#include <DdGScan.hh>

Inheritance diagram for protocols::simple_ddg::DdGScan:

Public Member Functions
	DdGScan ()
	default constructor More...

	DdGScan (core::pack::task::TaskFactoryOP task_factory, core::Size const repeats, core::scoring::ScoreFunctionCOP scorefxn, bool report_diffs, bool write2pdb)
	constructor with arguments More...

	DdGScan (DdGScan const &rval)
	copy constructor More...

protocols::filters::FilterOP	clone () const override

protocols::filters::FilterOP	fresh_instance () const override

	~DdGScan () override
	destructor More...

void	initialize ()

void	task_factory (core::pack::task::TaskFactoryOP task_factory)

void	repeats (core::Size const r)

void	scorefxn (core::scoring::ScoreFunctionOP const scorefxn)

void	report_diffs (bool const report_diffs)

void	write2pdb (bool const write)

void	ddG_mover (protocols::simple_ddg::ddGOP const ddG_mover_op)

core::pack::task::TaskFactoryOP	task_factory () const

core::Size	repeats () const

bool	report_diffs () const

bool	write2pdb () const

protocols::simple_ddg::ddGOP	ddG_mover () const

bool	apply (core::pose::Pose const &) const override
	Dummy Filter apply function. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	parse xml More...

core::Real	ddG_for_single_residue (core::pose::Pose const &const_pose, core::Size const resi, core::pack::task::PackerTaskOP const general_task, core::pose::Pose &pose_to_mutate) const
	Calculate the binding ddG for a mutation at the specified position (or wildtype no-mutant if resi is 0) More...

void	write_to_pdb (core::pose::Pose const &pose, core::Size const &residue, core::Size const &output_resi, std::string const &residue_name, core::Real const &ddG) const

void	report (std::ostream &out, core::pose::Pose const &pose) const override
	Implementation of virtual report function. More...

utility::vector1< ddG_data_tuple >	calculate (std::ostream &out, core::pose::Pose const &pose) const
	calculate and report the per-residue ddGs More...

std::string	name () const override

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	~Filter () override

virtual core::Real	report_sm (core::pose::Pose const &) const
	used to report filter internals through a score or silent file More...

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 Attributes
core::pack::task::TaskFactoryOP	task_factory_

core::Size	repeats_

core::scoring::ScoreFunctionOP	scorefxn_

bool	report_diffs_

bool	write2pdb_

protocols::simple_ddg::ddGOP	ddG_mover_

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

Constructor & Destructor Documentation

◆ DdGScan() [1/3]

protocols::simple_ddg::DdGScan::DdGScan ( )

default constructor

References initialize().

◆ DdGScan() [2/3]

protocols::simple_ddg::DdGScan::DdGScan	(	core::pack::task::TaskFactoryOP	task_factory,
		core::Size const	repeats,
		core::scoring::ScoreFunctionCOP	scorefxn,
		bool	report_diffs,
		bool	write2pdb
	)

constructor with arguments

References initialize().

◆ DdGScan() [3/3]

protocols::simple_ddg::DdGScan::DdGScan ( DdGScan const & rval )

default

copy constructor

◆ ~DdGScan()

protocols::simple_ddg::DdGScan::~DdGScan ( )

overridedefault

destructor

Member Function Documentation

◆ apply()

bool protocols::simple_ddg::DdGScan::apply ( core::pose::Pose const & ) const

overridevirtual

Dummy Filter apply function.

Implements protocols::filters::Filter.

◆ calculate()

utility::vector1< ddG_data_tuple > protocols::simple_ddg::DdGScan::calculate	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

calculate and report the per-residue ddGs

References core::pack::task::TaskFactory::create_packer_task(), ddG_for_single_residue(), core::chemical::element::F, core::conformation::Residue::is_protein(), core::conformation::Residue::name3(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), report_diffs(), core::pose::Pose::residue(), core::pose::Pose::size(), task_factory_, protocols::simple_ddg::TR(), write2pdb(), and write_to_pdb().

Referenced by report().

◆ class_name()

std::string protocols::simple_ddg::DdGScan::class_name ( )

static

Referenced by protocols::simple_ddg::DdGScanCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::simple_ddg::DdGScan::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ ddG_for_single_residue()

core::Real protocols::simple_ddg::DdGScan::ddG_for_single_residue	(	core::pose::Pose const &	const_pose,
		core::Size const	resi,
		core::pack::task::PackerTaskOP const	general_task,
		core::pose::Pose &	pose_to_mutate
	)		const

Calculate the binding ddG for a mutation at the specified position (or wildtype no-mutant if resi is 0)

References protocols::jd2::current_output_name(), ddG_mover_, core::conformation::Residue::name3(), core::pack::pack_rotamers(), repeats(), core::pose::Pose::residue(), scorefxn_, core::pose::Pose::size(), and protocols::simple_ddg::TR().

Referenced by calculate().

◆ ddG_mover() [1/2]

protocols::simple_ddg::ddGOP protocols::simple_ddg::DdGScan::ddG_mover ( ) const

References ddG_mover_.

