graph

Bindings for core::pack::guidance_scoreterms::buried_unsat_penalty::graph namespace

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge

Bases: pyrosetta.rosetta.utility.graph.Edge

Each BuriedUnsatPenaltyEdge represents a hydrogen bonding interaction between two residues, and stores information about (a) the number of hydrogen bonds, and (b) the atoms involved.

copy_from(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge, src: pyrosetta.rosetta.utility.graph.Edge) None

Initialize this edge from another.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge::copy_from(const class utility::graph::Edge *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.utility.graph.Edge) int
how much memory is dynamically allocated by this edge – must be recursively invoked

by a derived class.

C++: utility::graph::Edge::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.utility.graph.Edge) int

how much memory is statically allocated by this edge

C++: utility::graph::Edge::count_static_memory() const –> unsigned long

get_first_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) int

returns the index of the lower node

C++: utility::graph::Edge::get_first_node_ind() const –> unsigned long

get_other_ind(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) int
returns the index of the one node given the index of the other.

node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_ind(unsigned long) const –> unsigned long

get_other_node(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) pyrosetta.rosetta.utility.graph.Node
returns a non-const pointer to one node given the index of the other.

node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_node(unsigned long) –> class utility::graph::Node *

get_second_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) int

returns the index of the upper node

C++: utility::graph::Edge::get_second_node_ind() const –> unsigned long

hbond(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge, hbond_index: int) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond

Access a particular hbond in this edge.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge::hbond(const unsigned long) const –> const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond &

is_loop(self: pyrosetta.rosetta.utility.graph.Edge) bool

Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex.

C++: utility::graph::Edge::is_loop() const –> bool

n_hbonds(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge) int

Get the number of hbonds in this edge.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge::n_hbonds() const –> unsigned long

same_edge(self: pyrosetta.rosetta.utility.graph.Edge, node1: int, node2: int) bool
Is this the same edge as another edge (node1,node2)? Note:

this graph does not work for multi-graphs. Edges must be unique.

C++: utility::graph::Edge::same_edge(unsigned long, unsigned long) const –> bool

set_edge_data(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge, edge_data_in: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData) None

Set the data object for this edge.

Data object pointer is copied; object is NOT cloned.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge::set_edge_data(class std::shared_ptr<const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData>) –> void

set_pos_in_owners_list(self: pyrosetta.rosetta.utility.graph.Edge, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) None
called only by class Graph, this function gives the Edge the data it needs

to later delete itself from its owner’s edge list in constant time.

C++: utility::graph::Edge::set_pos_in_owners_list(class utility::graph::EdgeListIterator) –> void

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData

Bases: pybind11_builtins.pybind11_object

add_hbond(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData, lower_numbered_node_is_acceptor: bool, acceptor_group: int, donor_group: int, hbond_energy: float, lower_numbered_node_symmetry_copy_index: int, higher_numbered_node_symmetry_copy_index: int) None

Add a hydrogen bond to a newly-created edge data object.

Note that acceptor_group and donor_group are group indices in the respective nodes, not atom indices in the respective residues.

The symmetry copy indices should both be 1 in the asymmetric case.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData::add_hbond(const bool, const unsigned long, const unsigned long, const double, const unsigned long, const unsigned long) –> void

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData, : pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData::operator=(const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData &) –> class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData &

hbonds_list(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData) pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond

Access the hbonds list (const access).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData::hbonds_list() const –> const class utility::vector1<class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond, class std::allocator<class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond> > &

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph

Bases: pyrosetta.rosetta.utility.graph.Graph

The BuriedUnsatPenaltyGraph consists of nodes representing resiudues (or rotamers in packing mode) and edges representing hydrogen-bonding interactions. Each node stores a list of hydrogen bond donor and acceptor atoms that we’re seeking to satisfy; each edge stores the donors and acceptors that are connected by hydrogen bonds when two residues (or rotamers) interact.

add_edge(*args, **kwargs)

Overloaded function.

