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core::conformation::carbohydrates::GlycanTreeSet Class Reference

Class to store info on all glycan trees of a pose. More...

#include <GlycanTreeSet.hh>

Inheritance diagram for core::conformation::carbohydrates::GlycanTreeSet:
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Public Member Functions

 GlycanTreeSet ()
 
 GlycanTreeSet (conformation::Conformation const &conf)
 Construct which populates the glycan trees. More...
 
 ~GlycanTreeSet () override
 
 GlycanTreeSet (GlycanTreeSet const &src)
 
GlycanTreeSetOP clone () const
 
bool has_tree (core::Size const glycan_start_position) const
 
bool is_residue_in_tree (const core::uint glycan_residue) const
 Is this residue a part of a glycan tree? More...
 
GlycanTreeCOP get_tree (core::Size const glycan_start_position) const
 Get a glycan tree corresponding to a particular starting residue. More...
 
GlycanTreeCOP get_tree_containing_residue (core::Size const glycan_residue) const
 Convenience function to the tree of a particular residue. More...
 
std::map< Size, GlycanTreeOP >
const & 
get_tree_map () const
 Get a map of the tree start to the glycan tree. More...
 
utility::vector1
< GlycanTreeCOP > const 
get_all_trees () const
 Get a list of all the glycan trees. More...
 
utility::vector1< Sizeget_start_points () const
 
void setup_glycan_trees (conformation::Conformation const &pose)
 Setup the glycan trees. Done by other classes if contained in Pose. Unless you know what you are doing, you should not need to use this function. More...
 
core::Size n_trees () const
 Get the number of glycan trees. More...
 
core::Size get_size () const
 Get the number of glycan trees. More...
 
core::Size size () const
 Get the number of glycan trees. More...
 
core::Size get_largest_glycan_tree_length () const
 
core::Size get_largest_glycan_tree_layer () const
 Get the largest glycan tree layer (from 0 to N). More...
 
core::Size get_largest_glycan_tree_layer (utility::vector1< bool > const &subset) const
 Get the largest glycan tree layer (from 0 to N). of the glycan node residues passed in. More...
 
core::Size get_smallest_glycan_tree_layer () const
 Get the smallest glycan tree layer (from 0 to N). More...
 
core::Size get_smallest_glycan_tree_layer (utility::vector1< bool > const &subset) const
 Get the smallest glycan tree layer (from 0 to N). More...
 
bool has_node (core::Size glycan_residue) const
 Does the current glycan tree set have the node? More...
 
GlycanNodeCOP get_node (core::Size glycan_residue) const
 Convenience function to get the node of a particular residue. More...
 
core::Size get_parent (core::Size glycan_residue) const
 Convenience function to get the parent residue number from a GlycanNode. More...
 
core::uint get_mainchain_child (core::Size glycan_residue) const
 Convenience function to get the main-chain child residue number from a GlycanNode. More...
 
core::Size get_tree_start_of_glycan_residue (core::Size resnum) const
 Convenience function to get the starting position of a particular tree which contains the residue. This is the first Glycan Residue of the tree. Accessed from a stored GlycanTree class. More...
 
core::Size get_tree_root_of_glycan_residue (core::Size resnum) const
 Convenience function to get the root of a particular tree which contains the residue. This is the residue that 'roots' the glycan. It should be protein. If this is 0, it means the glycan is a 'free' glycan. Accessed from a stored GlycanTree class. More...
 
core::Size get_distance_to_start (core::Size glycan_residue) const
 Get the residue distance from this glycan residue to the root of the glycan. Used for Layer-based glycan sampling. More...
 
core::uint get_linkage_position (core::Size const resnum) const
 Linkage number on the parent residue. More...
 
bool has_exocyclic_glycosidic_linkage (core::Size resnum) const
 Convenience function to get whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon. More...
 
void on_length_change (core::conformation::signals::LengthEvent const &event)
 Respond to a length change event. Do not use this manually. It is used by the GlcyanTreeObserver. The observer is attached to your pose and will respond. More...
 

Private Attributes

std::map< Size, GlycanTreeOPglycan_tree_set_
 
std::map< Size, GlycanTreeOPglycan_res_to_tree_
 

Detailed Description

Class to store info on all glycan trees of a pose.

This class contains a map, where the key is the first glycan residue If the key would be the root residue (Asn), we couldn't work with pure glycans.

Constructor & Destructor Documentation

core::conformation::carbohydrates::GlycanTreeSet::GlycanTreeSet ( )
core::conformation::carbohydrates::GlycanTreeSet::GlycanTreeSet ( conformation::Conformation const &  conf)

Construct which populates the glycan trees.

Standard constructor.

References setup_glycan_trees().

core::conformation::carbohydrates::GlycanTreeSet::~GlycanTreeSet ( )
overridedefault
core::conformation::carbohydrates::GlycanTreeSet::GlycanTreeSet ( GlycanTreeSet const &  src)

Member Function Documentation

GlycanTreeSetOP core::conformation::carbohydrates::GlycanTreeSet::clone ( ) const
utility::vector1< GlycanTreeCOP > const core::conformation::carbohydrates::GlycanTreeSet::get_all_trees ( ) const

Get a list of all the glycan trees.

References glycan_tree_set_.

core::Size core::conformation::carbohydrates::GlycanTreeSet::get_distance_to_start ( core::Size  glycan_residue) const

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

References get_node().

Referenced by get_largest_glycan_tree_layer(), and get_smallest_glycan_tree_layer().

Size core::conformation::carbohydrates::GlycanTreeSet::get_largest_glycan_tree_layer ( ) const

Get the largest glycan tree layer (from 0 to N).

