#include <AtomicContactCountFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::AtomicContactCountFilter:

Public Member Functions
	AtomicContactCountFilter ()

	AtomicContactCountFilter (core::Real distance_cutoff)

	AtomicContactCountFilter (AtomicContactCountFilter const &copy)

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

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

	~AtomicContactCountFilter () override

void	initialize_all_atoms (core::pack::task::TaskFactoryOP task_factoryA=nullptr, bool individual_tasks=false, core::pack::task::TaskFactoryOP task_factoryB=nullptr, bool normalize_by_carbon_count=false, bool non_local=false, bool res_contact=false, bool count_SD_NE1=false)

void	initialize_cross_jump (core::Size jump=0, std::string sym_dof_name="", core::pack::task::TaskFactoryOP task_factoryA=nullptr, bool normalize_by_sasa=false, bool individual_tasks=false, core::pack::task::TaskFactoryOP task_factoryB=nullptr, bool normalize_by_carbon_count=false, bool non_local=false, bool res_contact=false, bool count_SD_NE1=false)

void	initialize_cross_chain (core::pack::task::TaskFactoryOP task_factoryA=nullptr, bool normalize_by_sasa=false, bool detect_chains_for_interface_by_task=false, bool individual_tasks=false, core::pack::task::TaskFactoryOP task_factoryB=nullptr, bool normalize_by_carbon_count=false, bool non_local=false, bool res_contact=false, bool count_SD_NE1=false)

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...

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

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

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

std::string	name () const override

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

	Filter (std::string const &)

	~Filter () override

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

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	Mode { ALL , CROSS_CHAIN_DETECTED , CROSS_CHAIN_ALL , CROSS_JUMP }

Private Attributes
core::pack::task::TaskFactoryOP	task_factoryA_

core::pack::task::TaskFactoryOP	task_factoryB_

core::Real	distance_cutoff_

bool	non_local_

bool	res_contact_

bool	count_SD_NE1_

Mode	filter_mode_

bool	normalize_by_sasa_

bool	ss_only_

bool	normalize_by_carbon_count_

bool	individual_tasks_

core::Size	jump_

std::string	sym_dof_name_

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

Member Enumeration Documentation

◆ Mode

enum protocols::protein_interface_design::filters::AtomicContactCountFilter::Mode

private

Enumerator
ALL
CROSS_CHAIN_DETECTED
CROSS_CHAIN_ALL
CROSS_JUMP

Constructor & Destructor Documentation

◆ AtomicContactCountFilter() [1/3]

protocols::protein_interface_design::filters::AtomicContactCountFilter::AtomicContactCountFilter ( )

References initialize_all_atoms().

◆ AtomicContactCountFilter() [2/3]

protocols::protein_interface_design::filters::AtomicContactCountFilter::AtomicContactCountFilter ( core::Real distance_cutoff )

References initialize_all_atoms().

◆ AtomicContactCountFilter() [3/3]

protocols::protein_interface_design::filters::AtomicContactCountFilter::AtomicContactCountFilter ( AtomicContactCountFilter const & copy )

default

◆ ~AtomicContactCountFilter()

protocols::protein_interface_design::filters::AtomicContactCountFilter::~AtomicContactCountFilter ( )

overridedefault

Member Function Documentation

◆ apply()

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

inlineoverridevirtual

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

Implements protocols::filters::Filter.

◆ class_name()

std::string protocols::protein_interface_design::filters::AtomicContactCountFilter::class_name ( )

static

Referenced by protocols::protein_interface_design::filters::AtomicContactCountFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

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

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::protein_interface_design::filters::AtomicContactCountFilter::compute ( core::pose::Pose const & pose ) const

References ALL, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::chain(), core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::simple_filters::InterfaceSasaFilter::compute(), core::pose::Pose::conformation(), count_SD_NE1_, core::pack::task::TaskFactory::create_packer_task(), CROSS_CHAIN_ALL, CROSS_CHAIN_DETECTED, CROSS_JUMP, core::conformation::Conformation::delete_residue_range_slow(), distance_cutoff_, protocols::simple_filters::dssp(), core::chemical::AtomType::element(), filter_mode_, core::conformation::Residue::first_sidechain_atom(), core::pose::Pose::fold_tree(), core::pose::symmetry::get_sym_aware_jump_num(), individual_tasks_, core::pose::symmetry::is_symmetric(), jump_, protocols::simple_filters::InterfaceSasaFilter::jumps(), core::pack::make_new_symmetric_PackerTask_by_requested_method(), core::conformation::Residue::nheavyatoms(), non_local_, normalize_by_carbon_count_, normalize_by_sasa_, core::conformation::Conformation::num_chains(), core::pose::Pose::num_jump(), core::kinematics::FoldTree::partition_by_jump(), core::pose::symmetry::partition_by_symm_jumps(), res_contact_, core::pose::Pose::residue(), core::pose::Pose::size(), ss_only_, core::pose::symmetry::sym_dof_jump_num(), sym_dof_name_, protocols::simple_filters::InterfaceSasaFilter::sym_dof_names(), core::pose::symmetry::symmetry_info(), task_factoryA_, task_factoryB_, protocols::protein_interface_design::filters::TR(), and core::conformation::Residue::xyz().

Referenced by report_sm().

◆ fresh_instance()

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

overridevirtual

Implements protocols::filters::Filter.