  1. add_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) -> pyrosetta.rosetta.utility.graph.Edge

add an edge between two vertices. Invokes “create_edge” from the derived class.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

  1. add_edge(self: pyrosetta.rosetta.utility.graph.Graph, example_edge: pyrosetta.rosetta.utility.graph.Edge) -> pyrosetta.rosetta.utility.graph.Edge

add an edge to this graph copying the data from an edge in another graph.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(const class utility::graph::Edge *) –> class utility::graph::Edge *

all_pairs_shortest_paths(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t
O(V^3). Computes all pairs shortest paths using Warshall’s algorithm

and writes all the path distances to the two-dimensional table.

C++: utility::graph::Graph::all_pairs_shortest_paths() const –> class ObjexxFCL::FArray2D<int>

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, : pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::operator=(const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph &) –> class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph &

compute_unsats_all_nodes(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph) None
Given this BuriedUnsatPenaltyGraph with some number of nodes, iterate through each node and update the

internally-stored counts for unsats and oversats based on the edges connected to that node.

Calls compute_unsats_for_node().

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_all_nodes() –> void

compute_unsats_changed_nodes(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, changed_node_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, changed_node_partners: pyrosetta.rosetta.utility.vector1_unsigned_long) None
Given two lists (one of changed nodes, one of their partners), update the internally-stored counts for unsats and oversats for

those nodes only.

calls compute_unsats_for_node().

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_changed_nodes(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

compute_unsats_for_node(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, node_index: int) None
Given this BuriedUnsatPenaltyGraph with some number of nodes and the index of a node, update the

internally-stored counts for unsats and oversats based on the edges connected to that node.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_for_node(const unsigned long) –> void

static configure_hbond_options(hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) None

Set up options for hbond detection.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(class core::scoring::hbonds::HBondOptions &) –> void

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.EdgeListConstIterator
returns a const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::const_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.EdgeListConstIterator
returns a const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::const_edge_list_end() const –> class utility::graph::EdgeListConstIterator

copy_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, source: pyrosetta.rosetta.utility.graph.Graph) None
copy the edge connectivity from a source graph with a potentially

unknown type.

C++: utility::graph::Graph::copy_connectivity(const class utility::graph::Graph &) –> void

copy_node_and_connected_edges(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, node_index_in_this_graph: int, other_graph: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, node_index_in_other_graph: int) None
Given an index of a node in this graph, an owning pointer to another graph, and a node index in the other graph, copy the node

from the other graph to the node in this graph, flush the edges that were connected to the node in this graph, and copy those edges from the other graph that can be connected to nodes in this graph.

Note that the logic for determining whether an edge from the other graph can be related to this graph is based on ResidueCOPs.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::copy_node_and_connected_edges(const unsigned long, const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph &, const unsigned long) –> void

delete_edge(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, edge: pyrosetta.rosetta.utility.graph.Edge) None

Needed override from base class.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::delete_edge(class utility::graph::Edge *) –> void

delete_node(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, node: pyrosetta.rosetta.utility.graph.Node) None

Needed override from base class.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::delete_node(class utility::graph::Node *) –> void

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Graph) None

delete all the edges present in the graph

C++: utility::graph::Graph::drop_all_edges() –> void

drop_all_edges_for_node(self: pyrosetta.rosetta.utility.graph.Graph, node: int) None

delete all the edges for a single vertex in the graph

C++: utility::graph::Graph::drop_all_edges_for_node(unsigned long) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.EdgeListIterator
returns a non-const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::edge_list_begin() –> class utility::graph::EdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.EdgeListIterator
returns a non-const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::edge_list_end() –> class utility::graph::EdgeListIterator

find_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) pyrosetta.rosetta.utility.graph.Edge
returns a pointer to the edge connecting nodes node1 and node2, if that edge exists

in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval.

C++: utility::graph::Graph::find_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

focused_edge(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.Edge

returns a pointer to the focused edge

C++: utility::graph::Graph::focused_edge() –> class utility::graph::Edge *

getTotalMemoryUsage(self: pyrosetta.rosetta.utility.graph.Graph) int
returns a count of all the memory used by every vertex and edge in a graph

by invoking the polymorphic count_static_memory and count_dynamic_memory of each (possibly derived) node and edge object as well as for the (possibly derived) graph class.

C++: utility::graph::Graph::getTotalMemoryUsage() const –> unsigned long

get_edge_exists(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) bool

is an edge already present in the graph? O(V) worst case. O(1) iff all vertices have O(1) edges

C++: utility::graph::Graph::get_edge_exists(unsigned long, unsigned long) const –> bool

get_node(self: pyrosetta.rosetta.utility.graph.Graph, index: int) pyrosetta.rosetta.utility.graph.Node

C++: utility::graph::Graph::get_node(unsigned long) –> class utility::graph::Node *

get_node_index(*args, **kwargs)

Overloaded function.

  1. get_node_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, seqpos: int, rotamer_index: int) -> int

Given the sequence position and rotamer index of a residue, get the corresponding node index.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::get_node_index(const unsigned long, const unsigned long) const –> unsigned long

  1. get_node_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, residue: pyrosetta.rosetta.core.conformation.Residue) -> int

Given a const owning pointer to a residue, get the corresponding node index.

Will throw an error if the owning pointer corresponds to no node in this object.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::get_node_index(class std::shared_ptr<const class core::conformation::Residue>) const –> unsigned long

get_self_ptr(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.Graph

C++: utility::graph::Graph::get_self_ptr() –> class std::shared_ptr<class utility::graph::Graph>

has_node_corresponding_to_residue(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, residue: pyrosetta.rosetta.core.conformation.Residue) bool

Given a const owning pointer to a residue, determine whether a corresponding node exists.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::has_node_corresponding_to_residue(class std::shared_ptr<const class core::conformation::Residue>) const –> bool

initialize_graph_for_packing(*args, **kwargs)

Overloaded function.

  1. initialize_graph_for_packing(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, pose: pyrosetta.rosetta.core.pose.Pose, rotamersets: core::pack::rotamer_set::RotamerSets) -> None

  2. initialize_graph_for_packing(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, pose: pyrosetta.rosetta.core.pose.Pose, rotamersets: core::pack::rotamer_set::RotamerSets, only_scoring: bool) -> None

  3. initialize_graph_for_packing(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, pose: pyrosetta.rosetta.core.pose.Pose, rotamersets: core::pack::rotamer_set::RotamerSets, only_scoring: bool, prevent_pruning: bool) -> None

Initialize a BuriedUnsatPenaltyGraph from a pose and a residue set, for packing.

If prevent_pruning is true, then we DISABLE pruning of groups that are not packable and not able to hydrogen bond to packable residues.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(const class core::pose::Pose &, const class core::pack::rotamer_set::RotamerSets &, const bool, const bool) –> void

initialize_graph_for_scoring(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, pose: pyrosetta.rosetta.core.pose.Pose) None

Initialize a BuriedUnsatPenaltyGraph from a pose, for scoring.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_scoring(const class core::pose::Pose &) –> void

nodeindex_to_residue_memory_address(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, nodeindex: int) pyrosetta.rosetta.core.conformation.Residue

Get the memory address of the residue corresponding to a particular node.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::nodeindex_to_residue_memory_address(const unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

num_edges(self: pyrosetta.rosetta.utility.graph.Graph) int

C++: utility::graph::Graph::num_edges() const –> unsigned long

num_nodes(self: pyrosetta.rosetta.utility.graph.Graph) int

the number of nodes in the graph

C++: utility::graph::Graph::num_nodes() const –> unsigned long

output_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) None

send an edge list to the stream os.

C++: utility::graph::Graph::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) None

describe this graph in dimacs form to the stream os.

C++: utility::graph::Graph::output_dimacs(std::ostream &) const –> void

print_vertices(self: pyrosetta.rosetta.utility.graph.Graph) None

send summary information to the screen for all vertices in the graph

C++: utility::graph::Graph::print_vertices() const –> void

provide_pymol_commands_to_show_groups(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None
Provide Pymol commands to colour the pose grey, non-buried donor and acceptor groups cyan, and buried acceptor

and donor groups orange. Useful for debugging degree of burial.

To use, pass in a pose. If this graph contains residues corresponding to those in the pose, commands for colouring them will be written out.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::provide_pymol_commands_to_show_groups(std::ostream &, const class core::pose::Pose &) const –> void

set_always_rotamer_one(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph, setting: bool) None

Set whether this is a graph that just stores one rotamer per position.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::set_always_rotamer_one(const bool) –> void

set_num_nodes(self: pyrosetta.rosetta.utility.graph.Graph, num_nodes: int) None

set the number of nodes in the graph – deletes any existing edges in the graph

C++: utility::graph::Graph::set_num_nodes(unsigned long) –> void

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

A container for the BuriedUnsatPenaltyGraph, to allow it to be cached in a pose while skirting multiple inheritance issues.

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer, : pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphContainer::operator=(const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphContainer &) –> class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphContainer &

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer) pyrosetta.rosetta.basic.datacache.CacheableData

Copy this object and return an owning pointer to the copy.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphContainer::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

graph(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph

Access the graph.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphContainer::graph() –> class std::shared_ptr<class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph>

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond

Bases: pybind11_builtins.pybind11_object

A hydrogen bond between two atoms in two residues. Since this is tied to a BuriedUnsatPenaltyEdge (which in turn is associated with two residues), it stores only donor group index and acceptor group index. The group indices match the indexing in the corresponding node.

A “donor group” can be a single atom or a collection of related atoms (e.g. the pair of NH2 protons in an aspartate side-chain). This allows us to impose a little bit of prior knowledge: sometimes, you’re satisfied if one of the protons in a group is making a hydrogen bond.

acceptor_group(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond) int

Get the index of the Hbond acceptor group in the donor residue.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::acceptor_group() const –> unsigned long

acceptor_symmetry_copy_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond) int

Get the symmetry copy index of the node that’s the acceptor.

Returns 1 in the asymmetric case.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::acceptor_symmetry_copy_index() const –> unsigned long

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond, src: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond

Assignment operator.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::operator=(const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond &) –> class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond &

donor_group(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond) int

Get the index of the Hbond donor group in the donor residue.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::donor_group() const –> unsigned long

donor_symmetry_copy_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond) int

Get the symmetry copy index of the node that’s the donor.

Returns 1 in the asymmetric case.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::donor_symmetry_copy_index() const –> unsigned long

first_node_is_the_acceptor(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond) bool

Is the first node the acceptor?

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::first_node_is_the_acceptor() const –> bool

higher_numbered_node_symmetry_copy_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond) int

Get the symmetry copy index of the higher-numbered node.

Returns 1 in the asymmetric case.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::higher_numbered_node_symmetry_copy_index() const –> unsigned long

lower_numbered_node_symmetry_copy_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond) int

Get the symmetry copy index of the lower-numbered node.

Returns 1 in the asymmetric case.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::lower_numbered_node_symmetry_copy_index() const –> unsigned long

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup

Bases: pybind11_builtins.pybind11_object

A class for a hydrogen bond donor group or acceptor group.

An “acceptor group” is (usually) just an acceptor atom (with the exception noted below). A “donor group” is a donor proton and its parent heavyatom, plus any other protons on that parent.

In rare cases (e.g. a hydroxyl), a group can be both donor and acceptor.

add_proton_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup, index_in: int) None

Add a proton to the list of protons in this group.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::add_proton_index(const unsigned long) –> void

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup, src: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup

Assignment operator.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::operator=(const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup &) –> class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup &

static determine_max_accepted_hbond_count(is_acceptor: bool, heavyatom_index: int, residue: pyrosetta.rosetta.core.conformation.Residue) int

Determine the maximum number of hydrogen bonds that a group can accept, based on the identity of the heavyatom.

