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:

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< Size >	get_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, GlycanTreeOP >	glycan_tree_set_
std::map< Size, GlycanTreeOP >	glycan_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

)

References glycan_res_to_tree_, and glycan_tree_set_.

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

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

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

Convenience function to get the node of a particular residue.

References get_parent(), glycan_res_to_tree_, glycan_tree_set_, has_node(), core::scoring::pair, core::id::to_string(), and core::conformation::TR().

Referenced by get_distance_to_start(), get_largest_glycan_tree_layer(), get_linkage_position(), get_mainchain_child(), get_parent(), get_smallest_glycan_tree_layer(), and has_exocyclic_glycosidic_linkage().

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

)

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.

References core::conformation::signals::GeneralEvent::conformation, core::conformation::carbohydrates::find_seqpos_of_saccharides_mainchain_child(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::id::SequenceMapping::get_corresponding_residue_in_current(), get_start_points(), glycan_res_to_tree_, glycan_tree_set_, core::conformation::signals::LengthEvent::INVALIDATE, core::conformation::Residue::is_carbohydrate(), core::conformation::signals::LengthEvent::position, core::conformation::signals::LengthEvent::residue, core::conformation::Conformation::residue(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, core::conformation::signals::LengthEvent::RESIDUE_DELETE, core::conformation::signals::LengthEvent::RESIDUE_PREPEND, core::conformation::Residue::seqpos(), core::conformation::signals::LengthEvent::tag, and core::conformation::TR().

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

Referenced by get_node(), get_tree_containing_residue(), get_tree_root_of_glycan_residue(), get_tree_start_of_glycan_residue(), GlycanTreeSet(), has_node(), is_residue_in_tree(), on_length_change(), and setup_glycan_trees().

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

private

Referenced by get_all_trees(), get_largest_glycan_tree_layer(), get_largest_glycan_tree_length(), get_node(), get_smallest_glycan_tree_layer(), get_start_points(), get_tree(), get_tree_map(), GlycanTreeSet(), has_tree(), n_trees(), on_length_change(), and setup_glycan_trees().

---

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

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