protocols::simple_ddg::AlaScan Class Reference

#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 (Filter 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

protocols::simple_ddg::AlaScan::AlaScan

(

)

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_.

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

overridedefault

Member Function Documentation

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.

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

inline

References chain1_.

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

inline

References chain1_.

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

inline

References chain2_.

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

inline

References chain2_.

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

static

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

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

inlineoverridevirtual

Implements protocols::filters::Filter.

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(), protocols::simple_ddg::DdgFilter::repack(), repack(), repeats_, core::pose::Pose::residue(), scorefxn_, and core::pose::Pose::size().

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

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

inline

References distance_threshold_.

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

inline

References distance_threshold_.

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

inlineoverridevirtual

Implements protocols::filters::Filter.

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().

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

inline

References jump_.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

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_, and symmetry_.

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().

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().

bool protocols::simple_ddg::AlaScan::repack

(

)

const

References repack_.

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

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().

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

inline

References repeats_.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References chain1_, chain2_, protocols::simple_ddg::DdgFilter::compute(), core::pose::Pose::conformation(), ddG_for_single_residue(), distance_threshold_, core::kinematics::FoldTree::downstream_jump_residue(), core::chemical::element::F, core::conformation::Conformation::fold_tree(), core::conformation::Residue::is_protein(), protocols::scoring::Interface::jump(), jump_, core::conformation::Residue::name3(), 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().

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.

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

References core::chemical::aa_ala, protocols::scoring::Interface::calculate(), protocols::simple_ddg::DdgFilter::compute(), core::pose::Pose::conformation(), protocols::scoring::Interface::distance(), distance_threshold_, core::chemical::element::F, protocols::scoring::Interface::is_interface(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::name3(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), core::pose::Pose::pdb_info(), repeats_, core::pose::Pose::residue(), scorefxn_, core::pose::Pose::size(), and core::pose::Pose::update_residue_neighbors().

Referenced by report().

void protocols::simple_ddg::AlaScan::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn

)

References scorefxn_.

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

Member Data Documentation

bool protocols::simple_ddg::AlaScan::chain1_

private

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

bool protocols::simple_ddg::AlaScan::chain2_

private

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

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

private

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

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

private

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

bool protocols::simple_ddg::AlaScan::repack_

private

Referenced by parse_my_tag(), and repack().

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

private

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

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

private

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

bool protocols::simple_ddg::AlaScan::symmetry_

private

Referenced by parse_my_tag(), and report().

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

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