Oxygens can accept 2; nitrogens can accept 1. For now, the rule is that simple. At some point, we might look up the information from a database lookup table based on the details of the oxygen type or nitrogen type or whatnot.

Returns 0 if “is_acceptor” is false. This is a static function.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::determine_max_accepted_hbond_count(const bool, const unsigned long, const class core::conformation::Residue &) –> unsigned long

heavyatom_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup) int

Get the atom index in the relevant residue of the heavyatom for this group.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::heavyatom_index() const –> unsigned long

is_acceptor(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup) bool

Is this group an acceptor?

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_acceptor() const –> bool

is_counted(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup) bool

Is this group a group to count (e.g. a buried group)?

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_counted() const –> bool

is_donor(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup) bool

Is this group a donor?

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_donor() const –> bool

max_accepted_hbond_count(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup) int

Get the maximum accepted hydrogen bond count.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_accepted_hbond_count() const –> unsigned long

max_donated_hbond_count(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup) int

Get the maximum donated hydrogen bond count.

Synonym for n_protons().

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_donated_hbond_count() const –> unsigned long

n_protons(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup) int

Get the number of protons in this group.

Synonymous with max_donated_hbond_count().

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::n_protons() const –> unsigned long

proton_indices(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup) pyrosetta.rosetta.utility.vector1_unsigned_long

Get the vector of atom indices in the relevant residue of the protons attached to the heavyatom.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::proton_indices() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

set_counted(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup, setting: bool) None

Set whether this is a group to count.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::set_counted(const bool) –> void

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions

Bases: pybind11_builtins.pybind11_object

Options container for the BuriedUnsatPenaltyGraph. Initialized by the BuriedUnsatPenalty energy method.

angle_exponent(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions) float

Get the angle exponent, for determining burial by the method of sidechain neighbor cones.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::angle_exponent() const –> double

angle_shift_factor(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions) float

Get the angle shift factor, for determining burial by the method of sidechain neighbor cones.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::angle_shift_factor() const –> double

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions, : pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::operator=(const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions &) –> class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions &

burial_threshold(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions) float
Get the minimum number of cones that a point must fall within, for determining burial by the

method of sidechain neighbor cones.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::burial_threshold() const –> double

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions

Clone method: return a copy of the original object, by owning pointer.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::clone() const –> class std::shared_ptr<class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions>

dist_exponent(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions) float

Get the distance exponent, for determining burial by the method of sidechain neighbor cones.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::dist_exponent() const –> double

dist_midpoint(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions) float

Get the distance midpoint, for determining burial by the method of sidechain neighbor cones.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::dist_midpoint() const –> double

hbond_energy_threshold(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions) float

Get the maximum hydrogen bond energy allowed, above which a hydrogen bond is not counted.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::hbond_energy_threshold() const –> double

show(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions, out: pyrosetta.rosetta.std.ostream) None

Print information about this object.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode

Bases: pyrosetta.rosetta.utility.graph.Node

Each BuriedUnsatPenaltyNode represents a rotamer from the RotamerSets object, or a residue (if we’re doing a simple scoring pass).

Internally, this stores a list of hydrogen bond donor and acceptor atoms that must be satisfied.

add_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_ptr: utility::graph::Edge, : pyrosetta.rosetta.utility.graph.EdgeListIterator) None
adds edge pointer to edge list; returns an iterator to the new

list element

C++: utility::graph::Node::add_edge(class utility::graph::Edge *, class utility::graph::EdgeListIterator &) –> void

clear_hbond_counts(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode) None

For every donor/acceptor group, reset the counts of hydrogen bonds to/from that group.

