A Residue Selector for selecting specific parts of arbitrary glycans by 'position'. More...

#include <GlycanPositionSelector.hh>

Inheritance diagram for core::select::residue_selector::GlycanPositionSelector:

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

	GlycanPositionSelector (GlycanPositionSelector const &src)
	Copy Constructor. Use if you have non-basic private variables (classes, OPs, etc.) More...

void	add_range (ResidueRange const &range)
	Add a range to the list. More...

void	set_range (utility::vector1< ResidueRange > const &ranges)
	Set the range of glycan positions to select from. More...

void	set_positions (utility::vector1< Size > const &positions)
	Set a specific set of positions to select on. More...

void	set_select_from_residue_position (Size const select_from_residue_position)
	Set the position from which to select all outer foliage from, (and includeing) this position. More...

void	set_select_to_residue_position (Size const select_to_residue_position)
	Set the position where we will select all glycan residues up to this specific glycan position. More...

	~GlycanPositionSelector () override
	Destructor. More...

core::select::residue_selector::ResidueSelectorOP	clone () const override
	Clone operator. More...

core::select::residue_selector::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...

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< ResidueRange >	ranges_

utility::vector1< Size >	positions_

Size	from_residue_

Size	to_residue_

Detailed Description

A Residue Selector for selecting specific parts of arbitrary glycans by 'position'.

Background

Lets assume that the ASN that a particular N-linked Glycan is attached to, starts from Residue 0. The residues off this continue with 1 being the next residue, 2, and so on. Each branch corresponds to a number.

This allows you to choose parts of the glycan, without knowing the actual glycan residue numbers. For example, maybe you want to select the outer part of all glycans or between specific positions.

Tips For use

This Selector works on all glycans of the pose at once.

Settings are:

range (start, end) positions (specific resnums, such as the carbohydrate at position 4) from_residue (all glycan foliage from this and including this residue.) to_residue (all glycan foliage up to and including this residue.)

Use the 'glycan_info' application to determine the glycan position numbers from a pose.

Combine with the GlycanResidueSelector to get unions of specific glycans (such as the leaf of all Man5 residues or the stem of the glycan that starts at ASN85.)

Constructor & Destructor Documentation

core::select::residue_selector::GlycanPositionSelector::GlycanPositionSelector ( )

Constructor.

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

default

Copy Constructor. Use if you have non-basic private variables (classes, OPs, etc.)

core::select::residue_selector::GlycanPositionSelector::~GlycanPositionSelector ( )

overridedefault

Destructor.

Member Function Documentation

void core::select::residue_selector::GlycanPositionSelector::add_range ( ResidueRange const & range )

Add a range to the list.

References ranges_.

ResidueSubset core::select::residue_selector::GlycanPositionSelector::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::select::residue_selector::GlycanResidueSelector::apply(), from_residue_, core::pose::carbohydrates::get_resnums_from_glycan_positions(), core::pose::Pose::glycan_tree_set(), positions_, ranges_, protocols::loops::start, to_residue_, and core::select::residue_selector::TR().

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

static

Get the mover class name.

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

core::select::residue_selector::ResidueSelectorOP core::select::residue_selector::GlycanPositionSelector::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.

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

overridevirtual

Get the mover class name.

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

References class_name().

void core::select::residue_selector::GlycanPositionSelector::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 core::sequence::end, from_residue_, positions_, protocols::sic_dock::range(), ranges_, protocols::loops::start, and to_residue_.

void core::select::residue_selector::GlycanPositionSelector::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::GlycanPositionSelectorCreator::provide_xml_schema().

void core::select::residue_selector::GlycanPositionSelector::set_positions ( utility::vector1< Size > const & positions )

Set a specific set of positions to select on.

References positions_.

void core::select::residue_selector::GlycanPositionSelector::set_range ( utility::vector1< ResidueRange > const & ranges )

Set the range of glycan positions to select from.

References ranges_.

void core::select::residue_selector::GlycanPositionSelector::set_select_from_residue_position ( Size const select_from_residue_position )

Set the position from which to select all outer foliage from, (and includeing) this position.

References from_residue_.

void core::select::residue_selector::GlycanPositionSelector::set_select_to_residue_position ( Size const select_to_residue_position )

Set the position where we will select all glycan residues up to this specific glycan position.

References to_residue_.

Member Data Documentation

Size core::select::residue_selector::GlycanPositionSelector::from_residue_

private

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

utility::vector1< Size > core::select::residue_selector::GlycanPositionSelector::positions_

private

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

utility::vector1< ResidueRange > core::select::residue_selector::GlycanPositionSelector::ranges_

private

Referenced by add_range(), apply(), parse_my_tag(), and set_range().

Size core::select::residue_selector::GlycanPositionSelector::to_residue_

private

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

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation