#include <AlaScan.hh>

Inheritance diagram for protocols::simple_ddg::AlaScan:

Public Member Functions
	AlaScan ()

	AlaScan (bool const chain1, bool const chain2, core::Size const repeats, core::Real const dist, core::scoring::ScoreFunctionCOP scorefxn, core::Size const jump, bool const symmetry)

bool	apply (core::pose::Pose const &) const override
	Returns true if the given pose passes the filter, false otherwise. More...

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

void	report (std::ostream &out, core::pose::Pose const &pose) const override

void	report_symmetry (std::ostream &out, core::pose::Pose const &pose) const

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

void	chain1 (bool const c1)

void	chain2 (bool const c2)

void	dist (core::Real const d)

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

core::Real	ddG_for_single_residue (core::pose::Pose const &pose, core::Size const resi) const

bool	chain1 () const

bool	chain2 () const

core::Size	repeats () const

void	repeats (core::Size const r)

core::Size	jump () const

void	jump (core::Size const j)

core::Real	dist () const

	~AlaScan () override

void	repack (bool const repack)

bool	repack () const

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 Attributes
bool	chain1_

bool	chain2_

core::Size	repeats_

core::Real	distance_threshold_

core::Size	jump_

bool	symmetry_

core::scoring::ScoreFunctionOP	scorefxn_

bool	repack_

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

Constructor & Destructor Documentation

◆ AlaScan() [1/2]

protocols::simple_ddg::AlaScan::AlaScan ( )

◆ AlaScan() [2/2]

protocols::simple_ddg::AlaScan::AlaScan	(	bool const	chain1,
		bool const	chain2,
		core::Size const	repeats,
		core::Real const	dist,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size const	jump = `1`,
		bool const	symmetry = `false`
	)

References scorefxn(), and scorefxn_.

◆ ~AlaScan()

protocols::simple_ddg::AlaScan::~AlaScan ( )

overridedefault

Member Function Documentation

◆ apply()

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

inlineoverridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

◆ chain1() [1/2]

bool protocols::simple_ddg::AlaScan::chain1 ( ) const

inline

References chain1_.

◆ chain1() [2/2]

void protocols::simple_ddg::AlaScan::chain1 ( bool const c1 )

inline

References chain1_.

◆ chain2() [1/2]

bool protocols::simple_ddg::AlaScan::chain2 ( ) const

inline

References chain2_.

◆ chain2() [2/2]

void protocols::simple_ddg::AlaScan::chain2 ( bool const c2 )

inline

References chain2_.

◆ class_name()

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

static

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

◆ clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ ddG_for_single_residue()

core::Real protocols::simple_ddg::AlaScan::ddG_for_single_residue	(	core::pose::Pose const &	pose,
		core::Size const	resi
	)		const

References core::chemical::aa_ala, protocols::simple_ddg::DdgFilter::compute(), core::conformation::Residue::is_protein(), jump_, core::chemical::num_canonical_aas, core::pack::pack_rotamers(), repack(), protocols::simple_ddg::DdgFilter::repack(), repeats_, core::pose::Pose::residue(), scorefxn_, core::pose::Pose::size(), and protocols::simple_ddg::TR().

Referenced by protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), and report().

◆ dist() [1/2]

core::Real protocols::simple_ddg::AlaScan::dist ( ) const

inline

References distance_threshold_.

◆ dist() [2/2]

void protocols::simple_ddg::AlaScan::dist ( core::Real const d )

inline

References distance_threshold_.

◆ fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ jump() [1/2]

core::Size protocols::simple_ddg::AlaScan::jump ( ) const

inline

References jump_.

Referenced by protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), and protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan().

◆ jump() [2/2]

void protocols::simple_ddg::AlaScan::jump ( core::Size const j )

inline

References jump_.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

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

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References chain1_, chain2_, distance_threshold_, jump_, core::scoring::parse_score_function(), repack(), repack_, repeats_, scorefxn_, symmetry_, and protocols::simple_ddg::TR().

◆ provide_xml_schema()

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

static

References core::scoring::attributes_for_parse_score_function(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_ddg::AlaScanFilterCreator::provide_xml_schema().