The donated_hbond_count_ and accepted_hbond_count_ vars are initialized to the intra-residue donated and intra-residue accepted counts, respectively (i.e. inter-residue donated and inter-residue accepted counts have not yet been added in).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::clear_hbond_counts() –> void

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of its edge list

C++: utility::graph::Node::const_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of its edge list

C++: utility::graph::Node::const_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_end() const –> class utility::graph::EdgeListConstIterator

copy_from(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode, other_node: pyrosetta.rosetta.utility.graph.Node) None

Given another node, set this node to copy that one.

Note: this does NOT copy the rotamer index, but instead sets it to 1. The donated_hbond_count_ and accepted_hbond_count_ vars are initialized to the intra-residue donated and intra-residue accepted counts, respectively (i.e. inter-residue donated and inter-residue accepted counts have not yet been added in).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::copy_from(const class utility::graph::Node *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.utility.graph.Node) int

memory accounting scheme

C++: utility::graph::Node::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.utility.graph.Node) int

memory accounting scheme

C++: utility::graph::Node::count_static_memory() const –> unsigned long

decrement_counts(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode, unsat_acceptor_count: int, unsat_donor_count: int, unsat_acceptor_and_donor_count: int, oversat_acceptor_count: int, oversat_donor_count: int, oversat_acceptor_and_donor_count: int, data: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) None

After hydrogen bonds from edges have been counted, report the number of donor/acceptor groups in each of several categories.

The integer instances passed in are DECREMENTED appropriately by this function. (So if there is an incoming count of 5 unsaturated acceptors, and the current node accounts for 3 unsaturated acceptors, the unsat_acceptor_count will drop to 2).

The number of acceptor (and not donor) groups that are unsatisfied.

The number of donor (and not acceptor) groups that are unsatisfied.

The number of groups that are both donors and acceptors (e.g. hydroxyls) that are unsatisfied (i.e. lack either a donated hbond or an accepted hbond).

The number of acceptor (and not donor) groups that are oversatisfied.

The number of donor (and not acceptor) groups that are oversatisfied. (This generally doesn’t happen).

The number of groups that are both donors and acceptors (e.g. hydroxyls) that are unsatisfied (i.e. have either too many donated hbonds or too many accepted hbonds).

The BuriedUnsatPenaltyNodeData to use. Since this has often been replaced by the time this function is called, we need to pass it in separately.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::decrement_counts(unsigned long &, unsigned long &, unsigned long &, unsigned long &, unsigned long &, unsigned long &, class std::shared_ptr<const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData>) const –> void

donor_acceptor_group(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode, donor_acceptor_group_index: int) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup

Get a donor or acceptor group, by donor or acceptor group index.

This version provides const access.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::donor_acceptor_group(const unsigned long) const –> const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup &

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Node) None

deletes all edges incident upon this node

C++: utility::graph::Node::drop_all_edges() –> void

drop_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) None

removes an edge iterator from the node’s edge list. Only called by Edge class.

C++: utility::graph::Node::drop_edge(class utility::graph::EdgeListIterator) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of its edge list

C++: utility::graph::Node::edge_list_begin() –> class utility::graph::EdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of its edge list

C++: utility::graph::Node::edge_list_end() –> class utility::graph::EdgeListIterator

find_edge(self: pyrosetta.rosetta.utility.graph.Node, other_node_index: int) utility::graph::Edge

C++: utility::graph::Node::find_edge(unsigned long) –> class utility::graph::Edge *

get_donor_acceptor_group_from_heavyatom_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode, heavyatom_index: int) int

Given the index of a donor or acceptor heavyatom, get the donor/acceptor group index.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::get_donor_acceptor_group_from_heavyatom_index(const unsigned long) const –> unsigned long

get_node_index(self: pyrosetta.rosetta.utility.graph.Node) int

the index for this node

C++: utility::graph::Node::get_node_index() const –> unsigned long

get_num_edges_to_larger_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) int
the number of upper neighbors – which “self” neighborness is counted if a loop edge

is present

C++: utility::graph::Node::get_num_edges_to_larger_indexed_nodes() const –> unsigned long

get_num_edges_to_smaller_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) int

the number of lower neighbors

C++: utility::graph::Node::get_num_edges_to_smaller_indexed_nodes() const –> unsigned long

increment_accepted_hbond_count_for_group(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode, group_index: int) None

Add one to the number of accepted hydrogen bonds for the Nth donor/acceptor group in this node.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_accepted_hbond_count_for_group(const unsigned long) –> void

increment_counts(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode, unsat_acceptor_count: int, unsat_donor_count: int, unsat_acceptor_and_donor_count: int, oversat_acceptor_count: int, oversat_donor_count: int, oversat_acceptor_and_donor_count: int) None

After hydrogen bonds from edges have been counted, report the number of donor/acceptor groups in each of several categories.

