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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:
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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, Sizedownstream_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< Sizechildren_
 directly connected residues (downstream residues) (Downstream = this->end of glycan More...
 
utility::vector1< connectiondownstream_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

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)

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
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().


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