The SSElementSelector allows you to select objects based on their secondary structure defintion. Language: "A,B,C" or "A,B", "c_term","n_term","middle" A = numerical position of THAT type of secondary structure. So if the secondary structure was Helix-Sheet-Helix. 2,H would refer to the second helix A could be positive or negative depending if you're counting from the n_term(positive) or c_term negative B = secondary structure type as assigned by DSSP , "H","E","L" C = S=Start, E=End, M=Middle. More...

#include <SSElementSelector.hh>

Inheritance diagram for core::select::residue_selector::SSElementSelector:

[legend]

Classes
struct	SSElement

Public Member Functions
	SSElementSelector ()

	SSElementSelector (SSElementSelector const &src)
	Copy constructor. More...

ResidueSelectorOP	clone () const override
	Clone operator. More...

	~SSElementSelector () override
	Destructor. More...

utility::vector1< SSElement >	parse_ss (core::pose::Pose const &pose) const
	parses the secondary structure elements More...

SSElementSelector::SSElement	get_SSElement (utility::vector1< SSElementSelector::SSElement > const &ss_elements, int goal_position, char type, std::string const &description) const

utility::vector1< Size >	convert_string_to_residues (utility::vector1< SSElementSelector::SSElement > ss_elements, std::string description) const

ResidueSubset	combine_residue_selections (utility::vector1< Size > start_selection_residues, utility::vector1< Size > end_selection_residues, core::pose::Pose const &pose) const

ResidueSubset	apply (core::pose::Pose const &pose) const override
	apply. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	tag parsing More...

std::string	get_name () const override

Public Member Functions inherited from core::select::residue_selector::ResidueSelector
	ResidueSelector ()
	Constructor. More...

	~ResidueSelector () override
	Destructor. More...

utility::vector1< core::Size >	selection_positions (core::pose::Pose const &pose) const
	Calls apply and returns the Rosetta numbering corresponding to the selected residues. More...

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	start_

std::string	end_

std::string	chain_

core::Size	reassign_short_terminal_loop_

Detailed Description

The SSElementSelector allows you to select objects based on their secondary structure defintion. Language: "A,B,C" or "A,B", "c_term","n_term","middle" A = numerical position of THAT type of secondary structure. So if the secondary structure was Helix-Sheet-Helix. 2,H would refer to the second helix A could be positive or negative depending if you're counting from the n_term(positive) or c_term negative B = secondary structure type as assigned by DSSP , "H","E","L" C = S=Start, E=End, M=Middle.

you can also select with n_term or c_term. Examples: selection="3,H,S" to_selection="4,H,E" Would select from the start of Helix 3 to the end of helix 4. selection="-1,H,S" to_selection="4,L,E" Would select from the start of the last helix and go to the end of the fourth loop. (order is not important) selection="n_term" to_selection="3,L,M" Would select from the n_term to the middle of the third loop

Constructor & Destructor Documentation

◆ SSElementSelector() [1/2]

core::select::residue_selector::SSElementSelector::SSElementSelector ( )

default

◆ SSElementSelector() [2/2]

core::select::residue_selector::SSElementSelector::SSElementSelector ( SSElementSelector const & src )

default

Copy constructor.

◆ ~SSElementSelector()

core::select::residue_selector::SSElementSelector::~SSElementSelector ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

ResidueSubset core::select::residue_selector::SSElementSelector::apply ( core::pose::Pose const & pose ) const

overridevirtual

apply.

Implements core::select::residue_selector::ResidueSelector.

References combine_residue_selections(), convert_string_to_residues(), end_, parse_ss(), and start_.

◆ class_name()

std::string core::select::residue_selector::SSElementSelector::class_name ( )

static

Referenced by get_name(), core::select::residue_selector::SSElementSelectorCreator::keyname(), and provide_xml_schema().

◆ clone()

ResidueSelectorOP core::select::residue_selector::SSElementSelector::clone ( ) const

overridevirtual

Clone operator.

Copy this object and return an owning pointer to the new object.

Implements core::select::residue_selector::ResidueSelector.

◆ combine_residue_selections()

ResidueSubset core::select::residue_selector::SSElementSelector::combine_residue_selections	(	utility::vector1< Size >	start_selection_residues,
		utility::vector1< Size >	end_selection_residues,
		core::pose::Pose const &	pose
	)		const

References core::pose::Pose::size().

Referenced by apply().

◆ convert_string_to_residues()

utility::vector1< Size > core::select::residue_selector::SSElementSelector::convert_string_to_residues	(	utility::vector1< SSElementSelector::SSElement >	ss_elements,
		std::string	description
	)		const

References core::select::residue_selector::SSElementSelector::SSElement::end_res, get_SSElement(), and core::select::residue_selector::SSElementSelector::SSElement::start_res.

Referenced by apply().

◆ get_name()

std::string core::select::residue_selector::SSElementSelector::get_name ( ) const

overridevirtual

Implements core::select::residue_selector::ResidueSelector.

References class_name().

◆ get_SSElement()

SSElementSelector::SSElement core::select::residue_selector::SSElementSelector::get_SSElement	(	utility::vector1< SSElementSelector::SSElement > const &	ss_elements,
		int	goal_position,
		char	type,
		std::string const &	description
	)		const

Referenced by convert_string_to_residues().

◆ parse_my_tag()

void core::select::residue_selector::SSElementSelector::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

tag parsing

Reimplemented from core::select::residue_selector::ResidueSelector.

References chain_, end_, reassign_short_terminal_loop_, and start_.

◆ parse_ss()

utility::vector1< SSElementSelector::SSElement > core::select::residue_selector::SSElementSelector::parse_ss ( core::pose::Pose const & pose ) const

parses the secondary structure elements

References chain_, protocols::simple_filters::dssp(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::get_resnums_for_chain(), core::pose::has_chain(), core::pose::symmetry::is_symmetric(), reassign_short_terminal_loop_, core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), and core::select::residue_selector::TR().

Referenced by apply().

◆ provide_xml_schema()

void core::select::residue_selector::SSElementSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and core::select::residue_selector::xsd_type_definition_w_attributes().

Referenced by core::select::residue_selector::SSElementSelectorCreator::provide_xml_schema().

Member Data Documentation

◆ chain_

std::string core::select::residue_selector::SSElementSelector::chain_

private

Referenced by parse_my_tag(), and parse_ss().

◆ end_

std::string core::select::residue_selector::SSElementSelector::end_

private

Referenced by apply(), and parse_my_tag().

◆ reassign_short_terminal_loop_

core::Size core::select::residue_selector::SSElementSelector::reassign_short_terminal_loop_

private

Referenced by parse_my_tag(), and parse_ss().

◆ start_

std::string core::select::residue_selector::SSElementSelector::start_

private

Referenced by apply(), and parse_my_tag().

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

src/core/select/residue_selector/SSElementSelector.hh
src/core/select/residue_selector/SSElementSelector.cc

Classes

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SSElementSelector() [1/2]

◆ SSElementSelector() [2/2]

◆ ~SSElementSelector()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ combine_residue_selections()

◆ convert_string_to_residues()

◆ get_name()

◆ get_SSElement()

◆ parse_my_tag()

◆ parse_ss()

◆ provide_xml_schema()

Member Data Documentation

◆ chain_

◆ end_

◆ reassign_short_terminal_loop_

◆ start_