The integer instances passed in are incremented appropriately by this function. (So if there is an incoming count of 5 unsaturated acceptors, and the current node has 3 more, the unsat_acceptor_count will end up being 8).

The number of acceptor (and not donor) groups that are unsatisfied.

The number of donor (and not acceptor) groups that are unsatisfied.

The number of groups that are both donors and acceptors (e.g. hydroxyls) that are unsatisfied (i.e. lack either a donated hbond or an accepted hbond).

The number of acceptor (and not donor) groups that are oversatisfied.

The number of donor (and not acceptor) groups that are oversatisfied. (This generally doesn’t happen).

The number of groups that are both donors and acceptors (e.g. hydroxyls) that are unsatisfied (i.e. have either too many donated hbonds or too many accepted hbonds).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_counts(unsigned long &, unsigned long &, unsigned long &, unsigned long &, unsigned long &, unsigned long &) const –> void

increment_donated_hbond_count_for_group(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode, group_index: int) None

Add one to the number of donated hydrogen bonds for the Nth donor/acceptor group in this node.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_donated_hbond_count_for_group(const unsigned long) –> void

initialize_node(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode, residue_position: int, rotamer_index: int, residue: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, options: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions, hbond_options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbond_database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, is_symmetric: bool) None

Initialize this node, setting its residue_position, rotamer_index,

The options owning pointer is stored directly; the options are not cloned.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::initialize_node(const unsigned long, const unsigned long, class std::shared_ptr<const class core::conformation::Residue>, const class core::pose::Pose &, class std::shared_ptr<const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions>, class std::shared_ptr<const class core::scoring::hbonds::HBondOptions>, const class core::scoring::hbonds::HBondDatabase &, const bool) –> void

loop_incident(self: pyrosetta.rosetta.utility.graph.Node) bool

NOTE TO SELF: remove loop support

C++: utility::graph::Node::loop_incident() const –> bool

lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::lower_edge_list_begin() –> class utility::graph::EdgeListIterator

lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of its lower-edge list

C++: utility::graph::Node::lower_edge_list_end() –> class utility::graph::EdgeListIterator

num_donor_acceptor_groups(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode) int

Get the number of donor/acceptor groups.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::num_donor_acceptor_groups() const –> unsigned long

num_edges(self: pyrosetta.rosetta.utility.graph.Node) int

the number of edges incident on this node, which may include a loop edge

C++: utility::graph::Node::num_edges() const –> unsigned long

num_neighbors_counting_self(self: pyrosetta.rosetta.utility.graph.Node) int

the number of neighbors counting “self” as a neighbor.

C++: utility::graph::Node::num_neighbors_counting_self() const –> unsigned long

num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node) int
the number of neighbors counting “self” as neighbor. Defaults to

num_neighbors_counting_self() but can be set to other values as well. Useful in calculation of symmetrical structures.

