#include <InterfaceHbondsFilter.hh>

Inheritance diagram for protocols::simple_filters::InterfaceHbondsFilter:

Public Member Functions
	InterfaceHbondsFilter ()

	InterfaceHbondsFilter (core::Size hbonds_num_threshold_in, core::Real hbonds_energy_cutoff_in=0.0, core::Size jump_in=1, core::scoring::ScoreFunctionOP scorefxn_in=nullptr, bool salt_bridge_mode_in=false, bool include_His_chain_terminus_in=false, core::Real salt_bridge_distance_cutoff_in=4.0)

bool	apply (core::pose::Pose const &pose) 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

InterfaceHbondsFilter &	operator= (InterfaceHbondsFilter const &ot)

	InterfaceHbondsFilter (InterfaceHbondsFilter const &init)

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

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

core::Size	compute (core::pose::Pose const &pose) const

	~InterfaceHbondsFilter () override

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

void	set_jump (core::Size const jump_in)

void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn_in)

void	set_hbonds_num_threshold (core::Size hbonds_num_threshold_in)

void	set_hbonds_energy_cutoff (core::Real hbonds_energy_cutoff_in)

void	set_salt_bridge_mode (bool salt_bridge_mode_in)

void	set_include_His_chain_terminus (bool include_His_chain_terminus_in)

void	set_salt_bridge_distance_cutoff (bool salt_bridge_distance_cutoff_in)

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 Types
enum	CHARGE { POSITIVE, NEGATIVE }

typedef std::pair< std::string, CHARGE >	Charged_Group

Private Member Functions
core::Size	compute_hbonds (core::pose::Pose const &pose) const

core::Size	compute_salt_bridges (core::pose::Pose const &pose) const

void	initialize_charged_residue_map ()

Private Attributes
core::Size	hbonds_num_threshold_

core::Real	hbonds_energy_cutoff_

core::Size	jump_

core::scoring::ScoreFunctionOP	scorefxn_

bool	salt_bridge_mode_

bool	include_His_chain_terminus_

core::Real	salt_bridge_distance_cutoff_

std::unordered_map < std::string, std::vector < Charged_Group > >	charged_res_

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

Member Typedef Documentation

typedef std::pair<std::string, CHARGE> protocols::simple_filters::InterfaceHbondsFilter::Charged_Group

private

Member Enumeration Documentation

enum protocols::simple_filters::InterfaceHbondsFilter::CHARGE

private

Enumerator
POSITIVE
NEGATIVE

Constructor & Destructor Documentation

protocols::simple_filters::InterfaceHbondsFilter::InterfaceHbondsFilter ( )

References core::scoring::get_score_function(), and scorefxn_.

protocols::simple_filters::InterfaceHbondsFilter::InterfaceHbondsFilter	(	core::Size	hbonds_num_threshold_in,
		core::Real	hbonds_energy_cutoff_in = `0.0`,
		core::Size	jump_in = `1`,
		core::scoring::ScoreFunctionOP	scorefxn_in = `nullptr`,
		bool	salt_bridge_mode_in = `false`,
		bool	include_His_chain_terminus_in = `false`,
		core::Real	salt_bridge_distance_cutoff_in = `4.0`
	)

References charged_res_, core::scoring::get_score_function(), initialize_charged_residue_map(), salt_bridge_mode_, and scorefxn_.

protocols::simple_filters::InterfaceHbondsFilter::InterfaceHbondsFilter ( InterfaceHbondsFilter const & init )

inline

References core::init::init().

protocols::simple_filters::InterfaceHbondsFilter::~InterfaceHbondsFilter ( )

overridedefault

Member Function Documentation

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

overridevirtual

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

Implements protocols::filters::Filter.

References compute(), and hbonds_num_threshold_.

std::string protocols::simple_filters::InterfaceHbondsFilter::class_name ( )

static

Referenced by protocols::simple_filters::InterfaceHbondsFilterCreator::keyname(), name(), and provide_xml_schema().

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

inlineoverridevirtual

Implements protocols::filters::Filter.

core::Size protocols::simple_filters::InterfaceHbondsFilter::compute ( core::pose::Pose const & pose ) const

References compute_hbonds(), compute_salt_bridges(), core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), salt_bridge_mode_, and scorefxn_.

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

core::Size protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds ( core::pose::Pose const & pose ) const

private

References core::conformation::Residue::atom_name(), core::pose::Pose::chain(), core::conformation::Residue::chain(), core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::kinematics::FoldTree::downstream_jump_residue(), core::scoring::hbonds::fill_hbond_set(), core::pose::Pose::fold_tree(), core::scoring::hbonds::HBondSet::hbond_options(), hbonds_energy_cutoff_, jump_, core::pose::Pose::residue(), core::conformation::Residue::seqpos(), protocols::simple_filters::TR(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by compute().

core::Size protocols::simple_filters::InterfaceHbondsFilter::compute_salt_bridges ( core::pose::Pose const & pose ) const

private

References protocols::scoring::Interface::calculate(), charged_res_, protocols::scoring::Interface::distance(), protocols::scoring::Interface::is_pair(), jump_, core::pose::Pose::residue(), salt_bridge_distance_cutoff_, core::pose::Pose::size(), and protocols::simple_filters::TR().