◆ repack() [1/2]

bool protocols::simple_ddg::AlaScan::repack ( ) const

References repack_.

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

◆ repack() [2/2]

void protocols::simple_ddg::AlaScan::repack ( bool const repack )

References repack(), and repack_.

Referenced by protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), and protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan().

◆ repeats() [1/2]

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

inline

References repeats_.

Referenced by protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), and protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan().

◆ repeats() [2/2]

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

inline

References repeats_.

◆ report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References protocols::scoring::Interface::calculate(), chain1_, chain2_, protocols::simple_ddg::DdgFilter::compute(), core::pose::Pose::conformation(), ddG_for_single_residue(), protocols::scoring::Interface::distance(), distance_threshold_, core::kinematics::FoldTree::downstream_jump_residue(), core::chemical::element::F, core::conformation::Conformation::fold_tree(), protocols::scoring::Interface::is_interface(), core::conformation::Residue::is_protein(), protocols::scoring::Interface::jump(), jump_, core::conformation::Residue::name3(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), repeats_, report_symmetry(), core::pose::Pose::residue(), scorefxn_, core::pose::Pose::size(), symmetry_, core::pose::Pose::update_residue_neighbors(), and core::kinematics::FoldTree::upstream_jump_residue().

◆ report_sm()

core::Real protocols::simple_ddg::AlaScan::report_sm ( core::pose::Pose const & ) const

inlineoverridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

◆ report_symmetry()

void protocols::simple_ddg::AlaScan::report_symmetry	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

◆ scorefxn()

void protocols::simple_ddg::AlaScan::scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

References scorefxn_.

Referenced by AlaScan(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), and protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan().

Member Data Documentation

◆ chain1_

bool protocols::simple_ddg::AlaScan::chain1_

private

Referenced by chain1(), parse_my_tag(), and report().

◆ chain2_

bool protocols::simple_ddg::AlaScan::chain2_

private

Referenced by chain2(), parse_my_tag(), and report().

◆ distance_threshold_

core::Real protocols::simple_ddg::AlaScan::distance_threshold_

private

Referenced by dist(), parse_my_tag(), report(), and report_symmetry().

◆ jump_

core::Size protocols::simple_ddg::AlaScan::jump_

private

Referenced by ddG_for_single_residue(), jump(), parse_my_tag(), and report().

◆ repack_

bool protocols::simple_ddg::AlaScan::repack_

private

Referenced by parse_my_tag(), and repack().

◆ repeats_

core::Size protocols::simple_ddg::AlaScan::repeats_

private

Referenced by ddG_for_single_residue(), parse_my_tag(), repeats(), report(), and report_symmetry().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::simple_ddg::AlaScan::scorefxn_

private

Referenced by AlaScan(), ddG_for_single_residue(), parse_my_tag(), report(), report_symmetry(), and scorefxn().

◆ symmetry_

bool protocols::simple_ddg::AlaScan::symmetry_

private

Referenced by parse_my_tag(), and report().

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

src/protocols/simple_ddg/AlaScan.hh
src/protocols/simple_ddg/AlaScan.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ AlaScan() [1/2]

◆ AlaScan() [2/2]

◆ ~AlaScan()

Member Function Documentation

◆ apply()

◆ chain1() [1/2]

◆ chain1() [2/2]

◆ chain2() [1/2]

◆ chain2() [2/2]

◆ class_name()

◆ clone()

◆ ddG_for_single_residue()

◆ dist() [1/2]

◆ dist() [2/2]

◆ fresh_instance()

◆ jump() [1/2]

◆ jump() [2/2]

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ repack() [1/2]

◆ repack() [2/2]

◆ repeats() [1/2]

◆ repeats() [2/2]

◆ report()

◆ report_sm()

◆ report_symmetry()

◆ scorefxn()

Member Data Documentation

◆ chain1_

◆ chain2_

◆ distance_threshold_

◆ jump_

◆ repack_

◆ repeats_

◆ scorefxn_

◆ symmetry_