C++: utility::graph::Node::num_neighbors_counting_self_static() const –> unsigned long

print(self: pyrosetta.rosetta.utility.graph.Node) None

send summaray data about this node to the screen

C++: utility::graph::Node::print() const –> void

prune_donor_acceptor_groups_lacking_hbonds_to_packable(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode, rotsets: core::pack::rotamer_set::RotamerSets) None
Iterate through each donor and acceptor group in this node, and set to “do not count” if the group forms no hydrogen bonds to any packable

residue’s groups.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::prune_donor_acceptor_groups_lacking_hbonds_to_packable(const class core::pack::rotamer_set::RotamerSets &) –> void

residue_position(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode) int

Get the residue index (position in the pose) for this node.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::residue_position() const –> unsigned long

rotamer_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode) int

Get the rotamer index for this node.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::rotamer_index() const –> unsigned long

set_num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node, neighbor: int) None
manually change the number of neighbors for a Node. Used

for symmetry scoring

C++: utility::graph::Node::set_num_neighbors_counting_self_static(unsigned long) –> void

stored_data(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData

Const access to the stored data.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::stored_data() const –> class std::shared_ptr<const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData>

upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::upper_edge_list_begin() –> class utility::graph::EdgeListIterator

upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of its upper-edge list

C++: utility::graph::Node::upper_edge_list_end() –> class utility::graph::EdgeListIterator

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData

Bases: pybind11_builtins.pybind11_object

Data stored inside a BuriedUnsatPenaltyNode.

This is a separate class so that nodes can rapidly be “copied”, just by changing the stored pointer to the data object.

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData, : pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::operator=(const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData &) –> class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData &

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData

Create a copy by owning pointer and return the owning pointer to the copy.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::clone() const –> class std::shared_ptr<class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData>

donor_acceptor_groups(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup

Non-const access to the donor/acceptor groups.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::donor_acceptor_groups() –> class utility::vector1<class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup, class std::allocator<class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup> > &

donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_accepted(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) pyrosetta.rosetta.utility.vector1_unsigned_long

Access the donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_accepted_ vector (non-const).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_accepted() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_donated(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) pyrosetta.rosetta.utility.vector1_unsigned_long

Access the donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_donated_ vector (non-const).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_donated() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

donor_acceptor_groups_intrares_hbonds_accepted(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) pyrosetta.rosetta.utility.vector1_unsigned_long

Access the donor_acceptor_groups_intrares_hbonds_accepted_ vector (non-const).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::donor_acceptor_groups_intrares_hbonds_accepted() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

donor_acceptor_groups_intrares_hbonds_donated(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) pyrosetta.rosetta.utility.vector1_unsigned_long

Access the donor_acceptor_groups_intrares_hbonds_donated_ vector (non-const).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::donor_acceptor_groups_intrares_hbonds_donated() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

group_heavyatom_index_to_group_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) pyrosetta.rosetta.std.map_unsigned_long_unsigned_long

Access the group_heavyatom_index_to_group_index_ map (non-const).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::group_heavyatom_index_to_group_index() –> class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &

hbond_options(*args, **kwargs)

Overloaded function.

  1. hbond_options(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData, options_in: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> None

Set the hbonds options pointer.

This copies the input pointer; it doesn’t clone the object.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::hbond_options(class std::shared_ptr<const class core::scoring::hbonds::HBondOptions>) –> void

  1. hbond_options(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) -> pyrosetta.rosetta.core.scoring.hbonds.HBondOptions

Get the options.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::hbond_options() const –> class std::shared_ptr<const class core::scoring::hbonds::HBondOptions>

options(*args, **kwargs)

Overloaded function.

  1. options(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData, options_in: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions) -> None

Set the options pointer.

This copies the input pointer; it doesn’t clone the object.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::options(class std::shared_ptr<const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions>) –> void

  1. options(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) -> core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions

Get the options.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::options() const –> class std::shared_ptr<const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions>

residue_position(*args, **kwargs)

Overloaded function.

  1. residue_position(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData, setting: int) -> None

Set the residue position.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::residue_position(const unsigned long &) –> void

  1. residue_position(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) -> int

Get the residue position.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::residue_position() const –> unsigned long

rotamer_index(*args, **kwargs)

Overloaded function.

  1. rotamer_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData, setting: int) -> None

Set the residue position.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::rotamer_index(const unsigned long &) –> void

  1. rotamer_index(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData) -> int

Get the residue position.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData::rotamer_index() const –> unsigned long