Referenced by compute().

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

inlineoverridevirtual

Implements protocols::filters::Filter.

void protocols::simple_filters::InterfaceHbondsFilter::initialize_charged_residue_map ( )

private

References protocols::cluster::calibur::aa, charged_res_, include_His_chain_terminus_, NEGATIVE, and POSITIVE.

Referenced by InterfaceHbondsFilter(), parse_my_tag(), set_include_His_chain_terminus(), and set_salt_bridge_mode().

std::string protocols::simple_filters::InterfaceHbondsFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

InterfaceHbondsFilter& protocols::simple_filters::InterfaceHbondsFilter::operator= ( InterfaceHbondsFilter const & ot )

inline

References charged_res_, hbonds_energy_cutoff_, hbonds_num_threshold_, include_His_chain_terminus_, jump_, salt_bridge_distance_cutoff_, salt_bridge_mode_, and scorefxn_.

void protocols::simple_filters::InterfaceHbondsFilter::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 hbonds_energy_cutoff_, hbonds_num_threshold_, include_His_chain_terminus_, initialize_charged_residue_map(), jump_, core::scoring::parse_score_function(), salt_bridge_distance_cutoff_, salt_bridge_mode_, and set_scorefxn().

void protocols::simple_filters::InterfaceHbondsFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::simple_filters::InterfaceHbondsFilterCreator::provide_xml_schema().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and jump_.

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

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::simple_filters::InterfaceHbondsFilter::set_hbonds_energy_cutoff ( core::Real hbonds_energy_cutoff_in )

inline

References hbonds_energy_cutoff_.

void protocols::simple_filters::InterfaceHbondsFilter::set_hbonds_num_threshold ( core::Size hbonds_num_threshold_in )

inline

References hbonds_num_threshold_.

void protocols::simple_filters::InterfaceHbondsFilter::set_include_His_chain_terminus ( bool include_His_chain_terminus_in )

inline

References include_His_chain_terminus_, initialize_charged_residue_map(), and salt_bridge_mode_.

void protocols::simple_filters::InterfaceHbondsFilter::set_jump ( core::Size const jump_in )

inline

References jump_.

void protocols::simple_filters::InterfaceHbondsFilter::set_salt_bridge_distance_cutoff ( bool salt_bridge_distance_cutoff_in )

inline

References salt_bridge_distance_cutoff_.

void protocols::simple_filters::InterfaceHbondsFilter::set_salt_bridge_mode ( bool salt_bridge_mode_in )

inline

References initialize_charged_residue_map(), and salt_bridge_mode_.

void protocols::simple_filters::InterfaceHbondsFilter::set_scorefxn ( core::scoring::ScoreFunctionOP scorefxn_in )

inline

References scorefxn_.

Referenced by parse_my_tag().

Member Data Documentation

std::unordered_map<std::string, std::vector<Charged_Group > > protocols::simple_filters::InterfaceHbondsFilter::charged_res_

private

Referenced by compute_salt_bridges(), initialize_charged_residue_map(), InterfaceHbondsFilter(), and operator=().

core::Real protocols::simple_filters::InterfaceHbondsFilter::hbonds_energy_cutoff_

private

Referenced by compute_hbonds(), operator=(), parse_my_tag(), and set_hbonds_energy_cutoff().

core::Size protocols::simple_filters::InterfaceHbondsFilter::hbonds_num_threshold_

private

Referenced by apply(), operator=(), parse_my_tag(), and set_hbonds_num_threshold().

bool protocols::simple_filters::InterfaceHbondsFilter::include_His_chain_terminus_

private

Referenced by initialize_charged_residue_map(), operator=(), parse_my_tag(), and set_include_His_chain_terminus().

core::Size protocols::simple_filters::InterfaceHbondsFilter::jump_

private

Referenced by compute_hbonds(), compute_salt_bridges(), operator=(), parse_my_tag(), report(), and set_jump().

core::Real protocols::simple_filters::InterfaceHbondsFilter::salt_bridge_distance_cutoff_

private

Referenced by compute_salt_bridges(), operator=(), parse_my_tag(), and set_salt_bridge_distance_cutoff().

bool protocols::simple_filters::InterfaceHbondsFilter::salt_bridge_mode_

private

Referenced by compute(), InterfaceHbondsFilter(), operator=(), parse_my_tag(), set_include_His_chain_terminus(), and set_salt_bridge_mode().

core::scoring::ScoreFunctionOP protocols::simple_filters::InterfaceHbondsFilter::scorefxn_

private

Referenced by compute(), InterfaceHbondsFilter(), operator=(), and set_scorefxn().

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

src/protocols/simple_filters/InterfaceHbondsFilter.hh
src/protocols/simple_filters/InterfaceHbondsFilter.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation