carbohydrates

Bindings for core::conformation::carbohydrates namespace

class pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode

Bases: pybind11_object

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

assign(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode, : pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode

C++: core::conformation::carbohydrates::GlycanNode::operator=(const class core::conformation::carbohydrates::GlycanNode &) –> class core::conformation::carbohydrates::GlycanNode &

clone(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode

C++: core::conformation::carbohydrates::GlycanNode::clone() const –> class std::shared_ptr<class core::conformation::carbohydrates::GlycanNode>

get_children(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get all connected downstream residues

(Downstream = this->end of glycan)

C++: core::conformation::carbohydrates::GlycanNode::get_children() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

get_distance_to_start(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → int

Get the residue distance from this glycan residue to the start of the glycan.

Used for Layer-based glycan sampling.

C++: core::conformation::carbohydrates::GlycanNode::get_distance_to_start() const –> unsigned long

get_downstream_connections(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_std_pair_unsigned_long_unsigned_long_t

Get all downstream connections

(Downstream = this->end of glycan

C++: core::conformation::carbohydrates::GlycanNode::get_downstream_connections() –> const class utility::vector1<struct std::pair<unsigned long, struct std::pair<unsigned long, unsigned long> >, class std::allocator<struct std::pair<unsigned long, struct std::pair<unsigned long, unsigned long> > > > &

get_linkage_position(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → int

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.

C++: core::conformation::carbohydrates::GlycanNode::get_linkage_position() const –> unsigned long

get_mainchain_child(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → int

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)

C++: core::conformation::carbohydrates::GlycanNode::get_mainchain_child() const –> unsigned long

get_parent(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → int

Get parent residue number

C++: core::conformation::carbohydrates::GlycanNode::get_parent() const –> unsigned long

get_resnum(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → int

Get the residue corresponding to this node.

C++: core::conformation::carbohydrates::GlycanNode::get_resnum() const –> unsigned long

has_exocyclic_linkage(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode) → bool

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

carbon.

C++: core::conformation::carbohydrates::GlycanNode::has_exocyclic_linkage() const –> bool

remap_residue(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode, new_start: int, new_node: int) → None

Remap residue following length change.

C++: core::conformation::carbohydrates::GlycanNode::remap_residue(unsigned long, unsigned long) –> void

setup_info(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode, conf: pyrosetta.rosetta.core.conformation.Conformation, tree_start_pos: int, pos: int) → None

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.

C++: core::conformation::carbohydrates::GlycanNode::setup_info(const class core::conformation::Conformation &, const unsigned long, const unsigned long) –> void

update_connectivity_data(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode, conf: pyrosetta.rosetta.core.conformation.Conformation) → None

Update connectivity following a length-change event.

C++: core::conformation::carbohydrates::GlycanNode::update_connectivity_data(const class core::conformation::Conformation &) –> void

class pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree

Bases: pybind11_object

Class to store info a glycan tree

assign(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree, : pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree

C++: core::conformation::carbohydrates::GlycanTree::operator=(const class core::conformation::carbohydrates::GlycanTree &) –> class core::conformation::carbohydrates::GlycanTree &

clone(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree

C++: core::conformation::carbohydrates::GlycanTree::clone() const –> class std::shared_ptr<class core::conformation::carbohydrates::GlycanTree>

get_node(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree, resnum: int) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode

Get the GlycanNode of a particular glycan residue

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

C++: core::conformation::carbohydrates::GlycanTree::get_node(unsigned long) const –> class std::shared_ptr<const class core::conformation::carbohydrates::GlycanNode>

get_residues(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get all the residues of this glycan

C++: core::conformation::carbohydrates::GlycanTree::get_residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_root(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree) → int

Get the root of this tree. The connecting residue.

If it is zero, it means this tree is a free-glycan and not connected!

