protocols::simple_filters::InterfaceSasaFilter Class Reference

#include <InterfaceSasaFilter.hh>

Inheritance diagram for protocols::simple_filters::InterfaceSasaFilter:

Public Member Functions
	InterfaceSasaFilter ()
	InterfaceSasaFilter (core::Real const lower_threshold, bool const hydrophobic=false, bool const polar=false, core::Real const upper_threshold=100000000.0, std::string const &sym_dof_names="")
bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
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::Real	compute (core::pose::Pose const &pose) const
filters::FilterOP	clone () const override
filters::FilterOP	fresh_instance () const override
	~InterfaceSasaFilter () override
void	jump (core::Size const jump)
void	add_jump (core::Size const jump)
void	jumps (utility::vector1< core::Size > const &jumps)
void	sym_dof_names (std::string const &sym_dof_names)
void	sym_dof_names (utility::vector1< std::string > const &sym_dof_names)
void	add_sym_dof_name (std::string const &sym_dof_name)
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 () 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::Real	lower_threshold_
core::Real	upper_threshold_
bool	hydrophobic_
bool	polar_
utility::vector1< core::Size >	jumps_
	count only hydrophobics? polars? More...
utility::vector1< std::string >	sym_dof_names_

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

Constructor & Destructor Documentation

InterfaceSasaFilter() [1/2]

protocols::simple_filters::InterfaceSasaFilter::InterfaceSasaFilter

(

)

References jump().

InterfaceSasaFilter() [2/2]

protocols::simple_filters::InterfaceSasaFilter::InterfaceSasaFilter	(	core::Real const	lower_threshold,
		bool const	hydrophobic = false,
		bool const	polar = false,
		core::Real const	upper_threshold = 100000000.0,
		std::string const &	sym_dof_names = ""
	)

References jump(), and sym_dof_names().

~InterfaceSasaFilter()

protocols::simple_filters::InterfaceSasaFilter::~InterfaceSasaFilter ( )

overridedefault

Member Function Documentation

add_jump()

void protocols::simple_filters::InterfaceSasaFilter::add_jump

(

core::Size const

jump

)

References jump(), and jumps_.

add_sym_dof_name()

void protocols::simple_filters::InterfaceSasaFilter::add_sym_dof_name

(

std::string const &

sym_dof_name

)

References sym_dof_names_.

apply()

bool protocols::simple_filters::InterfaceSasaFilter::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(), lower_threshold_, protocols::simple_filters::TR(), and upper_threshold_.

class_name()

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

static

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

clone()

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

overridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::simple_filters::InterfaceSasaFilter::compute

(

core::pose::Pose const &

pose

)

const

References core::conformation::Residue::atom_type(), core::pose::symmetry::get_full_intracomponent_and_neighbor_subpose(), core::pose::symmetry::get_full_intracomponent_neighbor_subpose(), core::pose::symmetry::get_full_intracomponent_subpose(), core::pose::symmetry::get_jump_name_to_subunits(), core::pose::symmetry::get_sym_aware_jump_num(), hydrophobic_, core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::pose::symmetry::is_multicomponent(), core::chemical::AtomType::is_polar_hydrogen(), core::pose::symmetry::is_symmetric(), jump(), core::pose::symmetry::jump_num_sym_dof(), jumps_, core::pose::Pose::metric(), polar_, core::pose::Pose::residue(), core::pose::Pose::size(), protocols::stepwise::modeler::split_pose(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_names_, core::pose::symmetry::symmetry_info(), protocols::simple_filters::TR(), and protocols::toolbox::rigid_body::translate().

Referenced by apply(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), report(), and report_sm().

fresh_instance()

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

overridevirtual

Implements protocols::filters::Filter.

jump()

void protocols::simple_filters::InterfaceSasaFilter::jump

(

core::Size const

jump

)

References jumps_, and sym_dof_names_.

Referenced by add_jump(), compute(), and InterfaceSasaFilter().

jumps()

void protocols::simple_filters::InterfaceSasaFilter::jumps

(

utility::vector1< core::Size > const &

jumps

)

References jumps_.

Referenced by protocols::protein_interface_design::filters::AtomicContactCountFilter::compute().

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::simple_filters::InterfaceSasaFilter::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 hydrophobic_, jumps_, lower_threshold_, polar_, sym_dof_names_, protocols::simple_filters::TR(), and upper_threshold_.

provide_xml_schema()

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

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

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

report_sm()

core::Real protocols::simple_filters::InterfaceSasaFilter::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]

void protocols::simple_filters::InterfaceSasaFilter::sym_dof_names

(

std::string const &

sym_dof_names

)

References jumps_, and sym_dof_names_.

Referenced by protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), InterfaceSasaFilter(), and sym_dof_names().

sym_dof_names() [2/2]

void protocols::simple_filters::InterfaceSasaFilter::sym_dof_names

(

utility::vector1< std::string > const &

sym_dof_names

)

References sym_dof_names(), and sym_dof_names_.

Member Data Documentation

hydrophobic_

bool protocols::simple_filters::InterfaceSasaFilter::hydrophobic_

private

Referenced by compute(), and parse_my_tag().

jumps_

utility::vector1<core::Size> protocols::simple_filters::InterfaceSasaFilter::jumps_

private

count only hydrophobics? polars?

Referenced by add_jump(), compute(), jump(), jumps(), parse_my_tag(), and sym_dof_names().

lower_threshold_

core::Real protocols::simple_filters::InterfaceSasaFilter::lower_threshold_

private

Referenced by apply(), and parse_my_tag().

polar_

bool protocols::simple_filters::InterfaceSasaFilter::polar_

private

Referenced by compute(), and parse_my_tag().

sym_dof_names_

utility::vector1<std::string> protocols::simple_filters::InterfaceSasaFilter::sym_dof_names_

private

Referenced by add_sym_dof_name(), compute(), jump(), parse_my_tag(), and sym_dof_names().

upper_threshold_

core::Real protocols::simple_filters::InterfaceSasaFilter::upper_threshold_

private

Referenced by apply(), and parse_my_tag().

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

• src/protocols/simple_filters/InterfaceSasaFilter.hh
• src/protocols/simple_filters/InterfaceSasaFilter.cc