protocols::protein_interface_design::filters::SequenceRecoveryFilter Class Reference

#include <SequenceRecoveryFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::SequenceRecoveryFilter:

Collaboration diagram for protocols::protein_interface_design::filters::SequenceRecoveryFilter:

Public Member Functions
	SequenceRecoveryFilter ()
	default ctor More...
virtual bool	apply (core::pose::Pose const &pose) const
	Constructor with a single target residue. More...
virtual void	apply (core::io::serialization::PipeMap &pmap)
virtual void	report (std::ostream &out, core::pose::Pose const &pose) const
virtual core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
virtual protocols::filters::FilterOP	clone () const
virtual protocols::filters::FilterOP	fresh_instance () const
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...
virtual	~SequenceRecoveryFilter ()
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)
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::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
virtual	~Filter ()
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 void	score (core::io::serialization::PipeMap &pmap)
virtual core::Real	score (core::pose::Pose &pose)
virtual std::string	name () const

Private Types
typedef protocols::filters::Filter	parent

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_
core::pose::PoseCOP	reference_pose_
core::Real	rate_threshold_
core::Size	mutation_threshold_
bool	mutations_
bool	verbose_
bool	write2pdb_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Detailed Description

Definition at line 35 of file SequenceRecoveryFilter.hh.

Member Typedef Documentation

typedef protocols::filters::Filter protocols::protein_interface_design::filters::SequenceRecoveryFilter::parent

private

Definition at line 38 of file SequenceRecoveryFilter.hh.

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::SequenceRecoveryFilter::SequenceRecoveryFilter

(

)

default ctor

Definition at line 46 of file SequenceRecoveryFilter.cc.

Referenced by clone(), protocols::protein_interface_design::filters::SequenceRecoveryFilterCreator::create_filter(), and fresh_instance().

protocols::protein_interface_design::filters::SequenceRecoveryFilter::~SequenceRecoveryFilter ( )

virtual

Definition at line 342 of file SequenceRecoveryFilter.cc.

Member Function Documentation

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::apply ( core::pose::Pose const &  pose) const

virtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

Definition at line 148 of file SequenceRecoveryFilter.cc.

References compute(), mutation_threshold_, mutations_, rate_threshold_, and protocols::protein_interface_design::filters::TR().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::apply ( core::io::serialization::PipeMap &  pmap)

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 172 of file SequenceRecoveryFilter.cc.

References protocols::filters::Filter::apply(), reference_pose(), and core::io::serialization::size().

protocols::filters::FilterOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::clone ( ) const

virtual

Implements protocols::filters::Filter.

Definition at line 346 of file SequenceRecoveryFilter.cc.

References SequenceRecoveryFilter().

core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute	(	core::pose::Pose const &	pose,
		bool const &	write
	)		const

Definition at line 179 of file SequenceRecoveryFilter.cc.

References protocols::protein_interface_design::ReportSequenceDifferences::calculate(), core::pose::Pose::conformation(), core::scoring::ScoreFunctionFactory::create_score_function(), core::conformation::Conformation::delete_residue_slow(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::is_symmetric(), mutations_, core::chemical::ResidueType::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(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, task_factory(), task_factory_, core::pose::Pose::total_residue(), protocols::protein_interface_design::filters::TR(), verbose_, and write_to_pdb().

Referenced by apply(), report(), and report_sm().

protocols::filters::FilterOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::fresh_instance ( ) const

virtual

Implements protocols::filters::Filter.

Definition at line 338 of file SequenceRecoveryFilter.cc.

References SequenceRecoveryFilter().

core::Size protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutation_threshold

(

)

const

Definition at line 100 of file SequenceRecoveryFilter.cc.

References mutation_threshold_.

Referenced by parse_def(), and parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutation_threshold

(

core::Size const

mut)

Definition at line 106 of file SequenceRecoveryFilter.cc.

References mutation_threshold_.

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutations

(

)

const

Definition at line 112 of file SequenceRecoveryFilter.cc.

References mutations_.

Referenced by parse_def(), and parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutations

(

bool const

muts)

Definition at line 118 of file SequenceRecoveryFilter.cc.

