#include <OligomericAverageDegreeFilter.hh>

Inheritance diagram for protocols::matdes::OligomericAverageDegreeFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef protocols::filters::FilterOP	FilterOP

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	OligomericAverageDegreeFilter ()

	OligomericAverageDegreeFilter (core::pack::task::TaskFactoryOP task_factory, core::Real const t, core::Real const d, bool jump_set, core::Size jump, std::string const &dof_names, bool mcomp)

	OligomericAverageDegreeFilter (OligomericAverageDegreeFilter const &rval)

	~OligomericAverageDegreeFilter () override

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

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

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

void	threshold (core::Real const t)

void	distance_threshold (core::Real const d)

void	jump_set (bool const jump_set)

void	jump_id (core::Size const jump)

void	sym_dof_names (std::string const &dof_names)

void	write2pdb (bool const write)

void	verbose (bool const verb)

void	multicomp (bool const multicomp)

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

core::Real	threshold () const

core::Real	distance_threshold () const

bool	jump_set () const

core::Size	jump_id () const

std::string	sym_dof_names () const

bool	write2pdb () const

bool	verbose () const

bool	multicomp () const

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

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

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

core::Real	compute (core::pose::Pose const &pose, bool const &verbose, bool const &write) const
	calc oligomeric AverageDegree More...

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

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
core::pack::task::TaskFactoryOP	task_factory_

core::Real	threshold_

core::Real	distance_threshold_

bool	jump_set_

core::Size	jump_id_

std::string	sym_dof_names_

bool	write2pdb_

bool	verbose_

bool	multicomp_

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

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::matdes::OligomericAverageDegreeFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::matdes::OligomericAverageDegreeFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::matdes::OligomericAverageDegreeFilter::FilterOP

◆ Pose

typedef core::pose::Pose protocols::matdes::OligomericAverageDegreeFilter::Pose

◆ Real

typedef core::Real protocols::matdes::OligomericAverageDegreeFilter::Real

◆ Super

typedef protocols::filters::Filter protocols::matdes::OligomericAverageDegreeFilter::Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::matdes::OligomericAverageDegreeFilter::TagCOP

Constructor & Destructor Documentation

◆ OligomericAverageDegreeFilter() [1/3]

protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter ( )

◆ OligomericAverageDegreeFilter() [2/3]

protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter	(	core::pack::task::TaskFactoryOP	task_factory,
		core::Real const	t,
		core::Real const	d,
		bool	jump_set,
		core::Size	jump,
		std::string const &	dof_names,
		bool	mcomp
	)

◆ OligomericAverageDegreeFilter() [3/3]

protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter ( OligomericAverageDegreeFilter const & rval )

◆ ~OligomericAverageDegreeFilter()

protocols::matdes::OligomericAverageDegreeFilter::~OligomericAverageDegreeFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::matdes::OligomericAverageDegreeFilter::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 threshold().

◆ class_name()

std::string protocols::matdes::OligomericAverageDegreeFilter::class_name ( )

static

Referenced by protocols::matdes::OligomericAverageDegreeFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::matdes::OligomericAverageDegreeFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::matdes::OligomericAverageDegreeFilter::compute	(	core::pose::Pose const &	pose,
		bool const &	verbose,
		bool const &	write
	)		const

calc oligomeric AverageDegree

References core::conformation::Residue::aa(), core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::pose::Pose::conformation(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), core::kinematics::distance(), distance_threshold(), core::pose::Pose::fold_tree(), core::pose::symmetry::get_sym_aware_jump_num(), jump_id_, jump_set_, multicomp(), multicomp_, core::conformation::Residue::name3(), core::conformation::Residue::nbr_atom(), core::kinematics::FoldTree::partition_by_jump(), core::pose::symmetry::partition_by_symm_jumps(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::conformation::Conformation::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_names_, core::pose::symmetry::symmetry_info(), task_factory(), protocols::matdes::TR(), verbose(), write_to_pdb(), and core::conformation::Residue::xyz().

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

◆ distance_threshold() [1/2]

core::Real protocols::matdes::OligomericAverageDegreeFilter::distance_threshold ( ) const

References distance_threshold_.

Referenced by compute(), and parse_my_tag().

◆ distance_threshold() [2/2]

void protocols::matdes::OligomericAverageDegreeFilter::distance_threshold ( core::Real const d )

References distance_threshold_.

◆ fresh_instance()

protocols::filters::FilterOP protocols::matdes::OligomericAverageDegreeFilter::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ jump_id() [1/2]

core::Size protocols::matdes::OligomericAverageDegreeFilter::jump_id ( ) const

References jump_id_.

Referenced by parse_my_tag().

◆ jump_id() [2/2]

void protocols::matdes::OligomericAverageDegreeFilter::jump_id ( core::Size const jump )

References jump_id_.

◆ jump_set() [1/2]

bool protocols::matdes::OligomericAverageDegreeFilter::jump_set ( ) const

References jump_set_.

Referenced by jump_set(), and parse_my_tag().

◆ jump_set() [2/2]

void protocols::matdes::OligomericAverageDegreeFilter::jump_set ( bool const jump_set )

References jump_set(), and jump_set_.

◆ multicomp() [1/2]

bool protocols::matdes::OligomericAverageDegreeFilter::multicomp ( ) const

References multicomp_.

Referenced by compute(), and parse_my_tag().

