core::conformation::carbohydrates::GlycanNode Class Reference

Class to store info a node (residue) within a glycan tree. More...

#include <GlycanNode.hh>

Inheritance diagram for core::conformation::carbohydrates::GlycanNode:

Public Member Functions
	GlycanNode ()
	GlycanNode (conformation::Conformation const &conf, Size const tree_start_pos, Size const pos)
	Standard constructor tree_start_pos is the first residue of the tree in which this node is located in. pos is the glycan residue we are setting up. More...
	~GlycanNode () override
	GlycanNode (GlycanNode const &src)
GlycanNodeOP	clone () const
core::Size	get_resnum () const
	Get the residue corresponding to this node. More...
core::Size	get_distance_to_start () const
	Get the residue distance from this glycan residue to the start of the glycan. Used for Layer-based glycan sampling. More...
core::Size	get_parent () const
	Get parent residue number. More...
core::Size	get_linkage_position () const
	Linkage number on the parent residue. More...
bool	has_exocyclic_linkage () const
	Get whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon. More...
utility::vector1< Size > const &	get_children () const
	Get all connected downstream residues (Downstream = this->end of glycan) More...
core::Size	get_mainchain_child () const
	Get the downstream residue connecting to this residue that is part of the mainchain. If this has NO mainchain connection, we return zero. (Downstream = this->end of glycan) More...
utility::vector1< connection > const &	get_downstream_connections ()
	Get all downstream connections (Downstream = this->end of glycan. More...
void	setup_info (conformation::Conformation const &conf, Size const tree_start_pos, Size const pos)
	Setup all data for this glycan residue. More...
void	update_connectivity_data (conformation::Conformation const &conf)
	Update connectivity following a length-change event. More...
void	remap_residue (Size new_start, Size new_node)
	Remap residue following length change. More...

Private Types
typedef Size	upstream_atom
	Typedefs for storing connections. More...
typedef std::pair< Size, Size >	downstream_atom
typedef std::pair < upstream_atom, downstream_atom >	connection

Private Attributes
Size	node_residue_
	Member variables. More...
Size	parent_residue_
	The node's parent pose-internal residue number. More...
Size	tree_start_residue_
	The starting residue of this Node's Tree. Instead of holding a whole AP. More...
utility::vector1< Size >	children_
	directly connected residues (downstream residues) (Downstream = this->end of glycan More...
utility::vector1< connection >	downstream_connections_
	All connections of this node, i.e. connections to children: (Downstream = this->end of glycan. More...
Size	glycan_position_
	Position representation of the glycan residue. From 1 to N, N being the size of the glycan tree. More...
Size	distance_to_start_
	Residue distance to the glycan root. Used for Layer-Based Tree sampling. More...
bool	has_exocyclic_linkage_
	Whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon. More...
Size	linkage_position_
	Linkage number on the parent residue. More...
Size	mainchain_child_

Detailed Description

Class to store info a node (residue) within a glycan tree.

Member Typedef Documentation

typedef std::pair<upstream_atom,downstream_atom> core::conformation::carbohydrates::GlycanNode::connection

private

typedef std::pair< Size, Size > core::conformation::carbohydrates::GlycanNode::downstream_atom

private

typedef Size core::conformation::carbohydrates::GlycanNode::upstream_atom

private

Typedefs for storing connections.

Constructor & Destructor Documentation

core::conformation::carbohydrates::GlycanNode::GlycanNode

(

)

core::conformation::carbohydrates::GlycanNode::GlycanNode	(	conformation::Conformation const &	conf,
		Size const	tree_start_pos,
		Size const	pos
	)

Standard constructor tree_start_pos is the first residue of the tree in which this node is located in. pos is the glycan residue we are setting up.

References setup_info().

core::conformation::carbohydrates::GlycanNode::~GlycanNode ( )

overridedefault

core::conformation::carbohydrates::GlycanNode::GlycanNode

(

GlycanNode const &

src

)

Member Function Documentation

GlycanNodeOP core::conformation::carbohydrates::GlycanNode::clone

(

)

const

utility::vector1< Size > const& core::conformation::carbohydrates::GlycanNode::get_children ( ) const

inline

Get all connected downstream residues (Downstream = this->end of glycan)

References children_.

core::Size core::conformation::carbohydrates::GlycanNode::get_distance_to_start ( ) const

inline

Get the residue distance from this glycan residue to the start of the glycan. Used for Layer-based glycan sampling.

References distance_to_start_.

utility::vector1< connection > const& core::conformation::carbohydrates::GlycanNode::get_downstream_connections ( )

inline

Get all downstream connections (Downstream = this->end of glycan.

