A ResidueSelector for carbohydrates and individual carbohydrate trees. Selects all Glycan residues if no option is given or the branch going out from the root residue. Selecting from root residues allows you to choose the whole glycan branch or only tips, etc. More...

#include <GlycanResidueSelector.hh>

Inheritance diagram for core::select::residue_selector::GlycanResidueSelector:

[legend]

Public Member Functions
	GlycanResidueSelector ()
	Constructor. More...

	GlycanResidueSelector (utility::vector1< bool > root_residues, bool include_root=false)
	Constructor to select tree residues from branch roots. See set_branch_residues for more. More...

	GlycanResidueSelector (core::Size root_residue, bool include_root=false)

void	set_select_from_branch_residues (utility::vector1< bool > root_residues)
	Set the residue(s) to select from. These can be the branch points of the glycans or carbohydrate residues from which to select the downstream branch from. More...

void	set_select_from_branch_residue (core::Size root_residue)
	Set the residue to select from. These can be the branch points of the glycans or carbohydrate residues from which to select the downstream branch from. More...

void	set_include_root (bool include_root)
	Option to include the root(s) we are selecting from. Default FALSE. More...

	~GlycanResidueSelector () override
	Destructor. More...

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

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

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

std::string	get_name () const override
	Get the mover class name. More...

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 ()
	Get the mover class name. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Provide XSD information, enabling mechanical validation of input XML. More...

Private Attributes
utility::vector1< bool >	root_residues_

core::Size	root_residue_

utility::vector1< std::string >	parsed_positions_

std::string	ref_pose_name_

bool	include_root_

Detailed Description

A ResidueSelector for carbohydrates and individual carbohydrate trees. Selects all Glycan residues if no option is given or the branch going out from the root residue. Selecting from root residues allows you to choose the whole glycan branch or only tips, etc.

Constructor & Destructor Documentation

◆ GlycanResidueSelector() [1/3]

core::select::residue_selector::GlycanResidueSelector::GlycanResidueSelector ( )

Constructor.

References include_root_, and root_residue_.

◆ GlycanResidueSelector() [2/3]

core::select::residue_selector::GlycanResidueSelector::GlycanResidueSelector	(	utility::vector1< bool >	root_residues,
		bool	include_root = `false`
	)

Constructor to select tree residues from branch roots. See set_branch_residues for more.

References root_residue_, and set_select_from_branch_residues().

◆ GlycanResidueSelector() [3/3]

core::select::residue_selector::GlycanResidueSelector::GlycanResidueSelector	(	core::Size	root_residue,
		bool	include_root = `false`
	)

References set_select_from_branch_residue().

◆ ~GlycanResidueSelector()

core::select::residue_selector::GlycanResidueSelector::~GlycanResidueSelector ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

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

overridevirtual

"Apply" function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected ("true") or not ("false").

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

References core::pose::Pose::corresponding_residue_in_current(), core::conformation::carbohydrates::get_carbohydrate_residues_of_branch(), include_root_, core::conformation::Residue::is_carbohydrate(), core::pose::parse_resnum(), parsed_positions_, ref_pose_name_, core::pose::Pose::residue(), root_residue_, root_residues_, core::pose::Pose::size(), and core::pose::Pose::total_residue().

Referenced by core::select::residue_selector::GlycanPositionSelector::apply(), and core::select::residue_selector::RandomGlycanFoliageSelector::apply().

◆ class_name()

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

static

Get the mover class name.

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

◆ clone()

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

overridevirtual

Clone operator.

Clone function.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

Copy this object and return owning pointer to the copy (created on the heap).

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

◆ get_name()

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

overridevirtual

Get the mover class name.

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

References class_name().

◆ parse_my_tag()

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

overridevirtual

XML parse.

Parse RosettaScripts tags and set up this mover.

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

References include_root_, parsed_positions_, and ref_pose_name_.

◆ provide_xml_schema()

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

static

Provide XSD information, enabling mechanical validation of input XML.

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

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

◆ set_include_root()

void core::select::residue_selector::GlycanResidueSelector::set_include_root ( bool include_root )

Option to include the root(s) we are selecting from. Default FALSE.

References include_root_.

Referenced by core::select::residue_selector::RandomGlycanFoliageSelector::apply().

◆ set_select_from_branch_residue()

void core::select::residue_selector::GlycanResidueSelector::set_select_from_branch_residue ( core::Size root_residue )

Set the residue to select from. These can be the branch points of the glycans or carbohydrate residues from which to select the downstream branch from.

Like the rest of a tree from a particular position. That position could be the trunk or individual branches, which keep branching out.

Note that the Subset will not include the Root residue by default.

References root_residue_, and root_residues_.

Referenced by core::select::residue_selector::RandomGlycanFoliageSelector::apply(), and GlycanResidueSelector().

◆ set_select_from_branch_residues()

void core::select::residue_selector::GlycanResidueSelector::set_select_from_branch_residues ( utility::vector1< bool > root_residues )

Set the residue(s) to select from. These can be the branch points of the glycans or carbohydrate residues from which to select the downstream branch from.

Like the rest of a tree from a particular position. That position could be the trunk or individual branches, which keep branching out.

Note that the Subset will not include the Root residue by default.

References root_residue_, and root_residues_.

Referenced by GlycanResidueSelector().

Member Data Documentation

◆ include_root_

bool core::select::residue_selector::GlycanResidueSelector::include_root_

private

Referenced by apply(), GlycanResidueSelector(), parse_my_tag(), and set_include_root().

◆ parsed_positions_

utility::vector1< std::string > core::select::residue_selector::GlycanResidueSelector::parsed_positions_

private

Referenced by apply(), and parse_my_tag().

◆ ref_pose_name_

std::string core::select::residue_selector::GlycanResidueSelector::ref_pose_name_

private

Referenced by apply(), and parse_my_tag().

◆ root_residue_

core::Size core::select::residue_selector::GlycanResidueSelector::root_residue_

private

Referenced by apply(), GlycanResidueSelector(), set_select_from_branch_residue(), and set_select_from_branch_residues().

◆ root_residues_

utility::vector1< bool > core::select::residue_selector::GlycanResidueSelector::root_residues_

private

Referenced by apply(), set_select_from_branch_residue(), and set_select_from_branch_residues().

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ GlycanResidueSelector() [1/3]

◆ GlycanResidueSelector() [2/3]

◆ GlycanResidueSelector() [3/3]

◆ ~GlycanResidueSelector()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ get_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_include_root()

◆ set_select_from_branch_residue()

◆ set_select_from_branch_residues()

Member Data Documentation

◆ include_root_

◆ parsed_positions_

◆ ref_pose_name_

◆ root_residue_

◆ root_residues_