#include <FilterScan.hh>
Public Member Functions | |
| FilterScanFilter () | |
| default ctor More... | |
| ~FilterScanFilter () override | |
| bool | apply (core::pose::Pose const &pose) const override |
| Constructor with a single target residue. 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... | |
| protocols::filters::FilterOP | clone () const override |
| protocols::filters::FilterOP | fresh_instance () const override |
| core::pack::task::TaskFactoryOP | task_factory () const |
| Undefined, commenting out to fix PyRosetta build core::Real compute( core::pose::Pose const & pose ) const;. More... | |
| void | task_factory (core::pack::task::TaskFactoryOP task_factory) |
| void | resfile_name (std::string const &resfile_name) |
| void | score_log_file (std::string const &score_log_file) |
| std::string | resfile_name () const |
| std::string | score_log_file () const |
| protocols::filters::FilterOP | triage_filter () const |
| void | triage_filter (protocols::filters::FilterOP filter) |
| protocols::filters::FilterOP | filter () const |
| void | filter (protocols::filters::FilterOP filter) |
| std::string | resfile_general_property () const |
| void | resfile_general_property (std::string const &) |
| void | relax_mover (protocols::moves::MoverOP mover) |
| protocols::moves::MoverOP | relax_mover () const |
| core::scoring::ScoreFunctionOP | scorefxn () const |
| void | scorefxn (core::scoring::ScoreFunctionOP scorefxn) |
| 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... | |
| bool | unbound () const |
| void | unbound (bool const u) |
| core::Size | jump () const |
| void | jump (core::Size const j) |
| bool | delta () const |
| void | delta (bool const d) |
| bool | report_all () const |
| void | report_all (bool const ra) |
| void | dump_pdb (bool const d) |
| bool | dump_pdb () const |
| bool | rtmin () const |
| void | rtmin (bool const r) |
| void | single_substitution (core::pose::Pose &pose, core::Size const resi, core::chemical::AA const target_aa) const |
| introduces a single-point subsitution and then performs the repack, rtmin, and relax moves that are requested. More... | |
| utility::vector1< protocols::simple_filters::DeltaFilterOP > | delta_filters () const |
| void | delta_filters (utility::vector1< protocols::simple_filters::DeltaFilterOP > const &d) |
| std::string | dump_pdb_name () const |
| void | dump_pdb_name (std::string const &s) |
| bool | keep_native () const |
| void | keep_native (bool const k) |
| utility::vector1< core::Real > | delta_filter_thresholds () const |
| void | delta_filter_thresholds (utility::vector1< core::Real > const &) |
| std::string | name () const override |
| bool | log_pdb_number () const |
| void | log_pdb_number (bool const log) |
| std::string | log_separator () const |
| void | log_separator (std::string const &sep) |
 Public Member Functions inherited from protocols::filters::Filter | |
| 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 Types | |
| typedef protocols::filters::Filter | parent |
Private Member Functions | |
| void | unbind (core::pose::Pose &) const |
Private Attributes | |
| core::pack::task::TaskFactoryOP | task_factory_ |
| protocols::filters::FilterOP | triage_filter_ |
| protocols::filters::FilterOP | filter_ |
| std::string | score_log_file_ |
| std::string | resfile_name_ |
| std::string | resfile_general_property_ |
| protocols::moves::MoverOP | relax_mover_ |
| core::scoring::ScoreFunctionOP | scorefxn_ |
| bool | delta_ |
| bool | unbound_ |
| bool | report_all_ |
| core::Size | jump_ |
| bool | dump_pdb_ |
| bool | rtmin_ |
| utility::vector1< protocols::simple_filters::DeltaFilterOP > | delta_filters_ |
| std::string | dump_pdb_name_ |
| bool | keep_native_ |
| utility::vector1< core::Real > | delta_filter_thresholds_ |
| bool | log_pdb_number_ |
| std::string | log_separator_ |
Additional Inherited Members | |
| Protected Attributes inherited from protocols::filters::Filter | |
| std::string | scorename_ |
Member Typedef Documentation
◆ parent
|
private |
Constructor & Destructor Documentation
◆ FilterScanFilter()
| protocols::protein_interface_design::filters::FilterScanFilter::FilterScanFilter | ( | ) |
default ctor
References protocols::jd2::current_output_name(), delta_filter_thresholds_, delta_filters_, and resfile_name().
