protocols::simple_filters::TaskAwareScoreTypeFilter Class Reference

#include <TaskAwareScoreTypeFilter.hh>

Public Member Functions
	TaskAwareScoreTypeFilter ()
	default ctor More...
virtual bool	apply (core::pose::Pose const &pose) const
	Constructor with a single target residue. More...
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
virtual	~TaskAwareScoreTypeFilter ()
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::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)
core::pack::task::TaskFactoryOP	task_factory () const
core::scoring::ScoreFunctionOP	scorefxn () const
core::scoring::ScoreType	score_type () const
core::Real	threshold () const
bool	bb_bb () const
void	task_factory (core::pack::task::TaskFactoryOP task_factory)
void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)
void	score_type (core::scoring::ScoreType const st)
std::string	score_type_name () const
void	score_type_name (std::string const name)
void	threshold (core::Real const thresh)
void	bb_bb (bool const bb)
bool	unbound () const
void	unbound (bool const unbound)
std::string	sym_dof_names () const
void	sym_dof_names (std::string const sym_dofs)
core::Size	jump () const
void	jump (core::Size const jump)
std::string	mode () const
void	mode (std::string const mode)
void	write2pdb (bool const write)
bool	write2pdb () const
void	write_to_pdb (core::pose::Pose const &pose, core::Size const residue, std::string const residue_name, core::Real const score) const
bool	individual_hbonds () const
void	individual_hbonds (bool const individual_hbonds)
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	apply (core::io::serialization::PipeMap &pmap)
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::scoring::ScoreFunctionOP	scorefxn_
core::scoring::ScoreType	score_type_
std::string	score_type_name_
core::Real	threshold_
bool	bb_bb_
bool	unbound_
bool	write2pdb_
bool	individual_hbonds_
std::string	sym_dof_names_
core::Size	jump_
std::string	mode_

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

Member Typedef Documentation

typedef protocols::filters::Filter protocols::simple_filters::TaskAwareScoreTypeFilter::parent

private

Constructor & Destructor Documentation

protocols::simple_filters::TaskAwareScoreTypeFilter::TaskAwareScoreTypeFilter

(

)

default ctor

Referenced by clone(), and fresh_instance().

protocols::simple_filters::TaskAwareScoreTypeFilter::~TaskAwareScoreTypeFilter ( )

virtual

Member Function Documentation

bool protocols::simple_filters::TaskAwareScoreTypeFilter::apply ( core::pose::Pose const &  pose ) const

virtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

References compute(), mode(), protocols::filters::Filter::score(), threshold_, and protocols::simple_filters::TR.

bool protocols::simple_filters::TaskAwareScoreTypeFilter::bb_bb

(

)

const

References bb_bb_.

Referenced by parse_def(), and parse_my_tag().

void protocols::simple_filters::TaskAwareScoreTypeFilter::bb_bb

(

bool const

bb

)

References bb_bb_.

protocols::filters::FilterOP protocols::simple_filters::TaskAwareScoreTypeFilter::clone ( ) const

virtual

Implements protocols::filters::Filter.

References TaskAwareScoreTypeFilter().

Referenced by parse_def().

core::Real protocols::simple_filters::TaskAwareScoreTypeFilter::compute	(	core::pose::Pose const &	pose,
		bool const &	write
	)		const

References core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::pose::Pose::energies(), core::scoring::hbonds::fill_hbond_set(), core::pose::symmetry::get_sym_aware_jump_num(), protocols::filters::Filter::get_user_defined_name(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::methods::EnergyMethodOptions::hbond_options(), individual_hbonds_, interface_size, core::pose::symmetry::is_symmetric(), jump(), mode(), core::conformation::Residue::name3(), core::scoring::hbonds::HBondSet::nhbonds(), basic::options::option, core::pose::Pose::pdb_info(), basic::options::OptionKeys::out::file::renumber_pdb, resi, core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::scoring::Energies::residue_total_energy(), runtime_assert, score_type(), score_type_name(), scorefxn(), utility::string_split(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_names(), core::pose::symmetry::symmetry_info(), task_factory(), threshold(), core::pose::Pose::total_residue(), protocols::simple_filters::TR, protocols::stepwise::sampler::rigid_body::translate(), unbound(), utility_exit_with_message, and write_to_pdb().

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

protocols::filters::FilterOP protocols::simple_filters::TaskAwareScoreTypeFilter::fresh_instance ( ) const

virtual

Implements protocols::filters::Filter.

References TaskAwareScoreTypeFilter().

bool protocols::simple_filters::TaskAwareScoreTypeFilter::individual_hbonds

(

)

const

References individual_hbonds_.

Referenced by individual_hbonds(), and parse_my_tag().

void protocols::simple_filters::TaskAwareScoreTypeFilter::individual_hbonds

(

bool const

individual_hbonds

)

References individual_hbonds(), and individual_hbonds_.

core::Size protocols::simple_filters::TaskAwareScoreTypeFilter::jump

(

)

const

References jump_.

Referenced by compute(), jump(), and parse_my_tag().

void protocols::simple_filters::TaskAwareScoreTypeFilter::jump

(

core::Size const

jump

)

References jump(), and jump_.

std::string protocols::simple_filters::TaskAwareScoreTypeFilter::mode

(

)

const

References mode_.

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

void protocols::simple_filters::TaskAwareScoreTypeFilter::mode

(

std::string const

mode

)

References mode(), mode_, and utility_exit_with_message.

void protocols::simple_filters::TaskAwareScoreTypeFilter::parse_def ( utility::lua::LuaObject const &  def, utility::lua::LuaObject const &  score_fxns, utility::lua::LuaObject const &  tasks  )

virtual

Reimplemented from protocols::filters::Filter.

