hbnet

Bindings for protocols::hbnet namespace

class pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

sets allowed residue types to constrain HBNet residues in downstream design; add this Taskop to any design movers downstream of HBNet

apply(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::hbnet::ConstrainHBondNetwork::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork, : pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork) → pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork

C++: protocols::hbnet::ConstrainHBondNetwork::operator=(const class protocols::hbnet::ConstrainHBondNetwork &) –> class protocols::hbnet::ConstrainHBondNetwork &

clone(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::hbnet::ConstrainHBondNetwork::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname() → str

C++: protocols::hbnet::ConstrainHBondNetwork::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::hbnet::ConstrainHBondNetwork::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::hbnet::ConstrainHBondNetwork::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.hbnet.HBondNetStruct

Bases: pybind11_builtins.pybind11_object

struct that contains info needed for hbond networks

assign(self: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, : pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → pyrosetta.rosetta.protocols.hbnet.HBondNetStruct

C++: protocols::hbnet::HBondNetStruct::operator=(const struct protocols::hbnet::HBondNetStruct &) –> struct protocols::hbnet::HBondNetStruct &

class pyrosetta.rosetta.protocols.hbnet.HBondResStruct

Bases: pybind11_builtins.pybind11_object

struct that represents minimal info for residue in an h-bond network

assign(self: pyrosetta.rosetta.protocols.hbnet.HBondResStruct, : pyrosetta.rosetta.protocols.hbnet.HBondResStruct) → pyrosetta.rosetta.protocols.hbnet.HBondResStruct

C++: protocols::hbnet::HBondResStruct::operator=(const struct protocols::hbnet::HBondResStruct &) –> struct protocols::hbnet::HBondResStruct &

pyrosetta.rosetta.protocols.hbnet.add_reslabels_to_pose(*args, **kwargs)

Overloaded function.

  1. add_reslabels_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> None
  2. add_reslabels_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, label: str) -> None

C++: protocols::hbnet::add_reslabels_to_pose(class core::pose::Pose &, struct protocols::hbnet::HBondNetStruct &, class std::basic_string<char>) –> void

class pyrosetta.rosetta.protocols.hbnet.compare_by_x

Bases: pybind11_builtins.pybind11_object

pyrosetta.rosetta.protocols.hbnet.contains(atom_vec: pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_AtomInfo, local_atom_id: int) → bool

C++: protocols::hbnet::contains(const class utility::vector1<class core::scoring::hbonds::graph::AtomInfo, class std::allocator<class core::scoring::hbonds::graph::AtomInfo> > &, const unsigned short) –> bool

pyrosetta.rosetta.protocols.hbnet.edge_satisfies_heavy_unsat_for_node(current_state: pyrosetta.rosetta.protocols.hbnet.NetworkState, node: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode, edge: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge) → bool

C++: protocols::hbnet::edge_satisfies_heavy_unsat_for_node(const class protocols::hbnet::NetworkState &, const class core::scoring::hbonds::graph::AtomLevelHBondNode *, const class core::scoring::hbonds::graph::AtomLevelHBondEdge *) –> bool

pyrosetta.rosetta.protocols.hbnet.find_HBondResStruct(residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t, resnum: int) → __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::hbnet::HBondResStruct const> const*, std::vector<std::shared_ptr<protocols::hbnet::HBondResStruct const>, std::allocator<std::shared_ptr<protocols::hbnet::HBondResStruct const> > > >

C++: protocols::hbnet::find_HBondResStruct(const class utility::vector1<class std::shared_ptr<const struct protocols::hbnet::HBondResStruct>, class std::allocator<class std::shared_ptr<const struct protocols::hbnet::HBondResStruct> > > &, unsigned long) –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<const struct protocols::hbnet::HBondResStruct> *, class std::vector<class std::shared_ptr<const struct protocols::hbnet::HBondResStruct>, class std::allocator<class std::shared_ptr<const struct protocols::hbnet::HBondResStruct> > > >

pyrosetta.rosetta.protocols.hbnet.get_hbond_atom_pairs(*args, **kwargs)

Overloaded function.