◆ ~FilterScanFilter()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Constructor with a single target residue.
Implements protocols::filters::Filter.
References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::pose::Pose::conformation(), protocols::jd2::current_input_tag(), delta(), delta_filter_thresholds_, delta_filters_, dump_pdb(), dump_pdb_name(), dump_pdb_name_, core::pose::Pose::dump_scored_pdb(), protocols::buns::energy, core::chemical::element::F, filter(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), keep_native(), log_pdb_number_, log_separator_, core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::chemical::oneletter_code_from_aa(), core::conformation::membrane::out, core::scoring::pair, core::pose::Pose::pdb_info(), report_all_, report_sm(), resfile_general_property(), resfile_name(), core::pose::Pose::residue(), core::conformation::Conformation::residue(), score_log_file(), scorefxn(), single_substitution(), core::pose::Pose::size(), task_factory(), protocols::protein_interface_design::filters::TR(), protocols::protein_interface_design::filters::TR_residue_scan(), triage_filter(), and unbind().
◆ class_name()
|
static |
◆ clone()
|
overridevirtual |
Implements protocols::filters::Filter.
◆ delta() [1/2]
| bool protocols::protein_interface_design::filters::FilterScanFilter::delta | ( | ) | const |
References delta_.
Referenced by apply(), and parse_my_tag().
◆ delta() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::delta | ( | bool const | d | ) |
References delta_.
◆ delta_filter_thresholds() [1/2]
| utility::vector1< core::Real > protocols::protein_interface_design::filters::FilterScanFilter::delta_filter_thresholds | ( | ) | const |
References delta_filter_thresholds_.
◆ delta_filter_thresholds() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::delta_filter_thresholds | ( | utility::vector1< core::Real > const & | v | ) |
References delta_filter_thresholds_.
◆ delta_filters() [1/2]
| utility::vector1< protocols::simple_filters::DeltaFilterOP > protocols::protein_interface_design::filters::FilterScanFilter::delta_filters | ( | ) | const |
References delta_filters_.
◆ delta_filters() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::delta_filters | ( | utility::vector1< protocols::simple_filters::DeltaFilterOP > const & | d | ) |
References delta_filters_.
◆ dump_pdb() [1/2]
| bool protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb | ( | ) | const |
References dump_pdb_.
Referenced by apply(), and parse_my_tag().
◆ dump_pdb() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb | ( | bool const | d | ) |
References dump_pdb_.
◆ dump_pdb_name() [1/2]
|
inline |
References dump_pdb_name_.
Referenced by apply(), and parse_my_tag().
◆ dump_pdb_name() [2/2]
|
inline |
References dump_pdb_name_.
◆ filter() [1/2]
| protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::filter | ( | ) | const |
References filter_.
Referenced by apply(), filter(), parse_my_tag(), and triage_filter().
◆ filter() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::filter | ( | protocols::filters::FilterOP | filter | ) |
◆ fresh_instance()
|
overridevirtual |
Implements protocols::filters::Filter.
◆ jump() [1/2]
| core::Size protocols::protein_interface_design::filters::FilterScanFilter::jump | ( | ) | const |
References jump_.
Referenced by parse_my_tag(), and unbind().
◆ jump() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::jump | ( | core::Size const | j | ) |
References jump_.
◆ keep_native() [1/2]
|
inline |
References keep_native_.
Referenced by apply(), and parse_my_tag().
