protocols::protein_interface_design::filters::FilterScanFilter Class Reference

#include <FilterScan.hh>

Public Member Functions
	FilterScanFilter ()
	default ctor More...
virtual	~FilterScanFilter ()
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::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 &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
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)
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 void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
virtual std::string	name () const

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_

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

Member Typedef Documentation

typedef protocols::filters::Filter protocols::protein_interface_design::filters::FilterScanFilter::parent

private

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::FilterScanFilter::FilterScanFilter

(

)

default ctor

References protocols::jd2::current_output_name(), delta_filters_, and resfile_name().

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

protocols::protein_interface_design::filters::FilterScanFilter::~FilterScanFilter ( )

virtual

Member Function Documentation

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

virtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

References core::conformation::Residue::aa(), protocols::filters::Filter::apply(), core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), protocols::nonlocal::current_job(), delta(), delta_filters_, dump_pdb(), core::pose::Pose::dump_scored_pdb(), F, filter(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::Job::input_tag(), core::conformation::Residue::is_protein(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), oneletter_code_from_aa(), pair, core::pose::Pose::pdb_info(), report_all_, protocols::filters::Filter::report_sm(), resfile, resfile_general_property(), resfile_name(), resi, core::pose::Pose::residue(), core::conformation::Conformation::residue(), score_log_file(), scorefile, scorefxn(), single_substitution(), t, target_aa, task_factory(), core::pose::Pose::total_residue(), protocols::protein_interface_design::filters::TR, protocols::protein_interface_design::filters::TR_residue_scan, triage_filter(), and unbind().

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

virtual

Implements protocols::filters::Filter.

References FilterScanFilter().

bool protocols::protein_interface_design::filters::FilterScanFilter::delta

(

)

const

References delta_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::filters::FilterScanFilter::delta

(

bool const

d

)

References delta_.

utility::vector1< protocols::simple_filters::DeltaFilterOP > protocols::protein_interface_design::filters::FilterScanFilter::delta_filters

(

)

const

References delta_filters_.

void protocols::protein_interface_design::filters::FilterScanFilter::delta_filters

(

utility::vector1< protocols::simple_filters::DeltaFilterOP > const

d

)

References delta_filters_.

void protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb

(

bool const

d

)

References dump_pdb_.

bool protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb

(

)

const

References dump_pdb_.

Referenced by apply(), and parse_my_tag().

protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::filter

(

)

const

References filter_.

Referenced by apply(), filter(), parse_my_tag(), and triage_filter().

void protocols::protein_interface_design::filters::FilterScanFilter::filter

(

protocols::filters::FilterOP

filter

)

References filter(), and filter_.

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

virtual

Implements protocols::filters::Filter.

References FilterScanFilter().

core::Size protocols::protein_interface_design::filters::FilterScanFilter::jump

(

)

const

References jump_.

Referenced by parse_my_tag(), and unbind().

void protocols::protein_interface_design::filters::FilterScanFilter::jump

(

core::Size const

j

)

References jump_.

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

virtual

Reimplemented from protocols::filters::Filter.

References delta(), delta_filters_, dump_pdb(), filter(), jump(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), relax_mover(), report_all(), resfile_general_property(), resfile_name(), rtmin(), runtime_assert, score_log_file(), scorefxn(), utility::string_split(), task_factory(), protocols::protein_interface_design::filters::TR, triage_filter(), unbound(), and utility_exit_with_message.

void protocols::protein_interface_design::filters::FilterScanFilter::relax_mover

(

protocols::moves::MoverOP

mover

)

References relax_mover_.

protocols::moves::MoverOP protocols::protein_interface_design::filters::FilterScanFilter::relax_mover

(

)

const

References relax_mover_.

Referenced by parse_my_tag(), and single_substitution().

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

virtual

Reimplemented from protocols::filters::Filter.

bool protocols::protein_interface_design::filters::FilterScanFilter::report_all

(

)

const

References report_all_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::FilterScanFilter::report_all

(

bool const

ra

)

References report_all_.

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

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

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().

void protocols::protein_interface_design::filters::FilterScanFilter::resfile_general_property

(

std::string const

resfile_general_property

)

References resfile_general_property(), and resfile_general_property_.

void protocols::protein_interface_design::filters::FilterScanFilter::resfile_name

(

std::string const

resfile_name

)

References resfile_name(), and resfile_name_.

std::string protocols::protein_interface_design::filters::FilterScanFilter::resfile_name

(

)

const

References resfile_name_.