C++: core::conformation::carbohydrates::GlycanTree::get_root() const –> unsigned long

get_size(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree) → int

Get the length of this tree

C++: core::conformation::carbohydrates::GlycanTree::get_size() const –> unsigned long

get_start(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree) → int

Get the first glycan residue number of this tree.

This is also used to identify the tree. This is different than the root!

C++: core::conformation::carbohydrates::GlycanTree::get_start() const –> unsigned long

get_tips(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

C++: core::conformation::carbohydrates::GlycanTree::get_tips() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

has_glycan_residue(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree, resnum: int) → bool

Does this Tree have a particular residue?

C++: core::conformation::carbohydrates::GlycanTree::has_glycan_residue(unsigned long) const –> bool

has_node(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree, resnum: int) → bool

Does this node exist?

C++: core::conformation::carbohydrates::GlycanTree::has_node(unsigned long) const –> bool

is_connected(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree) → bool

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

C++: core::conformation::carbohydrates::GlycanTree::is_connected() const –> bool

setup_glycan_nodes(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree, conf: pyrosetta.rosetta.core.conformation.Conformation, start_pos: int) → None

Populate the glycan nodes of this GlycanTree

C++: core::conformation::carbohydrates::GlycanTree::setup_glycan_nodes(const class core::conformation::Conformation &, const unsigned long) –> void

size(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree) → int

Get the length of this tree

C++: core::conformation::carbohydrates::GlycanTree::size() const –> unsigned long

update_on_length_change(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree, event: core::conformation::signals::LengthEvent) → None

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

C++: core::conformation::carbohydrates::GlycanTree::update_on_length_change(const struct core::conformation::signals::LengthEvent &) –> void

update_start_position(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree, start_pos: int) → None

Update the starting position if the start has been deleted.

C++: core::conformation::carbohydrates::GlycanTree::update_start_position(const unsigned long) –> void

class pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet

Bases: pybind11_object

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.

assign(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, : pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet

C++: core::conformation::carbohydrates::GlycanTreeSet::operator=(const class core::conformation::carbohydrates::GlycanTreeSet &) –> class core::conformation::carbohydrates::GlycanTreeSet &

clone(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet

C++: core::conformation::carbohydrates::GlycanTreeSet::clone() const –> class std::shared_ptr<class core::conformation::carbohydrates::GlycanTreeSet>

get_distance_to_start(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, glycan_residue: int) → int

Get the residue distance from this glycan residue to the root of the glycan.

Used for Layer-based glycan sampling.

C++: core::conformation::carbohydrates::GlycanTreeSet::get_distance_to_start(unsigned long) const –> unsigned long

get_largest_glycan_tree_layer(*args, **kwargs)

Overloaded function.

1. get_largest_glycan_tree_layer(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) -> int

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

C++: core::conformation::carbohydrates::GlycanTreeSet::get_largest_glycan_tree_layer() const –> unsigned long

2. get_largest_glycan_tree_layer(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, subset: pyrosetta.rosetta.utility.vector1_bool) -> int

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

C++: core::conformation::carbohydrates::GlycanTreeSet::get_largest_glycan_tree_layer(const class utility::vector1<bool, class std::allocator<bool> > &) const –> unsigned long

get_largest_glycan_tree_length(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) → int

C++: core::conformation::carbohydrates::GlycanTreeSet::get_largest_glycan_tree_length() const –> unsigned long

get_linkage_position(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, resnum: int) → int

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.

C++: core::conformation::carbohydrates::GlycanTreeSet::get_linkage_position(const unsigned long) const –> unsigned long

get_mainchain_child(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, glycan_residue: int) → int

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

C++: core::conformation::carbohydrates::GlycanTreeSet::get_mainchain_child(unsigned long) const –> unsigned long

get_node(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, glycan_residue: int) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode

Convenience function to get the node of a particular residue

C++: core::conformation::carbohydrates::GlycanTreeSet::get_node(unsigned long) const –> class std::shared_ptr<const class core::conformation::carbohydrates::GlycanNode>

get_parent(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, glycan_residue: int) → int

Convenience function to get the parent residue number from a GlycanNode

C++: core::conformation::carbohydrates::GlycanTreeSet::get_parent(unsigned long) const –> unsigned long

get_size(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) → int

Get the number of glycan trees

C++: core::conformation::carbohydrates::GlycanTreeSet::get_size() const –> unsigned long

get_smallest_glycan_tree_layer(*args, **kwargs)

Overloaded function.

1. get_smallest_glycan_tree_layer(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) -> int

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

C++: core::conformation::carbohydrates::GlycanTreeSet::get_smallest_glycan_tree_layer() const –> unsigned long

2. get_smallest_glycan_tree_layer(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, subset: pyrosetta.rosetta.utility.vector1_bool) -> int

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

C++: core::conformation::carbohydrates::GlycanTreeSet::get_smallest_glycan_tree_layer(const class utility::vector1<bool, class std::allocator<bool> > &) const –> unsigned long

get_start_points(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::conformation::carbohydrates::GlycanTreeSet::get_start_points() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_tree(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, glycan_start_position: int) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree

Get a glycan tree corresponding to a particular starting residue.

C++: core::conformation::carbohydrates::GlycanTreeSet::get_tree(const unsigned long) const –> class std::shared_ptr<const class core::conformation::carbohydrates::GlycanTree>

get_tree_containing_residue(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, glycan_residue: int) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree

Convenience function to the tree of a particular residue

C++: core::conformation::carbohydrates::GlycanTreeSet::get_tree_containing_residue(const unsigned long) const –> class std::shared_ptr<const class core::conformation::carbohydrates::GlycanTree>

get_tree_map(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) → pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t

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

C++: core::conformation::carbohydrates::GlycanTreeSet::get_tree_map() const –> const class std::map<unsigned long, class std::shared_ptr<class core::conformation::carbohydrates::GlycanTree>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::shared_ptr<class core::conformation::carbohydrates::GlycanTree> > > > &

get_tree_root_of_glycan_residue(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, resnum: int) → int

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.

C++: core::conformation::carbohydrates::GlycanTreeSet::get_tree_root_of_glycan_residue(unsigned long) const –> unsigned long

get_tree_start_of_glycan_residue(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, resnum: int) → int

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.

C++: core::conformation::carbohydrates::GlycanTreeSet::get_tree_start_of_glycan_residue(unsigned long) const –> unsigned long

has_exocyclic_glycosidic_linkage(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, resnum: int) → bool

Convenience function to get whether the glycosidic linkage between the

residue and previous residue (parent residue) has an exocyclic carbon.

C++: core::conformation::carbohydrates::GlycanTreeSet::has_exocyclic_glycosidic_linkage(unsigned long) const –> bool

has_node(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, glycan_residue: int) → bool

Does the current glycan tree set have the node?

C++: core::conformation::carbohydrates::GlycanTreeSet::has_node(unsigned long) const –> bool

has_tree(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, glycan_start_position: int) → bool

C++: core::conformation::carbohydrates::GlycanTreeSet::has_tree(const unsigned long) const –> bool

is_residue_in_tree(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, glycan_residue: int) → bool

Is this residue a part of a glycan tree?

C++: core::conformation::carbohydrates::GlycanTreeSet::is_residue_in_tree(const unsigned long) const –> bool

n_trees(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) → int

Get the number of glycan trees

C++: core::conformation::carbohydrates::GlycanTreeSet::n_trees() const –> unsigned long

on_length_change(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, event: core::conformation::signals::LengthEvent) → None

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.

C++: core::conformation::carbohydrates::GlycanTreeSet::on_length_change(const struct core::conformation::signals::LengthEvent &) –> void

setup_glycan_trees(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet, pose: pyrosetta.rosetta.core.conformation.Conformation) → None

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.

C++: core::conformation::carbohydrates::GlycanTreeSet::setup_glycan_trees(const class core::conformation::Conformation &) –> void

size(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet) → int

Get the number of glycan trees

C++: core::conformation::carbohydrates::GlycanTreeSet::size() const –> unsigned long

class pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver

Bases: pybind11_object

The CacheablePoseObserver version of GlycanTreeSet that will react to pose length changes..

assign(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver, : pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver

C++: core::conformation::carbohydrates::GlycanTreeSetObserver::operator=(const class core::conformation::carbohydrates::GlycanTreeSetObserver &) –> class core::conformation::carbohydrates::GlycanTreeSetObserver &

attach_impl(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver, conf: pyrosetta.rosetta.core.conformation.Conformation) → None

Do the attachment to the length event signal

C++: core::conformation::carbohydrates::GlycanTreeSetObserver::attach_impl(class core::conformation::Conformation &) –> void

attach_to(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver, conf: pyrosetta.rosetta.core.conformation.Conformation) → None

Detach and attach to Conformation

C++: core::conformation::carbohydrates::GlycanTreeSetObserver::attach_to(class core::conformation::Conformation &) –> void

clone(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver

C++: core::conformation::carbohydrates::GlycanTreeSetObserver::clone() const –> class std::shared_ptr<class core::conformation::carbohydrates::GlycanTreeSetObserver>

detach_impl(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver) → None

C++: core::conformation::carbohydrates::GlycanTreeSetObserver::detach_impl() –> void

get_glycan_tree_set(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver) → pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet

Get the GlycanTreeSet that is maintained by this Observer.

C++: core::conformation::carbohydrates::GlycanTreeSetObserver::get_glycan_tree_set() const –> class std::shared_ptr<const class core::conformation::carbohydrates::GlycanTreeSet>

is_attached(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver) → bool

C++: core::conformation::carbohydrates::GlycanTreeSetObserver::is_attached() const –> bool

on_length_change(self: pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver, event: core::conformation::signals::LengthEvent) → None

C++: core::conformation::carbohydrates::GlycanTreeSetObserver::on_length_change(const struct core::conformation::signals::LengthEvent &) –> void

pyrosetta.rosetta.core.conformation.carbohydrates.align_virtual_atoms_in_carbohydrate_residue(conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → None

Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of the given

conformation.

C++: core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(class core::conformation::Conformation &, const unsigned long) –> void

pyrosetta.rosetta.core.conformation.carbohydrates.fill_downstream_children_res_and_tips(conf: pyrosetta.rosetta.core.conformation.Conformation, res: int, parent_residue: int, children_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, list_of_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, tips: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Find all children residues, list of residues, and any found tips from a given residue not including parent

Children Residues: Filled in list of children residues found if not tips. List Of Residues: All the residue nums found. Tips: All ‘ends’ of of children found.

See Also: get_carbohydrate_residues_and_tips_of_branch

trim_carbohydrate_branch_from_X

C++: core::conformation::carbohydrates::fill_downstream_children_res_and_tips(const class core::conformation::Conformation &, unsigned long, unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.conformation.carbohydrates.find_seqpos_of_saccharides_child_residue_at(residue: pyrosetta.rosetta.core.conformation.Residue, linkage_position: int) → int

Use a saccharide residue’s connections to find the residue following it from a given linkage position.

C++: core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(const class core::conformation::Residue &, unsigned long) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.find_seqpos_of_saccharides_mainchain_child(residue: pyrosetta.rosetta.core.conformation.Residue) → int

Use the mainchain acceptor to find the mainchain child.

Typically, this is N+1, but this is independent of the residue number. Returns 0 if it has no child.

C++: core::conformation::carbohydrates::find_seqpos_of_saccharides_mainchain_child(const class core::conformation::Residue &) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.find_seqpos_of_saccharides_parent_residue(residue: pyrosetta.rosetta.core.conformation.Residue) → int

Use a saccharide residue’s connections to find the residue from which it follows or branches.

Returns 0 if it has no parent.

C++: core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(const class core::conformation::Residue &) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.get_branching_residues(*args, **kwargs)

Overloaded function.

