hbonds

Bindings for core::pack::hbonds namespace

pyrosetta.rosetta.core.pack.hbonds.create_and_init_atom_level_hbond_graph(rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph

This combines the AtomLevelHBondGraph constructor and init_node_info(). The AtomLevelHBondGraph constructor can not take core.4 objects because it is in core.3 (as of the time this was written).

C++: core::pack::hbonds::create_and_init_atom_level_hbond_graph(const class core::pack::rotamer_set::RotamerSets &) –> class std::shared_ptr<class core::scoring::hbonds::graph::AtomLevelHBondGraph>

pyrosetta.rosetta.core.pack.hbonds.create_init_and_create_edges_for_atom_level_hbond_graph(rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, hydrogen_bond_threshold: float, clash_threshold: float) → pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph

Construct atom level hbond graph, initialize the node information, score rotamers to create hbonds. This will not work perfectly if you are using symmetry because it does not score one-body interactions, but can still provide a good template

C++: core::pack::hbonds::create_init_and_create_edges_for_atom_level_hbond_graph(class std::shared_ptr<class core::pack::rotamer_set::RotamerSets>, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, double, double) –> class std::shared_ptr<class core::scoring::hbonds::graph::AtomLevelHBondGraph>

pyrosetta.rosetta.core.pack.hbonds.delete_edges_with_degree_zero(hb_graph: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph) → None

If you only care about hbond networks, then you might not care about edges that have no incident edges. This function deletes those edges.

C++: core::pack::hbonds::delete_edges_with_degree_zero(class core::scoring::hbonds::graph::AtomLevelHBondGraph &) –> void

pyrosetta.rosetta.core.pack.hbonds.determine_atom_level_edge_info(*args, **kwargs)

Overloaded function.

1. determine_atom_level_edge_info(hb_edge: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, database: core::scoring::hbonds::HBondDatabase, tenA_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. determine_atom_level_edge_info(hb_edge: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, database: core::scoring::hbonds::HBondDatabase, tenA_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, pose: pyrosetta.rosetta.core.pose.Pose, hbond_energy_threshold_for_satisfaction: float) -> None
3. determine_atom_level_edge_info(hb_edge: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, database: core::scoring::hbonds::HBondDatabase, tenA_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, pose: pyrosetta.rosetta.core.pose.Pose, hbond_energy_threshold_for_satisfaction: float, symm_info: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> None

Add information regarding the atoms participating in hbonds (see find_hbonds_in_residue_pair() ). symm_info needs to be != 0 if and only if you want to evaluate symmetry.

C++: core::pack::hbonds::determine_atom_level_edge_info(class core::scoring::hbonds::graph::AtomLevelHBondEdge &, const class core::pack::rotamer_set::RotamerSets &, const class core::scoring::hbonds::HBondDatabase &, const class utility::graph::Graph &, const class core::pose::Pose &, double, class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>) –> void

pyrosetta.rosetta.core.pack.hbonds.determine_atom_level_edge_info_for_all_edges(*args, **kwargs)

Overloaded function.

1. determine_atom_level_edge_info_for_all_edges(hb_graph: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, database: core::scoring::hbonds::HBondDatabase, tenA_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. determine_atom_level_edge_info_for_all_edges(hb_graph: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, database: core::scoring::hbonds::HBondDatabase, tenA_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, pose: pyrosetta.rosetta.core.pose.Pose, skip_edges_with_degree_zero: bool) -> None
3. determine_atom_level_edge_info_for_all_edges(hb_graph: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, database: core::scoring::hbonds::HBondDatabase, tenA_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, pose: pyrosetta.rosetta.core.pose.Pose, skip_edges_with_degree_zero: bool, hbond_energy_threshold_for_satisfaction: float) -> None
4. determine_atom_level_edge_info_for_all_edges(hb_graph: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, database: core::scoring::hbonds::HBondDatabase, tenA_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, pose: pyrosetta.rosetta.core.pose.Pose, skip_edges_with_degree_zero: bool, hbond_energy_threshold_for_satisfaction: float, symm_info: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> None

Iterate through edges and calls determine_atom_level_edge_info(). skip_edges_with_degree_zero does not evaluate edges that have no incident edges and can not be part of a hydrogen bond network. symm_info needs to be != 0 if and only if you want to evaluate symmetry.