◆ initialize_all_atoms()

void protocols::protein_interface_design::filters::AtomicContactCountFilter::initialize_all_atoms	(	core::pack::task::TaskFactoryOP	task_factoryA = `nullptr`,
		bool	individual_tasks = `false`,
		core::pack::task::TaskFactoryOP	task_factoryB = `nullptr`,
		bool	normalize_by_carbon_count = `false`,
		bool	non_local = `false`,
		bool	res_contact = `false`,
		bool	count_SD_NE1 = `false`
	)

References ALL, count_SD_NE1_, filter_mode_, individual_tasks_, jump_, non_local_, normalize_by_carbon_count_, normalize_by_sasa_, res_contact_, ss_only_, sym_dof_name_, task_factoryA_, and task_factoryB_.

Referenced by AtomicContactCountFilter(), and parse_my_tag().

◆ initialize_cross_chain()

void protocols::protein_interface_design::filters::AtomicContactCountFilter::initialize_cross_chain	(	core::pack::task::TaskFactoryOP	task_factoryA = `nullptr`,
		bool	normalize_by_sasa = `false`,
		bool	detect_chains_for_interface_by_task = `false`,
		bool	individual_tasks = `false`,
		core::pack::task::TaskFactoryOP	task_factoryB = `nullptr`,
		bool	normalize_by_carbon_count = `false`,
		bool	non_local = `false`,
		bool	res_contact = `false`,
		bool	count_SD_NE1 = `false`
	)

References count_SD_NE1_, CROSS_CHAIN_ALL, CROSS_CHAIN_DETECTED, filter_mode_, individual_tasks_, jump_, non_local_, normalize_by_carbon_count_, normalize_by_sasa_, res_contact_, sym_dof_name_, task_factoryA_, and task_factoryB_.

Referenced by parse_my_tag().

◆ initialize_cross_jump()

void protocols::protein_interface_design::filters::AtomicContactCountFilter::initialize_cross_jump	(	core::Size	jump = `0`,
		std::string	sym_dof_name = `""`,
		core::pack::task::TaskFactoryOP	task_factoryA = `nullptr`,
		bool	normalize_by_sasa = `false`,
		bool	individual_tasks = `false`,
		core::pack::task::TaskFactoryOP	task_factoryB = `nullptr`,
		bool	normalize_by_carbon_count = `false`,
		bool	non_local = `false`,
		bool	res_contact = `false`,
		bool	count_SD_NE1 = `false`
	)

References count_SD_NE1_, CROSS_JUMP, filter_mode_, individual_tasks_, jump_, non_local_, normalize_by_carbon_count_, normalize_by_sasa_, res_contact_, sym_dof_name_, task_factoryA_, and task_factoryB_.

Referenced by parse_my_tag().

◆ name()

std::string protocols::protein_interface_design::filters::AtomicContactCountFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::protein_interface_design::filters::AtomicContactCountFilter::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 ALL, count_SD_NE1_, CROSS_CHAIN_DETECTED, distance_cutoff_, filter_mode_, initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), jump_, non_local_, normalize_by_sasa_, core::pack::task::parse_task_operations(), res_contact_, ss_only_, and protocols::protein_interface_design::filters::TR().

◆ provide_xml_schema()

void protocols::protein_interface_design::filters::AtomicContactCountFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::attributes_for_parse_task_operations(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::protein_interface_design::filters::AtomicContactCountFilterCreator::provide_xml_schema().

◆ report_sm()

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

inlineoverridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

Member Data Documentation

◆ count_SD_NE1_

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::count_SD_NE1_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), and parse_my_tag().

◆ distance_cutoff_

core::Real protocols::protein_interface_design::filters::AtomicContactCountFilter::distance_cutoff_

private

Referenced by compute(), and parse_my_tag().

◆ filter_mode_

Mode protocols::protein_interface_design::filters::AtomicContactCountFilter::filter_mode_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), and parse_my_tag().

◆ individual_tasks_

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::individual_tasks_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

◆ jump_

core::Size protocols::protein_interface_design::filters::AtomicContactCountFilter::jump_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), and parse_my_tag().

◆ non_local_

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::non_local_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), and parse_my_tag().

◆ normalize_by_carbon_count_

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::normalize_by_carbon_count_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

◆ normalize_by_sasa_

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::normalize_by_sasa_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), and parse_my_tag().

◆ res_contact_

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::res_contact_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), and parse_my_tag().

◆ ss_only_

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::ss_only_

private

Referenced by compute(), initialize_all_atoms(), and parse_my_tag().

◆ sym_dof_name_

std::string protocols::protein_interface_design::filters::AtomicContactCountFilter::sym_dof_name_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

◆ task_factoryA_

core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::AtomicContactCountFilter::task_factoryA_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

◆ task_factoryB_

core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::AtomicContactCountFilter::task_factoryB_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

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

src/protocols/protein_interface_design/filters/AtomicContactCountFilter.hh
src/protocols/protein_interface_design/filters/AtomicContactCountFilter.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Enumeration Documentation

◆ Mode

Constructor & Destructor Documentation

◆ AtomicContactCountFilter() [1/3]

◆ AtomicContactCountFilter() [2/3]

◆ AtomicContactCountFilter() [3/3]

◆ ~AtomicContactCountFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ fresh_instance()

◆ initialize_all_atoms()

◆ initialize_cross_chain()

◆ initialize_cross_jump()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report_sm()

Member Data Documentation

◆ count_SD_NE1_

◆ distance_cutoff_

◆ filter_mode_

◆ individual_tasks_

◆ jump_

◆ non_local_

◆ normalize_by_carbon_count_

◆ normalize_by_sasa_

◆ res_contact_

◆ ss_only_

◆ sym_dof_name_

◆ task_factoryA_

◆ task_factoryB_