1. get_branching_residues(conf: pyrosetta.rosetta.core.conformation.Conformation, parent_residue: int, children_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, list_of_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, tips: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. get_branching_residues(conf: pyrosetta.rosetta.core.conformation.Conformation, parent_residue: int, children_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, list_of_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, tips: pyrosetta.rosetta.utility.vector1_unsigned_long, ancestors: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

Recursive function to get branches of a set of residues, etc.

list_of_residues and tips are arrays are non-const references and modified by this function.

Children Residues: Residue nums of parent residue connected that we are interested in finding connected branches. List Of Residues: All the residue nums of the branching from children residues Tips: All ‘ends’ of all the branches found using this function.

See Also: get_carbohydrate_residues_and_tips_of_branch

trim_carbohydrate_branch_from_X

C++: core::conformation::carbohydrates::get_branching_residues(const class core::conformation::Conformation &, unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.conformation.carbohydrates.get_carbohydrate_residues_and_tips_of_branch(*args, **kwargs)

Overloaded function.

1. get_carbohydrate_residues_and_tips_of_branch(conf: pyrosetta.rosetta.core.conformation.Conformation, starting_position: int) -> Tuple[pyrosetta.rosetta.utility.vector1_unsigned_long, pyrosetta.rosetta.utility.vector1_unsigned_long]

2. get_carbohydrate_residues_and_tips_of_branch(conf: pyrosetta.rosetta.core.conformation.Conformation, starting_position: int, include_starting_position: bool) -> Tuple[pyrosetta.rosetta.utility.vector1_unsigned_long, pyrosetta.rosetta.utility.vector1_unsigned_long]

Get residues further down the branch from this residue. starting_position ->

Returns pair of all_upstream_residues, tips. Tips are the ends of linear glycan branches.

C++: core::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(const class core::conformation::Conformation &, const unsigned long, bool) –> struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > >

pyrosetta.rosetta.core.conformation.carbohydrates.get_carbohydrate_residues_of_branch(conf: pyrosetta.rosetta.core.conformation.Conformation, starting_position: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get residues further down the branch from this residue. starting_position ->

Convenience function. Calls get_carbohydrate_residues_and_tips_of_branch

C++: core::conformation::carbohydrates::get_carbohydrate_residues_of_branch(const class core::conformation::Conformation &, const unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_carbohydrate_tips_of_branch(conf: pyrosetta.rosetta.core.conformation.Conformation, starting_position: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get tips (end residue of linear components of branches) further down the branch from this residue. starting_position ->

Convenience function. Calls get_carbohydrate_residues_and_tips_of_branch

C++: core::conformation::carbohydrates::get_carbohydrate_tips_of_branch(const class core::conformation::Conformation &, const unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_distance_to_start(conf: pyrosetta.rosetta.core.conformation.Conformation, position: int) → int

Get the residue distance from the position to the root/end of the glycan.

On-the-fly calculation

C++: core::conformation::carbohydrates::get_distance_to_start(const class core::conformation::Conformation &, const unsigned long) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.get_downstream_residue_that_this_torsion_moves(conf: pyrosetta.rosetta.core.conformation.Conformation, torsion_id: core::id::TorsionID) → int

Return the sequence position of the immediate downstream (child) residue affected by this torsion.

C++: core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(const class core::conformation::Conformation &, const class core::id::TorsionID &) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.get_glycan_connecting_protein_branch_point(conf: pyrosetta.rosetta.core.conformation.Conformation, protein_branch_point_resnum: int) → int

Get the carbohydrate residue connecting the protein branch point.

Returns 0 if branch point is not connected to carbohydrate downstream.

C++: core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(const class core::conformation::Conformation &, const unsigned long) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.get_glycan_position_from_resnum(conf: pyrosetta.rosetta.core.conformation.Conformation, first_glycan_resnum: int, resnum: int) → int

Get the particular resnum from a glycan position, given the protein branch point.

The glycan_position is numbered 1 -> length of glycan. This is useful for easily identifying a particular glycan position. Returns 0 if that glycan_position is not part of the glycan we are interested in or not in pose.