C++: core::pack::hbonds::determine_atom_level_edge_info_for_all_edges(class core::scoring::hbonds::graph::AtomLevelHBondGraph &, const class core::pack::rotamer_set::RotamerSets &, const class core::scoring::hbonds::HBondDatabase &, const class utility::graph::Graph &, const class core::pose::Pose &, bool, double, class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>) –> void

pyrosetta.rosetta.core.pack.hbonds.determine_atom_level_node_info(node: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, include_these_resids: pyrosetta.rosetta.utility.vector1_bool) → None

Store atom information for every node with a corresponding resid set to true in include_these_resids. include_these_resids was originally meant to protray “resid_is_buried” so that we only store atom info for buried residues. I don’t care what you use this for so I gave it a more generalized name.

C++: core::pack::hbonds::determine_atom_level_node_info(class core::scoring::hbonds::graph::AtomLevelHBondNode &, const class core::pack::rotamer_set::RotamerSets &, const class utility::vector1<bool, class std::allocator<bool> > &) –> void

pyrosetta.rosetta.core.pack.hbonds.determine_atom_level_node_info_for_all_nodes(*args, **kwargs)

Overloaded function.

1. determine_atom_level_node_info_for_all_nodes(hb_graph: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, include_these_resids: pyrosetta.rosetta.utility.vector1_bool) -> None
2. determine_atom_level_node_info_for_all_nodes(hb_graph: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, include_these_resids: pyrosetta.rosetta.utility.vector1_bool, skip_nodes_with_no_edges: bool) -> None

Calls determine_atom_level_node_info() for all nodes. skip_nodes_with_no_edges is recommended to be set to true but depends on your protocol. The default is false for safety purposes.

C++: core::pack::hbonds::determine_atom_level_node_info_for_all_nodes(class core::scoring::hbonds::graph::AtomLevelHBondGraph &, const class core::pack::rotamer_set::RotamerSets &, const class utility::vector1<bool, class std::allocator<bool> > &, bool) –> void

pyrosetta.rosetta.core.pack.hbonds.find_hbonds_in_residue_pair(resA: pyrosetta.rosetta.core.conformation.Residue, resB: pyrosetta.rosetta.core.conformation.Residue, database: core::scoring::hbonds::HBondDatabase, tenA_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, set: core::scoring::hbonds::HBondSet) → None

Utility function used by other functions in this file. Given that an edge exists between two nodes, find all of the hbonds between those two residues. It does not matter which order resA and resB are. Output hbonds are put in the HBondSet provided. This should not be called before the graph is populated with edges (see MCHBNetInteractionGraph) - nothing will crash if this is called with no edges but it just does not make sense.

C++: core::pack::hbonds::find_hbonds_in_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::hbonds::HBondDatabase &, const class utility::graph::Graph &, class core::scoring::hbonds::HBondSet &) –> void

pyrosetta.rosetta.core.pack.hbonds.find_satisfying_interactions_with_background(*args, **kwargs)

Overloaded function.

1. find_satisfying_interactions_with_background(node: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, poly_ala_pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. find_satisfying_interactions_with_background(node: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, poly_ala_pose: pyrosetta.rosetta.core.pose.Pose, hbond_energy_threshold_for_satisfaction: float) -> None

CALL determine_atom_level_node_info() OR determine_atom_level_node_info_for_all_nodes() BEFORE CALLING THIS! After adding atom info to nodes, calling this function will result in removing atom info for atoms that hydrogen bond with the backbone or fixed sidechains.

C++: core::pack::hbonds::find_satisfying_interactions_with_background(class core::scoring::hbonds::graph::AtomLevelHBondNode &, const class core::pack::rotamer_set::RotamerSets &, const class utility::graph::Graph &, const class core::pose::Pose &, double) –> void

pyrosetta.rosetta.core.pack.hbonds.init_node_info(graph: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondGraph, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → None

This should be called immediately after creating the graph (and setting the number of nodes if need-be). This adds rotamer_sets info to the nodes for easier lookup later. Technically optional but recommended

C++: core::pack::hbonds::init_node_info(class core::scoring::hbonds::graph::AtomLevelHBondGraph &, const class core::pack::rotamer_set::RotamerSets &) –> void