References mutations_.

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_def ( utility::lua::LuaObject const &  def, utility::lua::LuaObject const &  score_fxns, utility::lua::LuaObject const &  tasks  )

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 314 of file SequenceRecoveryFilter.cc.

References mutation_threshold(), mutations(), protocols::elscripts::parse_taskdef(), core::import_pose::pose_from_pdb(), rate_threshold(), reference_pose(), task_factory(), protocols::protein_interface_design::filters::TR(), verbose(), and write2pdb().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag ( utility::tag::TagPtr const  tag, protocols::moves::DataMap &  data, protocols::filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &  pose  )

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 283 of file SequenceRecoveryFilter.cc.

References mutation_threshold(), mutations(), protocols::rosetta_scripts::parse_task_operations(), core::import_pose::pose_from_pdb(), rate_threshold(), reference_pose(), task_factory(), protocols::protein_interface_design::filters::TR(), verbose(), and write2pdb().

core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::rate_threshold

(

)

const

Definition at line 69 of file SequenceRecoveryFilter.cc.

References rate_threshold_.

Referenced by parse_def(), and parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::rate_threshold

(

core::Real const

rate)

Definition at line 75 of file SequenceRecoveryFilter.cc.

References rate_threshold_.

core::pose::PoseCOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose

(

)

const

Definition at line 82 of file SequenceRecoveryFilter.cc.

References reference_pose_.

Referenced by apply(), compute(), parse_def(), and parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose

(

core::pose::PoseCOP

reference_pose)

Definition at line 88 of file SequenceRecoveryFilter.cc.

References reference_pose_.

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose

(

core::pose::Pose const &

pose)

Definition at line 94 of file SequenceRecoveryFilter.cc.

References reference_pose_.

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 277 of file SequenceRecoveryFilter.cc.

References compute().

core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::report_sm ( core::pose::Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

Definition at line 271 of file SequenceRecoveryFilter.cc.

References compute(), and write2pdb().

core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::task_factory

(

)

const

Definition at line 57 of file SequenceRecoveryFilter.cc.

References task_factory_.

Referenced by compute(), parse_def(), parse_my_tag(), and task_factory().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::task_factory

(

core::pack::task::TaskFactoryOP

task_factory)

Definition at line 63 of file SequenceRecoveryFilter.cc.

References task_factory(), and task_factory_.

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::verbose

(

)

const

Definition at line 124 of file SequenceRecoveryFilter.cc.

References verbose_.

Referenced by parse_def(), and parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::verbose

(

bool const

verb)

Definition at line 130 of file SequenceRecoveryFilter.cc.

References verbose_.

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::write2pdb

(

)

const

Definition at line 136 of file SequenceRecoveryFilter.cc.

References write2pdb_.

Referenced by parse_def(), parse_my_tag(), and report_sm().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::write2pdb

(

bool const

write)

Definition at line 142 of file SequenceRecoveryFilter.cc.

References write2pdb_.

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.

Definition at line 256 of file SequenceRecoveryFilter.cc.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), and protocols::filters::Filter::get_user_defined_name().

Referenced by compute().

Member Data Documentation

core::Size protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutation_threshold_

private

Definition at line 81 of file SequenceRecoveryFilter.hh.

Referenced by apply(), and mutation_threshold().

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutations_

private

Definition at line 82 of file SequenceRecoveryFilter.hh.

Referenced by apply(), compute(), and mutations().

core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::rate_threshold_

private

Definition at line 80 of file SequenceRecoveryFilter.hh.

Referenced by apply(), and rate_threshold().

core::pose::PoseCOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose_

private

Definition at line 79 of file SequenceRecoveryFilter.hh.

Referenced by reference_pose().

core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::task_factory_

private

Definition at line 78 of file SequenceRecoveryFilter.hh.

Referenced by compute(), and task_factory().

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::verbose_

private

Definition at line 83 of file SequenceRecoveryFilter.hh.

Referenced by compute(), and verbose().

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::write2pdb_

private

Definition at line 84 of file SequenceRecoveryFilter.hh.

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