References downstream_connections_.

core::Size core::conformation::carbohydrates::GlycanNode::get_linkage_position ( ) const

inline

Linkage number on the parent residue.

an integer n of (1->n) of polysaccharide nomenclature, where n specifies the attachment point on the parent monosaccharide residue; e.g., 4 specifies O4; n = 0 specifies that the residue at <seqpos> is a lower terminus or connected to a non-sugar.

References linkage_position_.

Size core::conformation::carbohydrates::GlycanNode::get_mainchain_child

(

)

const

Get the downstream residue connecting to this residue that is part of the mainchain. If this has NO mainchain connection, we return zero. (Downstream = this->end of glycan)

References mainchain_child_.

core::Size core::conformation::carbohydrates::GlycanNode::get_parent ( ) const

inline

Get parent residue number.

References parent_residue_.

core::Size core::conformation::carbohydrates::GlycanNode::get_resnum ( ) const

inline

Get the residue corresponding to this node.

References node_residue_.

bool core::conformation::carbohydrates::GlycanNode::has_exocyclic_linkage ( ) const

inline

Get whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon.

References has_exocyclic_linkage_.

void core::conformation::carbohydrates::GlycanNode::remap_residue	(	Size	new_start,
		Size	new_node
	)

Remap residue following length change.

References node_residue_, and tree_start_residue_.

void core::conformation::carbohydrates::GlycanNode::setup_info	(	conformation::Conformation const &	conf,
		Size const	tree_start_pos,
		Size const	pos
	)

Setup all data for this glycan residue.

tree_start_pos is the first residue of the tree in which this node is located in. pos is the glycan residue we are setting up.

References downstream_connections_, node_residue_, tree_start_residue_, and update_connectivity_data().

Referenced by GlycanNode().

void core::conformation::carbohydrates::GlycanNode::update_connectivity_data

(

conformation::Conformation const &

conf

)

Update connectivity following a length-change event.

References children_, core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResConnID::connid(), distance_to_start_, downstream_connections_, core::conformation::carbohydrates::find_seqpos_of_saccharides_mainchain_child(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::conformation::carbohydrates::get_distance_to_start(), core::conformation::carbohydrates::get_glycan_position_from_resnum(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), glycan_position_, core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), has_exocyclic_linkage_, core::conformation::Residue::is_carbohydrate(), linkage_position_, mainchain_child_, core::conformation::Residue::n_possible_residue_connections(), node_residue_, parent_residue_, core::chemical::ResConnID::resid(), core::conformation::Conformation::residue(), and tree_start_residue_.

Referenced by setup_info().

Member Data Documentation

utility::vector1< Size > core::conformation::carbohydrates::GlycanNode::children_

private

directly connected residues (downstream residues) (Downstream = this->end of glycan

Referenced by get_children(), and update_connectivity_data().

Size core::conformation::carbohydrates::GlycanNode::distance_to_start_

private

Residue distance to the glycan root. Used for Layer-Based Tree sampling.

Referenced by get_distance_to_start(), and update_connectivity_data().

utility::vector1< connection > core::conformation::carbohydrates::GlycanNode::downstream_connections_

private

All connections of this node, i.e. connections to children: (Downstream = this->end of glycan.

Referenced by get_downstream_connections(), setup_info(), and update_connectivity_data().

Size core::conformation::carbohydrates::GlycanNode::glycan_position_

private

Position representation of the glycan residue. From 1 to N, N being the size of the glycan tree.

Referenced by update_connectivity_data().

bool core::conformation::carbohydrates::GlycanNode::has_exocyclic_linkage_

private

Whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon.

Referenced by has_exocyclic_linkage(), and update_connectivity_data().

Size core::conformation::carbohydrates::GlycanNode::linkage_position_

private

Linkage number on the parent residue.

an integer n of (1->n) of polysaccharide nomenclature, where n specifies the attachment point on the parent monosaccharide residue; e.g., 4 specifies O4; n = 0 specifies that the residue at <seqpos> is a lower terminus or connected to a non-sugar.

Referenced by get_linkage_position(), and update_connectivity_data().

Size core::conformation::carbohydrates::GlycanNode::mainchain_child_

private

Referenced by get_mainchain_child(), and update_connectivity_data().

Size core::conformation::carbohydrates::GlycanNode::node_residue_

private

Member variables.

The node's pose-internal residue number

Referenced by get_resnum(), remap_residue(), setup_info(), and update_connectivity_data().

Size core::conformation::carbohydrates::GlycanNode::parent_residue_

private

The node's parent pose-internal residue number.

Referenced by get_parent(), and update_connectivity_data().

Size core::conformation::carbohydrates::GlycanNode::tree_start_residue_

private

The starting residue of this Node's Tree. Instead of holding a whole AP.

Referenced by remap_residue(), setup_info(), and update_connectivity_data().

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

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