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core::select::residue_selector::GlycanPositionSelector Class Reference

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

#include <GlycanPositionSelector.hh>

Inheritance diagram for core::select::residue_selector::GlycanPositionSelector:
Inheritance graph
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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 bool residue_selector_provides_citation_info () const
 Does this residue selector provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool residue_selector_is_unpublished () const
 Does this residue selector indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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< ResidueRangeranges_
 
utility::vector1< Sizepositions_
 
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
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
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
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
Size core::select::residue_selector::GlycanPositionSelector::to_residue_
private

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