  1. get_hbond_atom_pairs(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, pose: pyrosetta.rosetta.core.pose.Pose) -> None
  2. get_hbond_atom_pairs(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, pose: pyrosetta.rosetta.core.pose.Pose, bb_exlcusion: bool) -> None

C++: protocols::hbnet::get_hbond_atom_pairs(struct protocols::hbnet::HBondNetStruct &, class core::pose::Pose &, bool) –> void

pyrosetta.rosetta.protocols.hbnet.get_num_edges_for_res(res: int, path_dists: ObjexxFCL::FArray2D<int>) → int

C++: protocols::hbnet::get_num_edges_for_res(const unsigned long, class ObjexxFCL::FArray2D<int> &) –> unsigned long

pyrosetta.rosetta.protocols.hbnet.get_num_protein_sc_sc_hbonds(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → int

C++: protocols::hbnet::get_num_protein_sc_sc_hbonds(class core::pose::Pose &, struct protocols::hbnet::HBondNetStruct &) –> unsigned long

pyrosetta.rosetta.protocols.hbnet.hbnet_one_body_energies(pose: pyrosetta.rosetta.core.pose.Pose, rotset_op: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) → None

C++: protocols::hbnet::hbnet_one_body_energies(const class core::pose::Pose &, class core::pack::rotamer_set::RotamerSet &, const class core::scoring::ScoreFunction &, class utility::vector1<float, class std::allocator<float> > &) –> void

pyrosetta.rosetta.protocols.hbnet.hbnet_symm_one_body_energies(pose: pyrosetta.rosetta.core.pose.Pose, rotset_op: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float) → None

C++: protocols::hbnet::hbnet_symm_one_body_energies(const class core::pose::Pose &, class core::pack::rotamer_set::RotamerSet &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, const class utility::graph::Graph &, class utility::vector1<float, class std::allocator<float> > &) –> void

pyrosetta.rosetta.protocols.hbnet.hbond_exists_in_vector(hbond_vec: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t, h2: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

C++: protocols::hbnet::hbond_exists_in_vector(const class utility::vector1<class std::shared_ptr<const class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<const class core::scoring::hbonds::HBond> > > &, class std::shared_ptr<const class core::scoring::hbonds::HBond> &) –> bool

pyrosetta.rosetta.protocols.hbnet.his_tyr_connectivity(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool

C++: protocols::hbnet::his_tyr_connectivity(const class core::pose::Pose &, struct protocols::hbnet::HBondNetStruct &) –> bool

pyrosetta.rosetta.protocols.hbnet.network_contains_aa(*args, **kwargs)

Overloaded function.

  1. network_contains_aa(aa_one_letter: str, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> bool

C++: protocols::hbnet::network_contains_aa(char, const struct protocols::hbnet::HBondNetStruct &) –> bool

  1. network_contains_aa(aa_one_letter: str, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t) -> bool

C++: protocols::hbnet::network_contains_aa(char, const class utility::vector1<class std::shared_ptr<const struct protocols::hbnet::HBondResStruct>, class std::allocator<class std::shared_ptr<const struct protocols::hbnet::HBondResStruct> > > &) –> bool

pyrosetta.rosetta.protocols.hbnet.print_headers() → str

C++: protocols::hbnet::print_headers() –> std::string

pyrosetta.rosetta.protocols.hbnet.print_list_to_string(*args, **kwargs)

Overloaded function.

  1. print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> str
  2. print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool) -> str
  3. print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool) -> str
  4. print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool, term_w_cycle: bool) -> str
  5. print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool, term_w_cycle: bool, term_w_bb: bool) -> str

C++: protocols::hbnet::print_list_to_string(const struct protocols::hbnet::HBondNetStruct &, bool, bool, bool, bool) –> std::string

  1. print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> str
  2. print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool) -> str
  3. print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool) -> str
  4. print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool, term_w_cycle: bool) -> str
  5. print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool, term_w_cycle: bool, term_w_bb: bool) -> str
  6. print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool, term_w_cycle: bool, term_w_bb: bool, use_pdb_numbering: bool) -> str

C++: protocols::hbnet::print_list_to_string(const class core::pose::Pose &, const struct protocols::hbnet::HBondNetStruct &, bool, bool, bool, bool, bool) –> std::string

pyrosetta.rosetta.protocols.hbnet.print_network(*args, **kwargs)

Overloaded function.

  1. print_network(i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> str
  2. print_network(i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool) -> str

C++: protocols::hbnet::print_network(const struct protocols::hbnet::HBondNetStruct &, bool) –> std::string

pyrosetta.rosetta.protocols.hbnet.print_network_w_pdb_numbering(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool) → str

C++: protocols::hbnet::print_network_w_pdb_numbering(const class core::pose::Pose &, const struct protocols::hbnet::HBondNetStruct &, bool) –> std::string