◆ keep_native() [2/2]
|
inline |
References keep_native_.
◆ log_pdb_number() [1/2]
|
inline |
References log_pdb_number_.
Referenced by parse_my_tag().
◆ log_pdb_number() [2/2]
|
inline |
References log_pdb_number_.
◆ log_separator() [1/2]
|
inline |
References log_separator_.
Referenced by parse_my_tag().
◆ log_separator() [2/2]
|
inline |
References log_separator_.
◆ name()
|
overridevirtual |
Reimplemented from protocols::filters::Filter.
References class_name().
◆ parse_my_tag()
|
overridevirtual |
Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.
Reimplemented from protocols::filters::Filter.
References delta(), delta_filter_thresholds_, delta_filters_, dump_pdb(), dump_pdb_name(), dump_pdb_name_, filter(), jump(), keep_native(), log_pdb_number(), log_separator(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_filter_or_null(), protocols::rosetta_scripts::parse_mover_or_null(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), relax_mover(), report_all(), resfile_general_property(), resfile_name(), rtmin(), score_log_file(), scorefxn(), task_factory(), protocols::protein_interface_design::filters::TR(), triage_filter(), and unbound().
◆ provide_xml_schema()
|
static |
References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().
Referenced by protocols::protein_interface_design::filters::FilterScanFilterCreator::provide_xml_schema().
◆ relax_mover() [1/2]
| protocols::moves::MoverOP protocols::protein_interface_design::filters::FilterScanFilter::relax_mover | ( | ) | const |
References relax_mover_.
Referenced by parse_my_tag(), and single_substitution().
◆ relax_mover() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::relax_mover | ( | protocols::moves::MoverOP | mover | ) |
References relax_mover_.
◆ report()
|
overridevirtual |
Reimplemented from protocols::filters::Filter.
◆ report_all() [1/2]
| bool protocols::protein_interface_design::filters::FilterScanFilter::report_all | ( | ) | const |
References report_all_.
Referenced by parse_my_tag().
◆ report_all() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::report_all | ( | bool const | ra | ) |
References report_all_.
◆ report_sm()
|
overridevirtual |
used to report filter internals through a score or silent file
Reimplemented from protocols::filters::Filter.
Referenced by apply().
◆ resfile_general_property() [1/2]
| std::string protocols::protein_interface_design::filters::FilterScanFilter::resfile_general_property | ( | ) | const |
References resfile_general_property_.
Referenced by apply(), parse_my_tag(), and resfile_general_property().
◆ resfile_general_property() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::resfile_general_property | ( | std::string const & | resfile_general_property | ) |
References resfile_general_property(), and resfile_general_property_.
◆ resfile_name() [1/2]
| std::string protocols::protein_interface_design::filters::FilterScanFilter::resfile_name | ( | ) | const |
References resfile_name_.
Referenced by apply(), FilterScanFilter(), parse_my_tag(), and resfile_name().
◆ resfile_name() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::resfile_name | ( | std::string const & | resfile_name | ) |
References resfile_name(), and resfile_name_.
◆ rtmin() [1/2]
|
inline |
References rtmin_.
Referenced by parse_my_tag(), and single_substitution().
◆ rtmin() [2/2]
|
inline |
References rtmin_.
◆ score_log_file() [1/2]
| std::string protocols::protein_interface_design::filters::FilterScanFilter::score_log_file | ( | ) | const |
References score_log_file_.
Referenced by apply(), parse_my_tag(), and score_log_file().
◆ score_log_file() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::score_log_file | ( | std::string const & | score_log_file | ) |
References score_log_file(), and score_log_file_.
◆ scorefxn() [1/2]
| core::scoring::ScoreFunctionOP protocols::protein_interface_design::filters::FilterScanFilter::scorefxn | ( | ) | const |
References scorefxn_.
Referenced by apply(), parse_my_tag(), scorefxn(), and single_substitution().
