core::conformation::carbohydrates::GlycanTree Class Reference

Class to store info a glycan tree. More...

#include <GlycanTree.hh>

Inheritance diagram for core::conformation::carbohydrates::GlycanTree:

Public Member Functions
	GlycanTree ()
	~GlycanTree () override
	GlycanTree (GlycanTree const &src)
GlycanTreeOP	clone () const
	GlycanTree (conformation::Conformation const &conf, Size const start_pos)
	GlycanTree (Size const start_pos)
bool	is_connected () const
	Is this tree connected to a [protein] or is it free-standing? More...
bool	has_glycan_residue (core::Size resnum) const
	Does this Tree have a particular residue? More...
core::Size	get_size () const
	Get the length of this tree. More...
core::Size	size () const
	Get the length of this tree. More...
core::Size	get_start () const
	Get the first glycan residue number of this tree. This is also used to identify the tree. This is different than the root! More...
core::Size	get_root () const
	Get the root of this tree. The connecting residue. If it is zero, it means this tree is a free-glycan and not connected! More...
bool	has_node (core::Size resnum) const
	Does this node exist? More...
GlycanNodeCOP	get_node (core::Size resnum) const
	Get the GlycanNode of a particular glycan residue GlycanNode has lots of information on the particular residue as part of this glycan tree. More...
utility::vector1< core::Size > const &	get_tips () const
	Get the tips (ending residues) of each foliage end. More...
utility::vector1< core::Size >	get_residues () const
	Get all the residues of this glycan. More...
void	setup_glycan_nodes (conformation::Conformation const &conf, core::Size const start_pos)
	Populate the glycan nodes of this GlycanTree. More...
void	update_on_length_change (core::conformation::signals::LengthEvent const &event)
	Update the nodes connectivity and the tree root after a length-change event. More...
void	update_start_position (core::Size const start_pos)
	Update the starting position if the start has been deleted. More...

Private Attributes
std::map< Size, GlycanNodeOP >	tree_
utility::vector1< Size >	branch_tips_
core::Size	start_pos_
Size	root_

Detailed Description

Class to store info a glycan tree.

Constructor & Destructor Documentation

core::conformation::carbohydrates::GlycanTree::GlycanTree

(

)

core::conformation::carbohydrates::GlycanTree::~GlycanTree ( )

overridedefault

core::conformation::carbohydrates::GlycanTree::GlycanTree

(

GlycanTree const &

src

)

References tree_.

core::conformation::carbohydrates::GlycanTree::GlycanTree	(	conformation::Conformation const &	conf,
		Size const	start_pos
	)

References setup_glycan_nodes().

core::conformation::carbohydrates::GlycanTree::GlycanTree

(

Size const

start_pos

)

Member Function Documentation

GlycanTreeOP core::conformation::carbohydrates::GlycanTree::clone

(

)

const

GlycanNodeCOP core::conformation::carbohydrates::GlycanTree::get_node

(

core::Size

resnum

)

const

Get the GlycanNode of a particular glycan residue GlycanNode has lots of information on the particular residue as part of this glycan tree.

References has_node(), core::id::to_string(), core::conformation::TR(), and tree_.

utility::vector1< Size > core::conformation::carbohydrates::GlycanTree::get_residues

(

)

const

Get all the residues of this glycan.

References tree_.

core::Size core::conformation::carbohydrates::GlycanTree::get_root

(

)

const

Get the root of this tree. The connecting residue. If it is zero, it means this tree is a free-glycan and not connected!

References root_.

core::Size core::conformation::carbohydrates::GlycanTree::get_size

(

)

const

Get the length of this tree.

References tree_.

core::Size core::conformation::carbohydrates::GlycanTree::get_start

(

)

const

Get the first glycan residue number of this tree. This is also used to identify the tree. This is different than the root!

References start_pos_.

utility::vector1< Size > const & core::conformation::carbohydrates::GlycanTree::get_tips

(

)

const

Get the tips (ending residues) of each foliage end.

References branch_tips_.

bool core::conformation::carbohydrates::GlycanTree::has_glycan_residue

(

core::Size

resnum

)

const

Does this Tree have a particular residue?

References tree_.

Referenced by has_node().

bool core::conformation::carbohydrates::GlycanTree::has_node

(

core::Size

resnum

)

const

Does this node exist?

References has_glycan_residue().

Referenced by get_node().

bool core::conformation::carbohydrates::GlycanTree::is_connected

(

)

const

Is this tree connected to a [protein] or is it free-standing?

References root_.

void core::conformation::carbohydrates::GlycanTree::setup_glycan_nodes	(	conformation::Conformation const &	conf,
		core::Size const	start_pos
	)

Populate the glycan nodes of this GlycanTree.

References branch_tips_, core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(), core::conformation::Conformation::residue(), root_, start_pos_, core::id::to_string(), and tree_.

Referenced by GlycanTree(), and update_on_length_change().

core::Size core::conformation::carbohydrates::GlycanTree::size

(

)

const

Get the length of this tree.

References tree_.

void core::conformation::carbohydrates::GlycanTree::update_on_length_change

(

core::conformation::signals::LengthEvent const &

event

)

Update the nodes connectivity and the tree root after a length-change event.

References branch_tips_, core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(), core::id::SequenceMapping::get_corresponding_residue_in_current(), core::conformation::signals::LengthEvent::position, core::conformation::signals::LengthEvent::residue, core::conformation::signals::LengthEvent::RESIDUE_APPEND, core::conformation::signals::LengthEvent::RESIDUE_DELETE, core::conformation::signals::LengthEvent::RESIDUE_PREPEND, root_, core::conformation::Residue::seqpos(), setup_glycan_nodes(), start_pos_, core::conformation::signals::LengthEvent::tag, and tree_.

void core::conformation::carbohydrates::GlycanTree::update_start_position

(

core::Size const

start_pos

)

Update the starting position if the start has been deleted.

References start_pos_.

Member Data Documentation

utility::vector1< Size > core::conformation::carbohydrates::GlycanTree::branch_tips_

private

Referenced by get_tips(), setup_glycan_nodes(), and update_on_length_change().

Size core::conformation::carbohydrates::GlycanTree::root_

private

Referenced by get_root(), is_connected(), setup_glycan_nodes(), and update_on_length_change().

core::Size core::conformation::carbohydrates::GlycanTree::start_pos_

private

Referenced by get_start(), setup_glycan_nodes(), update_on_length_change(), and update_start_position().

std::map< Size, GlycanNodeOP > core::conformation::carbohydrates::GlycanTree::tree_

private

Referenced by get_node(), get_residues(), get_size(), GlycanTree(), has_glycan_residue(), setup_glycan_nodes(), size(), and update_on_length_change().

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

• src/core/conformation/carbohydrates/GlycanTree.hh
• src/core/conformation/carbohydrates/GlycanTree.cc