Referenced by initialize(), and parse_my_tag().

◆ ddG_mover() [2/2]

void protocols::simple_ddg::DdGScan::ddG_mover ( protocols::simple_ddg::ddGOP const ddG_mover_op )

References ddG_mover_.

◆ fresh_instance()

protocols::filters::FilterOP protocols::simple_ddg::DdGScan::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ initialize()

void protocols::simple_ddg::DdGScan::initialize ( )

References ddG_mover().

Referenced by DdGScan().

◆ name()

std::string protocols::simple_ddg::DdGScan::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_to_pdb().

◆ parse_my_tag()

void protocols::simple_ddg::DdGScan::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References ddG_mover(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), repeats(), report_diffs(), scorefxn_, task_factory(), and write2pdb().

◆ provide_xml_schema()

void protocols::simple_ddg::DdGScan::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

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::simple_ddg::DdGScanCreator::provide_xml_schema().

◆ repeats() [1/2]

core::Size protocols::simple_ddg::DdGScan::repeats ( ) const

References repeats_.

Referenced by ddG_for_single_residue(), and parse_my_tag().

◆ repeats() [2/2]

void protocols::simple_ddg::DdGScan::repeats ( core::Size const r )

References repeats_.

◆ report()

void protocols::simple_ddg::DdGScan::report	(	std::ostream &	out,
		core::pose::Pose const &	const_pose
	)		const

overridevirtual

Implementation of virtual report function.

Calls report function with return value

Reimplemented from protocols::filters::Filter.

References calculate(), and core::conformation::membrane::out.

◆ report_diffs() [1/2]

bool protocols::simple_ddg::DdGScan::report_diffs ( ) const

References report_diffs_.

Referenced by calculate(), parse_my_tag(), and report_diffs().

◆ report_diffs() [2/2]

void protocols::simple_ddg::DdGScan::report_diffs ( bool const report_diffs )

References report_diffs(), and report_diffs_.

◆ scorefxn()

void protocols::simple_ddg::DdGScan::scorefxn ( core::scoring::ScoreFunctionOP const scorefxn )

References scorefxn_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::simple_ddg::DdGScan::task_factory ( ) const

References task_factory_.

Referenced by parse_my_tag(), and task_factory().

◆ task_factory() [2/2]

void protocols::simple_ddg::DdGScan::task_factory ( core::pack::task::TaskFactoryOP task_factory )

References task_factory(), and task_factory_.

◆ write2pdb() [1/2]

bool protocols::simple_ddg::DdGScan::write2pdb ( ) const

References write2pdb_.

Referenced by calculate(), and parse_my_tag().

◆ write2pdb() [2/2]

void protocols::simple_ddg::DdGScan::write2pdb ( bool const write )

References write2pdb_.

◆ write_to_pdb()

void protocols::simple_ddg::DdGScan::write_to_pdb	(	core::pose::Pose const &	pose,
		core::Size const &	residue,
		core::Size const &	output_resi,
		std::string const &	residue_name,
		core::Real const &	ddG
	)		const

References protocols::jd2::add_string_to_current_job(), core::chemical::element::F, protocols::filters::Filter::get_user_defined_name(), name(), core::conformation::Residue::name3(), and core::pose::Pose::residue().

Referenced by calculate().

Member Data Documentation

◆ ddG_mover_

protocols::simple_ddg::ddGOP protocols::simple_ddg::DdGScan::ddG_mover_

private

Referenced by ddG_for_single_residue(), and ddG_mover().

◆ repeats_

core::Size protocols::simple_ddg::DdGScan::repeats_

private

Referenced by repeats().

◆ report_diffs_

bool protocols::simple_ddg::DdGScan::report_diffs_

private

Referenced by report_diffs().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::simple_ddg::DdGScan::scorefxn_

private

Referenced by ddG_for_single_residue(), parse_my_tag(), and scorefxn().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::simple_ddg::DdGScan::task_factory_

private

Referenced by calculate(), and task_factory().

◆ write2pdb_

bool protocols::simple_ddg::DdGScan::write2pdb_

private

Referenced by write2pdb().

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

src/protocols/simple_ddg/DdGScan.hh
src/protocols/simple_ddg/DdGScan.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ DdGScan() [1/3]

◆ DdGScan() [2/3]

◆ DdGScan() [3/3]

◆ ~DdGScan()

Member Function Documentation

◆ apply()

◆ calculate()

◆ class_name()

◆ clone()

◆ ddG_for_single_residue()

◆ ddG_mover() [1/2]

◆ ddG_mover() [2/2]

◆ fresh_instance()

◆ initialize()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ repeats() [1/2]

◆ repeats() [2/2]

◆ report()

◆ report_diffs() [1/2]

◆ report_diffs() [2/2]

◆ scorefxn()

◆ task_factory() [1/2]

◆ task_factory() [2/2]

◆ write2pdb() [1/2]

◆ write2pdb() [2/2]

◆ write_to_pdb()

Member Data Documentation

◆ ddG_mover_

◆ repeats_

◆ report_diffs_

◆ scorefxn_

◆ task_factory_

◆ write2pdb_