◆ multicomp() [2/2]

void protocols::matdes::OligomericAverageDegreeFilter::multicomp ( bool const multicomp )

References multicomp_.

◆ name()

std::string protocols::matdes::OligomericAverageDegreeFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_to_pdb().

◆ parse_my_tag()

void protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References distance_threshold(), jump_id(), jump_set(), multicomp(), core::pack::task::parse_task_operations(), sym_dof_names(), task_factory(), threshold(), protocols::matdes::TR(), verbose(), and write2pdb().

◆ provide_xml_schema()

void protocols::matdes::OligomericAverageDegreeFilter::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::matdes::OligomericAverageDegreeFilterCreator::provide_xml_schema().

◆ report()

void protocols::matdes::OligomericAverageDegreeFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), core::conformation::membrane::out, verbose_, and write2pdb_.

◆ report_sm()

core::Real protocols::matdes::OligomericAverageDegreeFilter::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().

◆ sym_dof_names() [1/2]

std::string protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names ( ) const

References sym_dof_names_.

Referenced by parse_my_tag().

◆ sym_dof_names() [2/2]

void protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names ( std::string const & dof_names )

References sym_dof_names_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::matdes::OligomericAverageDegreeFilter::task_factory ( ) const

References task_factory_.

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

◆ task_factory() [2/2]

void protocols::matdes::OligomericAverageDegreeFilter::task_factory ( core::pack::task::TaskFactoryOP task_factory )

References task_factory(), and task_factory_.

◆ threshold() [1/2]

core::Real protocols::matdes::OligomericAverageDegreeFilter::threshold ( ) const

References threshold_.

Referenced by apply(), and parse_my_tag().

◆ threshold() [2/2]

void protocols::matdes::OligomericAverageDegreeFilter::threshold ( core::Real const t )

References protocols::hybridization::t, and threshold_.

◆ verbose() [1/2]

bool protocols::matdes::OligomericAverageDegreeFilter::verbose ( ) const

References verbose_.

Referenced by compute(), and parse_my_tag().

◆ verbose() [2/2]

void protocols::matdes::OligomericAverageDegreeFilter::verbose ( bool const verb )

References verbose_.

◆ write2pdb() [1/2]

bool protocols::matdes::OligomericAverageDegreeFilter::write2pdb ( ) const

References write2pdb_.

Referenced by parse_my_tag().

◆ write2pdb() [2/2]

void protocols::matdes::OligomericAverageDegreeFilter::write2pdb ( bool const write )

References write2pdb_.

◆ write_to_pdb()

void protocols::matdes::OligomericAverageDegreeFilter::write_to_pdb	(	core::pose::Pose const &	pose,
		core::Size const	residue,
		std::string const &	residue_name,
		core::Size const	neighbors
	)		const

References protocols::jd2::add_string_to_current_job(), protocols::filters::Filter::get_user_defined_name(), name(), and core::pose::Pose::pdb_info().

Referenced by compute().

Member Data Documentation

◆ distance_threshold_

core::Real protocols::matdes::OligomericAverageDegreeFilter::distance_threshold_

private

Referenced by distance_threshold().

◆ jump_id_

core::Size protocols::matdes::OligomericAverageDegreeFilter::jump_id_

private

Referenced by compute(), and jump_id().

◆ jump_set_

bool protocols::matdes::OligomericAverageDegreeFilter::jump_set_

private

Referenced by compute(), and jump_set().

◆ multicomp_

bool protocols::matdes::OligomericAverageDegreeFilter::multicomp_

private

Referenced by compute(), and multicomp().

◆ sym_dof_names_

std::string protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names_

private

Referenced by compute(), and sym_dof_names().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::matdes::OligomericAverageDegreeFilter::task_factory_

private

Referenced by task_factory().

◆ threshold_

core::Real protocols::matdes::OligomericAverageDegreeFilter::threshold_

private

Referenced by threshold().

◆ verbose_

bool protocols::matdes::OligomericAverageDegreeFilter::verbose_

private

Referenced by report(), and verbose().

◆ write2pdb_

bool protocols::matdes::OligomericAverageDegreeFilter::write2pdb_

private

Referenced by report(), and write2pdb().

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

src/protocols/matdes/OligomericAverageDegreeFilter.hh
src/protocols/matdes/OligomericAverageDegreeFilter.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ OligomericAverageDegreeFilter() [1/3]

◆ OligomericAverageDegreeFilter() [2/3]

◆ OligomericAverageDegreeFilter() [3/3]

◆ ~OligomericAverageDegreeFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ distance_threshold() [1/2]

◆ distance_threshold() [2/2]

◆ fresh_instance()

◆ jump_id() [1/2]

◆ jump_id() [2/2]

◆ jump_set() [1/2]

◆ jump_set() [2/2]

◆ multicomp() [1/2]

◆ multicomp() [2/2]

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ sym_dof_names() [1/2]

◆ sym_dof_names() [2/2]

◆ task_factory() [1/2]

◆ task_factory() [2/2]

◆ threshold() [1/2]

◆ threshold() [2/2]

◆ verbose() [1/2]

◆ verbose() [2/2]

◆ write2pdb() [1/2]

◆ write2pdb() [2/2]

◆ write_to_pdb()

Member Data Documentation

◆ distance_threshold_

◆ jump_id_

◆ jump_set_

◆ multicomp_

◆ sym_dof_names_

◆ task_factory_

◆ threshold_

◆ verbose_

◆ write2pdb_