kinematics::distance(), distance_threshold_, core::conformation::Conformation::num_chains(), core::pose::parse_resnum(), residue(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), protocols::simple_filters::residue_burial_filter_tracer(), and core::pose::Pose::size().
Referenced by apply(), report(), and report_sm().
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References distance_threshold_.
Referenced by apply().
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inline |
References distance_threshold_.
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overridevirtual |
Implements protocols::filters::Filter.
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overridevirtual |
Reimplemented from protocols::filters::Filter.
References class_name().
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References neighbors_.
Referenced by apply().
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inline |
References neighbors_.
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overridevirtual |
Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.
Reimplemented from protocols::filters::Filter.
References distance_threshold_, neighbors_, core::pack::task::parse_task_operations(), residue(), protocols::simple_filters::residue_burial_filter_tracer(), residue_fraction_buried(), and task_factory().
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overridevirtual |
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overridevirtual |
used to report filter internals through a score or silent file
Reimplemented from protocols::filters::Filter.
References compute(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), and task_factory().
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inline |
References residue_.
Referenced by apply(), compute(), parse_my_tag(), and report().
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References residue_.
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inline |
References residue_fraction_buried_.
Referenced by apply(), and parse_my_tag().
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References residue_fraction_buried_.
core::pack::task::TaskFactoryOP protocols::simple_filters::ResidueBurialFilter::task_factory | ( | ) | const |
References task_factory_.
Referenced by apply(), parse_my_tag(), report(), and report_sm().
void protocols::simple_filters::ResidueBurialFilter::task_factory | ( | core::pack::task::TaskFactoryOP | tf | ) |
References task_factory_.
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private |
Referenced by compute(), distance_threshold(), and parse_my_tag().
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Referenced by apply(), neighbors(), and parse_my_tag().
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Referenced by residue().
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used to determine which residues to check for burial dynamically. All designable residues will be checked, and if any of them is buried, returns true
Referenced by residue_fraction_buried().
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Referenced by task_factory().