References bb_bb(), clone(), protocols::elscripts::parse_scoredef(), protocols::elscripts::parse_taskdef(), score_type(), core::scoring::score_type_from_name(), scorefxn(), task_factory(), threshold(), protocols::simple_filters::TR, and write2pdb().

void protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data, protocols::filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &    )

virtual

Reimplemented from protocols::filters::Filter.

References bb_bb(), individual_hbonds(), jump(), mode(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), score_type(), core::scoring::score_type_from_name(), score_type_name(), scorefxn(), sym_dof_names(), task_factory(), threshold(), protocols::simple_filters::TR, unbound(), utility_exit_with_message, and write2pdb().

void protocols::simple_filters::TaskAwareScoreTypeFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

virtual

Reimplemented from protocols::filters::Filter.

References compute(), and write2pdb_.

core::Real protocols::simple_filters::TaskAwareScoreTypeFilter::report_sm ( core::pose::Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), and protocols::filters::Filter::score().

core::scoring::ScoreType protocols::simple_filters::TaskAwareScoreTypeFilter::score_type

(

)

const

References score_type_.

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

void protocols::simple_filters::TaskAwareScoreTypeFilter::score_type

(

core::scoring::ScoreType const

st

)

References score_type_.

std::string protocols::simple_filters::TaskAwareScoreTypeFilter::score_type_name

(

)

const

References score_type_name_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::TaskAwareScoreTypeFilter::score_type_name

(

std::string const

name

)

References protocols::filters::Filter::name(), and score_type_name_.

core::scoring::ScoreFunctionOP protocols::simple_filters::TaskAwareScoreTypeFilter::scorefxn

(

)

const

References scorefxn_.

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

void protocols::simple_filters::TaskAwareScoreTypeFilter::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn

)

References scorefxn(), and scorefxn_.

std::string protocols::simple_filters::TaskAwareScoreTypeFilter::sym_dof_names

(

)

const

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::TaskAwareScoreTypeFilter::sym_dof_names

(

std::string const

sym_dofs

)

References sym_dof_names_.

core::pack::task::TaskFactoryOP protocols::simple_filters::TaskAwareScoreTypeFilter::task_factory

(

)

const

References task_factory_.

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

void protocols::simple_filters::TaskAwareScoreTypeFilter::task_factory

(

core::pack::task::TaskFactoryOP

task_factory

)

References task_factory(), and task_factory_.

core::Real protocols::simple_filters::TaskAwareScoreTypeFilter::threshold

(

)

const

References threshold_.

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

void protocols::simple_filters::TaskAwareScoreTypeFilter::threshold

(

core::Real const

thresh

)

References threshold_.

bool protocols::simple_filters::TaskAwareScoreTypeFilter::unbound

(

)

const

References unbound_.

Referenced by compute(), parse_my_tag(), and unbound().

void protocols::simple_filters::TaskAwareScoreTypeFilter::unbound

(

bool const

unbound

)

References unbound(), and unbound_.

void protocols::simple_filters::TaskAwareScoreTypeFilter::write2pdb

(

bool const

write

)

References write2pdb_.

bool protocols::simple_filters::TaskAwareScoreTypeFilter::write2pdb

(

)

const

References write2pdb_.

Referenced by parse_def(), and parse_my_tag().

void protocols::simple_filters::TaskAwareScoreTypeFilter::write_to_pdb	(	core::pose::Pose const &	pose,
		core::Size const	residue,
		std::string const	residue_name,
		core::Real const	score
	)		const

References protocols::jd2::Job::add_string(), protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), protocols::filters::Filter::get_user_defined_name(), protocols::filters::Filter::name(), basic::options::option, core::pose::Pose::pdb_info(), and basic::options::OptionKeys::out::file::renumber_pdb.

Referenced by compute().

Member Data Documentation

bool protocols::simple_filters::TaskAwareScoreTypeFilter::bb_bb_

private

Referenced by bb_bb().

bool protocols::simple_filters::TaskAwareScoreTypeFilter::individual_hbonds_

private

Referenced by compute(), and individual_hbonds().

core::Size protocols::simple_filters::TaskAwareScoreTypeFilter::jump_

private

Referenced by jump().

std::string protocols::simple_filters::TaskAwareScoreTypeFilter::mode_

private

Referenced by mode().

core::scoring::ScoreType protocols::simple_filters::TaskAwareScoreTypeFilter::score_type_

private

Referenced by score_type().

std::string protocols::simple_filters::TaskAwareScoreTypeFilter::score_type_name_

private

Referenced by score_type_name().

core::scoring::ScoreFunctionOP protocols::simple_filters::TaskAwareScoreTypeFilter::scorefxn_

private

Referenced by scorefxn().

std::string protocols::simple_filters::TaskAwareScoreTypeFilter::sym_dof_names_

private

Referenced by sym_dof_names().

core::pack::task::TaskFactoryOP protocols::simple_filters::TaskAwareScoreTypeFilter::task_factory_

private

Referenced by task_factory().

core::Real protocols::simple_filters::TaskAwareScoreTypeFilter::threshold_

private

Referenced by apply(), and threshold().

bool protocols::simple_filters::TaskAwareScoreTypeFilter::unbound_

private

Referenced by unbound().

bool protocols::simple_filters::TaskAwareScoreTypeFilter::write2pdb_

private

Referenced by report(), and write2pdb().

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The documentation for this class was generated from the following files:

• src/protocols/simple_filters/TaskAwareScoreTypeFilter.hh
• src/protocols/simple_filters/TaskAwareScoreTypeFilter.cc