protocols::simple_filters::SimpleHbondsToAtomFilter Class Reference

Simple filter for detercting Hbonds to atom with energy < energy cutoff. More...

#include <SimpleHbondsToAtomFilter.hh>

Inheritance diagram for protocols::simple_filters::SimpleHbondsToAtomFilter:

Public Member Functions
	SimpleHbondsToAtomFilter ()
	~SimpleHbondsToAtomFilter () override
bool	apply (core::pose::Pose const &pose) const override
	returns true if the structure passes the filter, false otherwise More...
core::Real	report_sm (core::pose::Pose const &pose) const override
	required for reporting score values More...
void	report (std::ostream &os, core::pose::Pose const &pose) const override
	allows printing data to a stream More...
std::string const &	get_target_residue () const
void	set_target_residue (std::string const &target_residue)
core::Size	get_n_partners () const
void	set_n_partners (core::Size n_partners)
std::string	get_target_atom_name () const
void	set_target_atom_name (std::string atom_name)
core::scoring::ScoreFunctionOP	get_scorefxn () const
void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
core::Real	get_hb_e_cutoff () const
void	set_hb_e_cutoff (core::Real hb_e_cutoff)
core::Size	compute (core::pose::Pose const &pose) const
std::string	name () const override
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Filter in Rosetta Scripts) More...
protocols::filters::FilterOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...
protocols::filters::FilterOP	clone () const override
	required in the context of the parser/scripting scheme More...
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
std::string	target_atom_name_
std::string	target_residue_
core::Size	n_partners_
core::scoring::ScoreFunctionOP	scorefxn_
core::Real	hb_e_cutoff_

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

Detailed Description

Simple filter for detercting Hbonds to atom with energy < energy cutoff.

Constructor & Destructor Documentation

protocols::simple_filters::SimpleHbondsToAtomFilter::SimpleHbondsToAtomFilter

(

)

protocols::simple_filters::SimpleHbondsToAtomFilter::~SimpleHbondsToAtomFilter ( )

overridedefault

Member Function Documentation

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

overridevirtual

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

References compute(), and get_n_partners().

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

static

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

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

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

core::Size protocols::simple_filters::SimpleHbondsToAtomFilter::compute

(

core::pose::Pose const &

pose

)

const

References core::scoring::hbonds::HBondSet::atom_hbonds(), core::conformation::Residue::atom_index(), core::conformation::Conformation::atom_tree(), core::pose::Pose::conformation(), core::scoring::hbonds::fill_hbond_set(), get_hb_e_cutoff(), get_n_partners(), get_scorefxn(), get_target_atom_name(), get_target_residue(), core::scoring::rna::chemical_shift::is_polar_hydrogen(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::parse_resnum(), core::pose::Pose::residue(), and protocols::simple_filters::TR().

Referenced by apply(), and report_sm().

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

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

core::Real protocols::simple_filters::SimpleHbondsToAtomFilter::get_hb_e_cutoff

(

)

const

References hb_e_cutoff_.

Referenced by compute().

core::Size protocols::simple_filters::SimpleHbondsToAtomFilter::get_n_partners

(

)

const

References n_partners_.

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

core::scoring::ScoreFunctionOP protocols::simple_filters::SimpleHbondsToAtomFilter::get_scorefxn

(

)

const

References scorefxn_.

Referenced by compute().

std::string protocols::simple_filters::SimpleHbondsToAtomFilter::get_target_atom_name

(

)

const

References target_atom_name_.

Referenced by compute(), and parse_my_tag().

std::string const & protocols::simple_filters::SimpleHbondsToAtomFilter::get_target_residue

(

)

const

References target_residue_.

Referenced by compute(), and parse_my_tag().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::SimpleHbondsToAtomFilter::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data  )

overridevirtual

parse XML tag (to use this Filter in Rosetta Scripts)

Reimplemented from protocols::filters::Filter.

References get_n_partners(), core::pose::get_resnum_string(), get_target_atom_name(), get_target_residue(), core::scoring::parse_score_function(), set_hb_e_cutoff(), set_n_partners(), set_scorefxn(), set_target_atom_name(), set_target_residue(), and protocols::simple_filters::TR().

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

static

References core::pose::attributes_for_get_resnum_string(), core::scoring::attributes_for_parse_score_function(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

void protocols::simple_filters::SimpleHbondsToAtomFilter::report ( std::ostream &  os, core::pose::Pose const &  pose  ) const

overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

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

overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::simple_filters::SimpleHbondsToAtomFilter::set_hb_e_cutoff

(

core::Real

hb_e_cutoff

)

References hb_e_cutoff_.

Referenced by parse_my_tag().

void protocols::simple_filters::SimpleHbondsToAtomFilter::set_n_partners

(

core::Size

n_partners

)

References n_partners_.

Referenced by parse_my_tag().

void protocols::simple_filters::SimpleHbondsToAtomFilter::set_scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn

)

References scorefxn_.

Referenced by parse_my_tag().

void protocols::simple_filters::SimpleHbondsToAtomFilter::set_target_atom_name

(

std::string

atom_name

)

References target_atom_name_.

Referenced by parse_my_tag().

void protocols::simple_filters::SimpleHbondsToAtomFilter::set_target_residue

(

std::string const &

target_residue

)

References target_residue_.

Referenced by parse_my_tag().

Member Data Documentation

core::Real protocols::simple_filters::SimpleHbondsToAtomFilter::hb_e_cutoff_

private

Referenced by get_hb_e_cutoff(), and set_hb_e_cutoff().

core::Size protocols::simple_filters::SimpleHbondsToAtomFilter::n_partners_

private

Referenced by get_n_partners(), and set_n_partners().

core::scoring::ScoreFunctionOP protocols::simple_filters::SimpleHbondsToAtomFilter::scorefxn_

private

Referenced by get_scorefxn(), and set_scorefxn().

std::string protocols::simple_filters::SimpleHbondsToAtomFilter::target_atom_name_

private

Referenced by get_target_atom_name(), and set_target_atom_name().

std::string protocols::simple_filters::SimpleHbondsToAtomFilter::target_residue_

private

Referenced by get_target_residue(), and set_target_residue().

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

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