C++: core::conformation::carbohydrates::get_glycan_position_from_resnum(const class core::conformation::Conformation &, const unsigned long, const unsigned long) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.get_glycan_start_points(conf: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.utility.vector1_bool

Get which residues denote starting a glycan.

These are the first residue of the glycan tree, and the tree can be branching from protein or not.

C++: core::conformation::carbohydrates::get_glycan_start_points(const class core::conformation::Conformation &) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_glycan_tree_size(conf: pyrosetta.rosetta.core.conformation.Conformation, first_glycan_resnum: int) → int

Get the size of the glycan tree given the first carbohydrate residue in the tree.

On-the-fly calculation

C++: core::conformation::carbohydrates::get_glycan_tree_size(const class core::conformation::Conformation &, const unsigned long) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.get_glycosidic_TorsionIDs(conf: pyrosetta.rosetta.core.conformation.Conformation, seq_pos: int) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID

Get a list of the TorsionIDs of all glycosidic torsions for the residue at this position.

C++: core::conformation::carbohydrates::get_glycosidic_TorsionIDs(const class core::conformation::Conformation &, const unsigned long) –> class utility::vector1<class core::id::TorsionID, class std::allocator<class core::id::TorsionID> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_glycosidic_bond_residues(conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → Tuple[pyrosetta.rosetta.core.conformation.Residue, pyrosetta.rosetta.core.conformation.Residue]

Return pointers to the two residues of the glycosidic bond.

C++: core::conformation::carbohydrates::get_glycosidic_bond_residues(const class core::conformation::Conformation &, const unsigned long) –> struct std::pair<class std::shared_ptr<const class core::conformation::Residue>, class std::shared_ptr<const class core::conformation::Residue> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_glycosidic_torsion(named_torsion: int, conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → float

Return the requested torsion angle between a saccharide residue of the given pose and the previous residue.

C++: core::conformation::carbohydrates::get_glycosidic_torsion(const unsigned long, const class core::conformation::Conformation &, const unsigned long) –> double

pyrosetta.rosetta.core.conformation.carbohydrates.get_largest_glycan_tree_size(conf: pyrosetta.rosetta.core.conformation.Conformation) → int

Get the largest glycan tree size int he pose.

C++: core::conformation::carbohydrates::get_largest_glycan_tree_size(const class core::conformation::Conformation &) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.get_linkage_position_of_saccharide_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, parent_rsd: pyrosetta.rosetta.core.conformation.Residue) → int

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.

C++: core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(const class core::conformation::Residue &, const class core::conformation::Residue &) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.get_n_glycosidic_torsions_in_res(conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → int

Get the number of glycosidic torsions for this residue. Up to 4 (omega2).

C++: core::conformation::carbohydrates::get_n_glycosidic_torsions_in_res(const class core::conformation::Conformation &, const unsigned long) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.get_non_NU_TorsionID_from_AtomIDs(conf: pyrosetta.rosetta.core.conformation.Conformation, atoms: pyrosetta.rosetta.utility.vector1_core_id_AtomID) → core::id::TorsionID

Get the main chain or branch TorsionID defined by these four AtomIDs.

C++: core::conformation::carbohydrates::get_non_NU_TorsionID_from_AtomIDs(const class core::conformation::Conformation &, const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &) –> class core::id::TorsionID

pyrosetta.rosetta.core.conformation.carbohydrates.get_reference_atoms(named_torsion: int, conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → pyrosetta.rosetta.utility.vector1_core_id_AtomID

Return the AtomIDs of the four reference atoms for the requested torsion.

Works for AA->Glycan connection as well.

C++: core::conformation::carbohydrates::get_reference_atoms(const unsigned long, const class core::conformation::Conformation &, const unsigned long) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_reference_atoms_for_1st_omega(conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → pyrosetta.rosetta.utility.vector1_core_id_AtomID

Return the AtomIDs of the four omega torsion reference atoms.