◆ scorefxn() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::scorefxn | ( | core::scoring::ScoreFunctionOP | scorefxn | ) |
References scorefxn(), and scorefxn_.
◆ single_substitution()
| void protocols::protein_interface_design::filters::FilterScanFilter::single_substitution | ( | core::pose::Pose & | pose, |
| core::Size const | resi, | ||
| core::chemical::AA const | target_aa | ||
| ) | const |
introduces a single-point subsitution and then performs the repack, rtmin, and relax moves that are requested.
References protocols::minimization_packing::RotamerTrialsMover::apply(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::name3(), core::chemical::num_canonical_aas, relax_mover(), core::pose::Pose::residue(), rtmin(), scorefxn(), core::pose::Pose::size(), task_factory(), and protocols::protein_interface_design::filters::TR().
Referenced by apply().
◆ task_factory() [1/2]
| core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::FilterScanFilter::task_factory | ( | ) | const |
Undefined, commenting out to fix PyRosetta build core::Real compute( core::pose::Pose const & pose ) const;.
References task_factory_.
Referenced by apply(), parse_my_tag(), single_substitution(), and task_factory().
◆ task_factory() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::task_factory | ( | core::pack::task::TaskFactoryOP | task_factory | ) |
References task_factory(), and task_factory_.
◆ triage_filter() [1/2]
| protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::triage_filter | ( | ) | const |
References triage_filter_.
Referenced by apply(), and parse_my_tag().
◆ triage_filter() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::triage_filter | ( | protocols::filters::FilterOP | filter | ) |
References filter(), and triage_filter_.
◆ unbind()
|
private |
References protocols::rigid::RigidBodyTransMover::apply(), jump(), protocols::rigid::RigidBodyTransMover::step_size(), and unbound().
Referenced by apply().
◆ unbound() [1/2]
| bool protocols::protein_interface_design::filters::FilterScanFilter::unbound | ( | ) | const |
References unbound_.
Referenced by parse_my_tag(), and unbind().
◆ unbound() [2/2]
| void protocols::protein_interface_design::filters::FilterScanFilter::unbound | ( | bool const | u | ) |
References protocols::hybridization::u, and unbound_.
Member Data Documentation
◆ delta_
|
private |
Referenced by delta().
◆ delta_filter_thresholds_
|
private |
Referenced by apply(), delta_filter_thresholds(), FilterScanFilter(), and parse_my_tag().
◆ delta_filters_
|
private |
Referenced by apply(), delta_filters(), FilterScanFilter(), and parse_my_tag().
◆ dump_pdb_
|
private |
Referenced by dump_pdb().
◆ dump_pdb_name_
|
private |
Referenced by apply(), dump_pdb_name(), and parse_my_tag().
◆ filter_
|
private |
Referenced by filter().
◆ jump_
|
private |
Referenced by jump().
◆ keep_native_
|
private |
Referenced by keep_native().
◆ log_pdb_number_
|
private |
Referenced by apply(), and log_pdb_number().
◆ log_separator_
|
private |
Referenced by apply(), and log_separator().
◆ relax_mover_
|
private |
Referenced by relax_mover().
◆ report_all_
|
private |
Referenced by apply(), and report_all().
◆ resfile_general_property_
|
private |
Referenced by resfile_general_property().
◆ resfile_name_
|
private |
Referenced by resfile_name().
◆ rtmin_
|
private |
Referenced by rtmin().
◆ score_log_file_
|
private |
Referenced by score_log_file().
◆ scorefxn_
|
private |
Referenced by scorefxn().
◆ task_factory_
|
private |
Referenced by task_factory().
◆ triage_filter_
|
private |
Referenced by triage_filter().
◆ unbound_
|
private |
Referenced by unbound().
The documentation for this class was generated from the following files:
- src/protocols/protein_interface_design/filters/FilterScan.hh
- src/protocols/protein_interface_design/filters/FilterScan.cc
