protocols::matdes::OligomericAverageDegreeFilter Class Reference

#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 (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
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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter

(

)

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
	)

protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter

(

OligomericAverageDegreeFilter const &

rval

)

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

overridedefault

Member Function Documentation

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().

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

static

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

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

overridevirtual

Implements protocols::filters::Filter.

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

calc oligomeric AverageDegree

References 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::kinematics::FoldTree::partition_by_jump(), core::pose::symmetry::partition_by_symm_jumps(), core::pose::Pose::pdb_info(), core::conformation::Conformation::residue(), core::pose::Pose::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(), and write_to_pdb().

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

void protocols::matdes::OligomericAverageDegreeFilter::distance_threshold

(

core::Real const

d

)

References distance_threshold_.

core::Real protocols::matdes::OligomericAverageDegreeFilter::distance_threshold

(

)

const

References distance_threshold_.

Referenced by compute(), and parse_my_tag().

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

overridevirtual

Implements protocols::filters::Filter.

void protocols::matdes::OligomericAverageDegreeFilter::jump_id

(

core::Size const

jump

)

References jump_id_.

core::Size protocols::matdes::OligomericAverageDegreeFilter::jump_id

(

)

const

References jump_id_.

Referenced by parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::jump_set

(

bool const

jump_set

)

References jump_set(), and jump_set_.

bool protocols::matdes::OligomericAverageDegreeFilter::jump_set

(

)

const

References jump_set_.

Referenced by jump_set(), and parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::multicomp

(

bool const

multicomp

)

References multicomp_.

bool protocols::matdes::OligomericAverageDegreeFilter::multicomp

(

)

const

References multicomp_.

Referenced by compute(), and parse_my_tag().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_to_pdb().

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().

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().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), verbose_, and write2pdb_.

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().

void protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names

(

std::string const &

dof_names

)

References sym_dof_names_.

std::string protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names

(

)

const

References sym_dof_names_.

Referenced by parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::task_factory

(

core::pack::task::TaskFactoryOP

task_factory

)

References task_factory(), and task_factory_.

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

(

)

const

References task_factory_.

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

void protocols::matdes::OligomericAverageDegreeFilter::threshold

(

core::Real const

t

)

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

core::Real protocols::matdes::OligomericAverageDegreeFilter::threshold

(

)

const

References threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::verbose

(

bool const

verb

)

References verbose_.

bool protocols::matdes::OligomericAverageDegreeFilter::verbose

(

)

const

References verbose_.

Referenced by parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::write2pdb

(

bool const

write

)

References write2pdb_.

bool protocols::matdes::OligomericAverageDegreeFilter::write2pdb

(

)

const

References write2pdb_.

Referenced by parse_my_tag().

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

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

private

Referenced by distance_threshold().

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

private

Referenced by compute(), and jump_id().

bool protocols::matdes::OligomericAverageDegreeFilter::jump_set_

private

Referenced by compute(), and jump_set().

bool protocols::matdes::OligomericAverageDegreeFilter::multicomp_

private

Referenced by compute(), and multicomp().

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

private

Referenced by compute(), and sym_dof_names().

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

private

Referenced by task_factory().

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

private

Referenced by threshold().

bool protocols::matdes::OligomericAverageDegreeFilter::verbose_

private

Referenced by report(), and verbose().

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