C++: core::conformation::carbohydrates::get_reference_atoms_for_1st_omega(const class core::conformation::Conformation &, const unsigned long) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_reference_atoms_for_2nd_omega(conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → pyrosetta.rosetta.utility.vector1_core_id_AtomID

Return the AtomIDs of the four omega2 torsion reference atoms.

C++: core::conformation::carbohydrates::get_reference_atoms_for_2nd_omega(const class core::conformation::Conformation &, const unsigned long) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_reference_atoms_for_phi(conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → pyrosetta.rosetta.utility.vector1_core_id_AtomID

Return the AtomIDs of the four phi torsion reference atoms.

C++: core::conformation::carbohydrates::get_reference_atoms_for_phi(const class core::conformation::Conformation &, const unsigned long) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_reference_atoms_for_psi(conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → pyrosetta.rosetta.utility.vector1_core_id_AtomID

Return the AtomIDs of the four psi torsion reference atoms.

C++: core::conformation::carbohydrates::get_reference_atoms_for_psi(const class core::conformation::Conformation &, const unsigned long) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.core.conformation.carbohydrates.get_resnum_from_glycan_position(conf: pyrosetta.rosetta.core.conformation.Conformation, first_glycan_resnum: int, glycan_position: int) → int

Get the particular resnum from a glycan position, given the protein branch point.

The glycan_position is numbered 1 -> length of glycan. This is useful for easily identifying a particular glycan position. Returns 0 if that glycan_position is not part of the glycan we are interested in or not in pose.

C++: core::conformation::carbohydrates::get_resnum_from_glycan_position(const class core::conformation::Conformation &, const unsigned long, const unsigned long) –> unsigned long

pyrosetta.rosetta.core.conformation.carbohydrates.has_exocyclic_glycosidic_linkage(*args, **kwargs)

Overloaded function.

1. has_exocyclic_glycosidic_linkage(conf: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) -> bool

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

carbon.

C++: core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(const class core::conformation::Conformation &, const unsigned long) –> bool

2. has_exocyclic_glycosidic_linkage(rsd: pyrosetta.rosetta.core.conformation.Residue, parent_rsd: pyrosetta.rosetta.core.conformation.Residue) -> bool

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

carbon.

C++: core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(const class core::conformation::Residue &, const class core::conformation::Residue &) –> bool

pyrosetta.rosetta.core.conformation.carbohydrates.is_glycosidic_omega_torsion(conf: pyrosetta.rosetta.core.conformation.Conformation, torsion_id: core::id::TorsionID) → bool

Is this is an omega torsion angle of a glycosidic linkage?

C++: core::conformation::carbohydrates::is_glycosidic_omega_torsion(const class core::conformation::Conformation &, const class core::id::TorsionID &) –> bool

pyrosetta.rosetta.core.conformation.carbohydrates.is_glycosidic_phi_torsion(conf: pyrosetta.rosetta.core.conformation.Conformation, torsion_id: core::id::TorsionID) → bool

Is this is the phi torsion angle of a glycosidic linkage?

C++: core::conformation::carbohydrates::is_glycosidic_phi_torsion(const class core::conformation::Conformation &, const class core::id::TorsionID &) –> bool

pyrosetta.rosetta.core.conformation.carbohydrates.is_glycosidic_psi_torsion(conf: pyrosetta.rosetta.core.conformation.Conformation, torsion_id: core::id::TorsionID) → bool

Is this is the psi torsion angle of a glycosidic linkage?

C++: core::conformation::carbohydrates::is_glycosidic_psi_torsion(const class core::conformation::Conformation &, const class core::id::TorsionID &) –> bool

pyrosetta.rosetta.core.conformation.carbohydrates.set_glycosidic_torsion(named_torsion: int, conf: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int, setting: float) → None

Set the requested torsion angle between a saccharide residue of the given pose and the previous residue.

C++: core::conformation::carbohydrates::set_glycosidic_torsion(const unsigned long, class core::conformation::Conformation &, const unsigned long, const double) –> void