References glycan_tree_set_, and protocols::mean_field::max().

core::Size core::conformation::carbohydrates::GlycanTreeSet::get_largest_glycan_tree_layer ( utility::vector1< bool > const &  subset) const

Get the largest glycan tree layer (from 0 to N). of the glycan node residues passed in.

Get the largest glycan tree layer (from 0 to N). of the glycan tree starts passed in.

References get_distance_to_start(), get_node(), and protocols::mean_field::max().

Size core::conformation::carbohydrates::GlycanTreeSet::get_largest_glycan_tree_length ( ) const
core::uint core::conformation::carbohydrates::GlycanTreeSet::get_linkage_position ( core::Size const  resnum) const

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 get_node().

core::uint core::conformation::carbohydrates::GlycanTreeSet::get_mainchain_child ( core::Size  glycan_residue) const

Convenience function to get the main-chain child residue number from a GlycanNode.

References get_node().

GlycanNodeCOP core::conformation::carbohydrates::GlycanTreeSet::get_node ( core::Size  glycan_residue) const
core::Size core::conformation::carbohydrates::GlycanTreeSet::get_parent ( core::Size  glycan_residue) const

Convenience function to get the parent residue number from a GlycanNode.

References get_node().

Referenced by get_node().

Size core::conformation::carbohydrates::GlycanTreeSet::get_size ( ) const

Get the number of glycan trees.

References n_trees().

Size core::conformation::carbohydrates::GlycanTreeSet::get_smallest_glycan_tree_layer ( ) const

Get the smallest glycan tree layer (from 0 to N).

References glycan_tree_set_, and protocols::mean_field::min().

core::Size core::conformation::carbohydrates::GlycanTreeSet::get_smallest_glycan_tree_layer ( utility::vector1< bool > const &  subset) const

Get the smallest glycan tree layer (from 0 to N).

Get the largest glycan tree layer (from 0 to N). of the glycan tree starts passed in.

References get_distance_to_start(), get_node(), and protocols::mean_field::min().

utility::vector1< Size > core::conformation::carbohydrates::GlycanTreeSet::get_start_points ( ) const

References glycan_tree_set_.

Referenced by on_length_change().

GlycanTreeCOP core::conformation::carbohydrates::GlycanTreeSet::get_tree ( core::Size const  glycan_start_position) const

Get a glycan tree corresponding to a particular starting residue.

References glycan_tree_set_, has_tree(), core::id::to_string(), and core::conformation::TR().

GlycanTreeCOP core::conformation::carbohydrates::GlycanTreeSet::get_tree_containing_residue ( core::Size const  glycan_residue) const

Convenience function to the tree of a particular residue.

References glycan_res_to_tree_.

std::map< Size, GlycanTreeOP > const & core::conformation::carbohydrates::GlycanTreeSet::get_tree_map ( ) const

Get a map of the tree start to the glycan tree.

References glycan_tree_set_.

core::Size core::conformation::carbohydrates::GlycanTreeSet::get_tree_root_of_glycan_residue ( core::Size  resnum) const

Convenience function to get the root of a particular tree which contains the residue. This is the residue that 'roots' the glycan. It should be protein. If this is 0, it means the glycan is a 'free' glycan. Accessed from a stored GlycanTree class.

References glycan_res_to_tree_.

core::Size core::conformation::carbohydrates::GlycanTreeSet::get_tree_start_of_glycan_residue ( core::Size  resnum) const

Convenience function to get the starting position of a particular tree which contains the residue. This is the first Glycan Residue of the tree. Accessed from a stored GlycanTree class.

References glycan_res_to_tree_.

bool core::conformation::carbohydrates::GlycanTreeSet::has_exocyclic_glycosidic_linkage ( core::Size  resnum) const

Convenience function to get whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon.

References get_node().

bool core::conformation::carbohydrates::GlycanTreeSet::has_node ( core::Size  glycan_residue) const

Does the current glycan tree set have the node?

/// Convenience functions that access stored data. /// ///

References glycan_res_to_tree_.

Referenced by get_node().

bool core::conformation::carbohydrates::GlycanTreeSet::has_tree ( core::Size const  glycan_start_position) const

References glycan_tree_set_.

Referenced by get_tree().

bool core::conformation::carbohydrates::GlycanTreeSet::is_residue_in_tree ( const core::uint  glycan_residue) const

Is this residue a part of a glycan tree?

Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References glycan_res_to_tree_.

Size core::conformation::carbohydrates::GlycanTreeSet::n_trees ( ) const

Get the number of glycan trees.

References glycan_tree_set_.

Referenced by get_size(), and size().

void core::conformation::carbohydrates::GlycanTreeSet::on_length_change ( core::conformation::signals::LengthEvent const &  event)
void core::conformation::carbohydrates::GlycanTreeSet::setup_glycan_trees ( conformation::Conformation const &  pose)

Setup the glycan trees. Done by other classes if contained in Pose. Unless you know what you are doing, you should not need to use this function.

References core::conformation::carbohydrates::get_glycan_start_points(), glycan_res_to_tree_, glycan_tree_set_, core::conformation::Conformation::size(), and core::conformation::TR().

Referenced by GlycanTreeSet().

Size core::conformation::carbohydrates::GlycanTreeSet::size ( ) const

Get the number of glycan trees.

References n_trees().

Member Data Documentation

std::map< Size, GlycanTreeOP > core::conformation::carbohydrates::GlycanTreeSet::glycan_res_to_tree_
private
std::map< Size, GlycanTreeOP > core::conformation::carbohydrates::GlycanTreeSet::glycan_tree_set_
private

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