protocols::fldsgn::filters::SecondaryStructureHasResidueFilter Class Reference

#include <SecondaryStructureHasResidueFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::SecondaryStructureHasResidueFilter:

Public Types
typedef protocols::filters::Filter	Filter
typedef std::string	String
typedef protocols::filters::FilterOP	FilterOP
typedef core::pose::Pose	Pose
typedef utility::tag::TagCOP	TagCOP
typedef basic::datacache::DataMap	DataMap

Public Member Functions
	SecondaryStructureHasResidueFilter ()
	~SecondaryStructureHasResidueFilter () override
FilterOP	clone () const override
FilterOP	fresh_instance () const override
void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
	parse xml More...
bool	apply (Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
core::Real	report_sm (Pose const &pose) const override
	used to report filter internals through a score or silent file More...
void	report (std::ostream &out, Pose const &pose) const override
core::Real	compute (Pose const &pose) const
core::Size	n_req_res_in_seq (std::string const &, utility::vector0< bool > const &is_checked) 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::Size	min_helix_length_
core::Size	max_helix_length_
core::Size	min_sheet_length_
core::Size	max_sheet_length_
core::Size	min_loop_length_
core::Size	max_loop_length_
core::Real	threshold_
std::string	req_residue_str_
core::Size	nres_req_per_secstruct_
core::pack::task::TaskFactoryOP	res_check_task_factory_
core::pack::task::TaskFactoryOP	ss_select_task_factory_
bool	filter_helix_
bool	filter_sheet_
bool	filter_loop_

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

Member Typedef Documentation

DataMap

typedef basic::datacache::DataMap protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::DataMap

Filter

typedef protocols::filters::Filter protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::Filter

FilterOP

typedef protocols::filters::FilterOP protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::FilterOP

Pose

typedef core::pose::Pose protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::Pose

String

typedef std::string protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::String

TagCOP

typedef utility::tag::TagCOP protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::TagCOP

Constructor & Destructor Documentation

SecondaryStructureHasResidueFilter()

protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::SecondaryStructureHasResidueFilter

(

)

~SecondaryStructureHasResidueFilter()

protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::~SecondaryStructureHasResidueFilter ( )

inlineoverride

Member Function Documentation

apply()

bool protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::apply ( 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::fldsgn::filters::SecondaryStructureHasResidueFilter::class_name ( )

static

Referenced by protocols::fldsgn::filters::SecondaryStructureHasResidueFilterCreator::keyname(), name(), and provide_xml_schema().

clone()

FilterOP protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::compute

(

Pose const &

pose

)

const

References core::pose::Pose::chain(), protocols::simple_filters::dssp(), filter_helix_, filter_loop_, filter_sheet_, core::conformation::Residue::is_protein(), max_helix_length_, max_loop_length_, max_sheet_length_, min_helix_length_, min_loop_length_, min_sheet_length_, n_req_res_in_seq(), nres_req_per_secstruct_, res_check_task_factory_, core::pose::Pose::residue(), core::pose::Pose::sequence(), ss_select_task_factory_, and tr().

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

fresh_instance()

FilterOP protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

n_req_res_in_seq()

core::Size protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::n_req_res_in_seq	(	std::string const &	seq,
		utility::vector0< bool > const &	is_checked
	)		const

References req_residue_str_.

Referenced by compute().

name()

std::string protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &  data  )

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References filter_helix_, filter_loop_, filter_sheet_, max_helix_length_, max_loop_length_, max_sheet_length_, min_helix_length_, min_loop_length_, min_sheet_length_, nres_req_per_secstruct_, core::pack::task::parse_task_operations(), req_residue_str_, res_check_task_factory_, ss_select_task_factory_, threshold_, and tr().

provide_xml_schema()

void protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

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

Referenced by protocols::fldsgn::filters::SecondaryStructureHasResidueFilterCreator::provide_xml_schema().

report()

void protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::report ( std::ostream &  out, Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

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

report_sm()

core::Real protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::report_sm ( Pose const &  ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

Member Data Documentation

filter_helix_

bool protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::filter_helix_

private

Referenced by compute(), and parse_my_tag().

filter_loop_

bool protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::filter_loop_

private

Referenced by compute(), and parse_my_tag().

filter_sheet_

bool protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::filter_sheet_

private

Referenced by compute(), and parse_my_tag().

max_helix_length_

core::Size protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::max_helix_length_

private

Referenced by compute(), and parse_my_tag().

max_loop_length_

core::Size protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::max_loop_length_

private

Referenced by compute(), and parse_my_tag().

max_sheet_length_

core::Size protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::max_sheet_length_

private

Referenced by compute(), and parse_my_tag().

min_helix_length_

core::Size protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::min_helix_length_

private

Referenced by compute(), and parse_my_tag().

min_loop_length_

core::Size protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::min_loop_length_

private

Referenced by compute(), and parse_my_tag().

min_sheet_length_

core::Size protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::min_sheet_length_

private

Referenced by compute(), and parse_my_tag().

nres_req_per_secstruct_

core::Size protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::nres_req_per_secstruct_

private

Referenced by compute(), and parse_my_tag().

req_residue_str_

std::string protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::req_residue_str_

private

Referenced by n_req_res_in_seq(), and parse_my_tag().

res_check_task_factory_

core::pack::task::TaskFactoryOP protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::res_check_task_factory_

private

Referenced by compute(), and parse_my_tag().

ss_select_task_factory_

core::pack::task::TaskFactoryOP protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::ss_select_task_factory_

private

Referenced by compute(), and parse_my_tag().

threshold_

core::Real protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::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/fldsgn/filters/SecondaryStructureHasResidueFilter.hh
• src/protocols/fldsgn/filters/SecondaryStructureHasResidueFilter.cc