#include <SequenceRecoveryFilter.hh>
Public Member Functions | |
| SequenceRecoveryFilter () | |
| default ctor More... | |
| 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::Real | compute (core::pose::Pose const &pose, bool const &write) const |
| void | write_to_pdb (std::map< core::Size, std::string > const &res_names1, std::map< core::Size, std::string > const &res_names2) const |
| Add each mutation to the output pdb if desired. More... | |
| ~SequenceRecoveryFilter () override | |
| core::pack::task::TaskFactoryOP | task_factory () const |
| void | task_factory (core::pack::task::TaskFactoryOP task_factory) |
| core::Real | rate_threshold () const |
| void | rate_threshold (core::Real const rate) |
| core::Size | mutation_threshold () const |
| void | mutation_threshold (core::Size const mut) |
| bool | mutations () const |
| void | mutations (bool const muts) |
| bool | verbose () const |
| void | verbose (bool const verb) |
| bool | write2pdb () const |
| void | write2pdb (bool const write) |
| void | scorefxn (core::scoring::ScoreFunctionCOP sfx) |
| core::pose::PoseCOP | reference_pose () const |
| void | reference_pose (core::pose::PoseCOP reference_pose) |
| void | reference_pose (core::pose::Pose const &pose) |
| 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... | |
| std::string | name () const override |
 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 |
Additional Inherited Members | |
| Protected Attributes inherited from protocols::filters::Filter | |
| std::string | scorename_ |
Member Typedef Documentation
◆ parent
|
private |
Constructor & Destructor Documentation
◆ SequenceRecoveryFilter()
| protocols::protein_interface_design::filters::SequenceRecoveryFilter::SequenceRecoveryFilter | ( | ) |
default ctor
◆ ~SequenceRecoveryFilter()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Constructor with a single target residue.
Implements protocols::filters::Filter.
References compute(), mutation_threshold_, mutations_, rate_threshold_, and protocols::protein_interface_design::filters::TR().
◆ class_name()
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static |
◆ clone()
|
overridevirtual |
Implements protocols::filters::Filter.
◆ compute()
| core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute | ( | core::pose::Pose const & | pose, |
| bool const & | write | ||
| ) | const |
References protocols::protein_interface_design::ReportSequenceDifferences::calculate(), core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::is_symmetric(), mutations_, core::chemical::ResidueTypeBase::name(), reference_pose(), protocols::protein_interface_design::ReportSequenceDifferences::report(), protocols::protein_interface_design::ReportSequenceDifferences::res_name1(), protocols::protein_interface_design::ReportSequenceDifferences::res_name2(), core::pose::Pose::residue_type(), scorefxn_, core::pose::Pose::size(), task_factory(), task_factory_, protocols::protein_interface_design::filters::TR(), verbose_, and write_to_pdb().
Referenced by apply(), report(), and report_sm().
◆ fresh_instance()
|
overridevirtual |
Implements protocols::filters::Filter.
◆ mutation_threshold() [1/2]
| core::Size protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutation_threshold | ( | ) | const |
References mutation_threshold_.
Referenced by parse_my_tag().
◆ mutation_threshold() [2/2]
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutation_threshold | ( | core::Size const | mut | ) |
References mutation_threshold_.
◆ mutations() [1/2]
| bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutations | ( | ) | const |
References mutations_.
Referenced by parse_my_tag().
◆ mutations() [2/2]
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutations | ( | bool const | muts | ) |
References mutations_.
◆ 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 class_name(), protocols::rosetta_scripts::legacy_saved_pose_or_input(), mutation_threshold(), mutations(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), rate_threshold(), reference_pose(), scorefxn(), task_factory(), protocols::protein_interface_design::filters::TR(), verbose(), and write2pdb().
◆ provide_xml_schema()
|
static |
References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), core::pose::attributes_for_saved_reference_pose(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().
Referenced by protocols::protein_interface_design::filters::SequenceRecoveryFilterCreator::provide_xml_schema().
◆ rate_threshold() [1/2]
| core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::rate_threshold | ( | ) | const |
References rate_threshold_.
Referenced by parse_my_tag().
◆ rate_threshold() [2/2]
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::rate_threshold | ( | core::Real const | rate | ) |
References rate_threshold_.
◆ reference_pose() [1/3]
| core::pose::PoseCOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose | ( | ) | const |
References reference_pose_.
Referenced by compute(), and parse_my_tag().
◆ reference_pose() [2/3]
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose | ( | core::pose::Pose const & | pose | ) |
References reference_pose_.
◆ reference_pose() [3/3]
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose | ( | core::pose::PoseCOP | reference_pose | ) |
References reference_pose_.
◆ report()
|
overridevirtual |
Reimplemented from protocols::filters::Filter.
References compute(), and core::conformation::membrane::out.
◆ report_sm()
|
overridevirtual |
used to report filter internals through a score or silent file
Reimplemented from protocols::filters::Filter.
References compute(), and write2pdb().
◆ scorefxn()
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::scorefxn | ( | core::scoring::ScoreFunctionCOP | sfx | ) |
References scorefxn_.
Referenced by parse_my_tag().
◆ task_factory() [1/2]
| core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::task_factory | ( | ) | const |
References task_factory_.
Referenced by compute(), parse_my_tag(), and task_factory().
◆ task_factory() [2/2]
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::task_factory | ( | core::pack::task::TaskFactoryOP | task_factory | ) |
References task_factory(), and task_factory_.
◆ verbose() [1/2]
| bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::verbose | ( | ) | const |
References verbose_.
Referenced by parse_my_tag().
◆ verbose() [2/2]
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::verbose | ( | bool const | verb | ) |
References verbose_.
◆ write2pdb() [1/2]
| bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::write2pdb | ( | ) | const |
References write2pdb_.
Referenced by parse_my_tag(), and report_sm().
◆ write2pdb() [2/2]
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::write2pdb | ( | bool const | write | ) |
References write2pdb_.
◆ write_to_pdb()
| void protocols::protein_interface_design::filters::SequenceRecoveryFilter::write_to_pdb | ( | std::map< core::Size, std::string > const & | res_names1, |
| std::map< core::Size, std::string > const & | res_names2 | ||
| ) | const |
Add each mutation to the output pdb if desired.
References protocols::jd2::add_string_to_current_job(), and protocols::filters::Filter::get_user_defined_name().
Referenced by compute().
Member Data Documentation
◆ mutation_threshold_
|
private |
Referenced by apply(), and mutation_threshold().
◆ mutations_
|
private |
Referenced by apply(), compute(), and mutations().
◆ rate_threshold_
|
private |
Referenced by apply(), and rate_threshold().
◆ reference_pose_
|
private |
Referenced by reference_pose().
◆ scorefxn_
|
private |
Referenced by compute(), and scorefxn().
◆ task_factory_
|
private |
Referenced by compute(), and task_factory().
◆ verbose_
|
private |
◆ write2pdb_
|
private |
Referenced by write2pdb().
The documentation for this class was generated from the following files:
- src/protocols/protein_interface_design/filters/SequenceRecoveryFilter.hh
- src/protocols/protein_interface_design/filters/SequenceRecoveryFilter.cc