Referenced by apply(), FilterScanFilter(), parse_my_tag(), and resfile_name().

bool protocols::protein_interface_design::filters::FilterScanFilter::rtmin ( ) const

inline

References rtmin_.

Referenced by parse_my_tag(), and single_substitution().

void protocols::protein_interface_design::filters::FilterScanFilter::rtmin ( bool const  r )

inline

References rtmin_.

void protocols::protein_interface_design::filters::FilterScanFilter::score_log_file

(

std::string const

score_log_file

)

References score_log_file(), and score_log_file_.

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().

core::scoring::ScoreFunctionOP protocols::protein_interface_design::filters::FilterScanFilter::scorefxn

(

)

const

References scorefxn_.

Referenced by apply(), parse_my_tag(), scorefxn(), and single_substitution().

void protocols::protein_interface_design::filters::FilterScanFilter::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn

)

References scorefxn(), and scorefxn_.

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::simple_moves::symmetry::SymRotamerTrialsMover::apply(), protocols::moves::Mover::apply(), protocols::toolbox::task_operations::DesignAroundOperation::design_shell(), core::pack::task::PackerTask::initialize_from_command_line(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::name3(), num_canonical_aas, core::pack::task::PackerTask::or_include_current(), relax_mover(), core::pose::Pose::residue(), resj, rtmin(), scorefxn(), task_factory(), core::pose::Pose::total_residue(), and protocols::protein_interface_design::filters::TR.

Referenced by apply().

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().

void protocols::protein_interface_design::filters::FilterScanFilter::task_factory

(

core::pack::task::TaskFactoryOP

task_factory

)

References task_factory(), and task_factory_.

protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::triage_filter

(

)

const

References triage_filter_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::filters::FilterScanFilter::triage_filter

(

protocols::filters::FilterOP

filter

)

References filter(), and triage_filter_.

void protocols::protein_interface_design::filters::FilterScanFilter::unbind ( core::pose::Pose &  pose ) const

private

References protocols::rigid::RigidBodyTransMover::apply(), jump(), protocols::rigid::RigidBodyTransMover::step_size(), and unbound().

Referenced by apply().

bool protocols::protein_interface_design::filters::FilterScanFilter::unbound

(

)

const

References unbound_.

Referenced by parse_my_tag(), and unbind().

void protocols::protein_interface_design::filters::FilterScanFilter::unbound

(

bool const

u

)

References unbound_.

Member Data Documentation

bool protocols::protein_interface_design::filters::FilterScanFilter::delta_

private

Referenced by delta().

utility::vector1< protocols::simple_filters::DeltaFilterOP > protocols::protein_interface_design::filters::FilterScanFilter::delta_filters_

private

Referenced by apply(), delta_filters(), FilterScanFilter(), and parse_my_tag().

bool protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb_

private

Referenced by dump_pdb().

protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::filter_

private

Referenced by filter().

core::Size protocols::protein_interface_design::filters::FilterScanFilter::jump_

private

Referenced by jump().

protocols::moves::MoverOP protocols::protein_interface_design::filters::FilterScanFilter::relax_mover_

private

Referenced by relax_mover().

bool protocols::protein_interface_design::filters::FilterScanFilter::report_all_

private

Referenced by apply(), and report_all().

std::string protocols::protein_interface_design::filters::FilterScanFilter::resfile_general_property_

private

Referenced by resfile_general_property().

std::string protocols::protein_interface_design::filters::FilterScanFilter::resfile_name_

private

Referenced by resfile_name().

bool protocols::protein_interface_design::filters::FilterScanFilter::rtmin_

private

Referenced by rtmin().

std::string protocols::protein_interface_design::filters::FilterScanFilter::score_log_file_

private

Referenced by score_log_file().

core::scoring::ScoreFunctionOP protocols::protein_interface_design::filters::FilterScanFilter::scorefxn_

private

Referenced by scorefxn().

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

private

Referenced by task_factory().

protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::triage_filter_

private

Referenced by triage_filter().

bool protocols::protein_interface_design::filters::FilterScanFilter::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