hbnet¶

Bindings for protocols::hbnet namespace

class pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork¶

Bases: 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>

static 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_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::hbnet::ConstrainHBondNetwork::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator, : pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator) → pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator¶: C++: protocols::hbnet::ConstrainHBondNetworkCreator::operator=(const class protocols::hbnet::ConstrainHBondNetworkCreator &) –> class protocols::hbnet::ConstrainHBondNetworkCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::hbnet::ConstrainHBondNetworkCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator) → str¶: C++: protocols::hbnet::ConstrainHBondNetworkCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::hbnet::ConstrainHBondNetworkCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool¶

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.protocols.hbnet.DecoratedNetworkState¶

Bases: pybind11_object

property n_unsat_Hpols¶

property saturation¶

class pyrosetta.rosetta.protocols.hbnet.HBNet¶

Bases: Mover

add_start_res(self: pyrosetta.rosetta.protocols.hbnet.HBNet, res: int) → None¶: C++: protocols::hbnet::HBNet::add_start_res(unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

atom_hbonds_to_bridging_water(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, at_id: pyrosetta.rosetta.core.id.AtomID) → bool¶: C++: protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(const class core::pose::Pose &, const class core::id::AtomID) –> bool

static attributes_for_hbnet(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::hbnet::HBNet::attributes_for_hbnet(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::hbnet::HBNet::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

find_native(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::find_native() –> bool

find_unsats(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → None¶: C++: protocols::hbnet::HBNet::find_unsats(const class core::pose::Pose &, struct protocols::hbnet::HBondNetStruct &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::hbnet::HBNet::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_aa_for_state(self: pyrosetta.rosetta.protocols.hbnet.HBNet, res: int, rot: int) → str¶: C++: protocols::hbnet::HBNet::get_aa_for_state(const unsigned long, const unsigned long) const –> char

get_additional_output(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.pose.Pose¶

used by the job distributor and MultiplePoseMover (MPM) to return poses OTF as requested (without need to store in memory)

C++: protocols::hbnet::HBNet::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_ala_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::hbnet::HBNet::get_ala_pose() –> const class core::pose::Pose &

get_boundary_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.utility.vector1_bool¶: C++: protocols::hbnet::HBNet::get_boundary_residues() –> class utility::vector1<bool, class std::allocator<bool> >

get_boundary_selector(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: protocols::hbnet::HBNet::get_boundary_selector() –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_core_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.utility.vector1_bool¶: C++: protocols::hbnet::HBNet::get_core_residues() –> class utility::vector1<bool, class std::allocator<bool> >

get_core_selector(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: protocols::hbnet::HBNet::get_core_selector() –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_extend_existing_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::get_extend_existing_networks() –> bool

get_file_name(self: pyrosetta.rosetta.protocols.hbnet.HBNet, id: int, prefix: str, extension: str) → str¶: C++: protocols::hbnet::HBNet::get_file_name(unsigned long, std::string, std::string) –> std::string

get_ind_res(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, res_i: int) → int¶: C++: protocols::hbnet::HBNet::get_ind_res(const class core::pose::Pose &, const unsigned long) –> unsigned long

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_keep_existing_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::get_keep_existing_networks() –> bool

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_max_networks_size(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → int¶: C++: protocols::hbnet::HBNet::get_max_networks_size() –> unsigned long

get_max_unsat(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → int¶: C++: protocols::hbnet::HBNet::get_max_unsat() –> unsigned long

get_min_networks_size(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → int¶: C++: protocols::hbnet::HBNet::get_min_networks_size() –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → str¶: C++: protocols::hbnet::HBNet::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_native_vec(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t¶: C++: protocols::hbnet::HBNet::get_native_vec() –> class std::vector<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct>, class std::allocator<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct> > > &

get_net_vec(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t¶

return all hbond networks, sorted with best networks at the front, THIS SHOULD RETURN A POINTER (OP)

C++: protocols::hbnet::HBNet::get_net_vec() –> class std::vector<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct>, class std::allocator<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct> > > &

get_network_by_id(self: pyrosetta.rosetta.protocols.hbnet.HBNet, id: int) → pyrosetta.rosetta.protocols.hbnet.HBondNetStruct¶: C++: protocols::hbnet::HBNet::get_network_by_id(unsigned long) –> class std::shared_ptr<struct protocols::hbnet::HBondNetStruct>

get_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t¶: C++: protocols::hbnet::HBNet::get_networks() –> class std::vector<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct>, class std::allocator<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct> > >

get_num_native_rot(*args, **kwargs)¶

Overloaded function.

get_num_native_rot(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t) -> int
get_num_native_rot(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t, sc_rmsd_cut: float) -> int
get_num_native_rot(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t, sc_rmsd_cut: float, super: bool) -> int

return the number of rotamers in a network that are identical in seq or rot to the original input pose:

C++: protocols::hbnet::HBNet::get_num_native_rot(class core::pose::Pose &, 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> > > &, double, bool) –> unsigned long

get_num_native_seq(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t) → int¶: C++: protocols::hbnet::HBNet::get_num_native_seq(class core::pose::Pose &, 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

get_only_extend_existing(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::get_only_extend_existing() –> bool

get_orig_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::hbnet::HBNet::get_orig_pose() –> const class core::pose::Pose &

get_output_vector(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.vector_std_set_unsigned_long_t¶: C++: protocols::hbnet::HBNet::get_output_vector() –> class std::vector<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::allocator<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > > > &

get_packer_graph(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.utility.graph.Graph¶: C++: protocols::hbnet::HBNet::get_packer_graph() –> class std::shared_ptr<class utility::graph::Graph>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_start_res_vec(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::hbnet::HBNet::get_start_res_vec() –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

get_symm_info(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo¶: C++: protocols::hbnet::HBNet::get_symm_info() const –> class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>

get_task(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.pack.task.PackerTask¶: C++: protocols::hbnet::HBNet::get_task() const –> class std::shared_ptr<class core::pack::task::PackerTask>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

ligand(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → int¶: C++: protocols::hbnet::HBNet::ligand() –> unsigned long

static mover_name() → str¶: C++: protocols::hbnet::HBNet::mover_name() –> std::string

multi_component(*args, **kwargs)¶

Overloaded function.

multi_component(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> bool

C++: protocols::hbnet::HBNet::multi_component() const –> bool

multi_component(self: pyrosetta.rosetta.protocols.hbnet.HBNet, multi_component: bool) -> None

C++: protocols::hbnet::HBNet::multi_component(const bool) –> void

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

net_clash(self: pyrosetta.rosetta.protocols.hbnet.HBNet, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, j: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶

checks if two h-bond networks clash; returns true if they do clash

C++: protocols::hbnet::HBNet::net_clash(const struct protocols::hbnet::HBondNetStruct &, const struct protocols::hbnet::HBondNetStruct &) –> bool

network_meets_final_criteria(self: pyrosetta.rosetta.protocols.hbnet.HBNet, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶

final criteria that reuqires network rotamers placed on pose

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

network_meets_initial_criteria(self: pyrosetta.rosetta.protocols.hbnet.HBNet, : pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶

initial criteria for screening that just reuqires HBondNetStruct (no scoring or placement of rotamers on the pose)

C++: protocols::hbnet::HBNet::network_meets_initial_criteria(const struct protocols::hbnet::HBondNetStruct &) –> bool

num_boundary_res(self: pyrosetta.rosetta.protocols.hbnet.HBNet, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → int¶: C++: protocols::hbnet::HBNet::num_boundary_res(const struct protocols::hbnet::HBondNetStruct &) –> unsigned long

num_core_res(self: pyrosetta.rosetta.protocols.hbnet.HBNet, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → int¶: C++: protocols::hbnet::HBNet::num_core_res(const struct protocols::hbnet::HBondNetStruct &) –> unsigned long

only_native(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::only_native() –> bool

pair_meets_starting_criteria(self: pyrosetta.rosetta.protocols.hbnet.HBNet, : int, : int, : int, : int) → bool¶: C++: protocols::hbnet::HBNet::pair_meets_starting_criteria(const unsigned long, const unsigned long, const unsigned long, const unsigned long) –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.hbnet.HBNet, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::hbnet::HBNet::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pdb_numbering(*args, **kwargs)¶

Overloaded function.

pdb_numbering(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> bool

C++: protocols::hbnet::HBNet::pdb_numbering() const –> bool

pdb_numbering(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pdb_numbering: bool) -> None

C++: protocols::hbnet::HBNet::pdb_numbering(const bool) –> void

place_rots_on_pose(*args, **kwargs)¶

Overloaded function.

place_rots_on_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> pyrosetta.rosetta.utility.vector1_unsigned_long
place_rots_on_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, use_pose: bool) -> pyrosetta.rosetta.utility.vector1_unsigned_long

places the rotamers of the provided h-bond network onto the provided pose

C++: protocols::hbnet::HBNet::place_rots_on_pose(class core::pose::Pose &, struct protocols::hbnet::HBondNetStruct &, bool) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

prepare_output(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → None¶: C++: protocols::hbnet::HBNet::prepare_output() –> void

print_additional_headers(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → str¶: C++: protocols::hbnet::HBNet::print_additional_headers() –> std::string

print_additional_info_for_net(self: pyrosetta.rosetta.protocols.hbnet.HBNet, : pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, : pyrosetta.rosetta.core.pose.Pose) → str¶: C++: protocols::hbnet::HBNet::print_additional_info_for_net(struct protocols::hbnet::HBondNetStruct &, const class core::pose::Pose &) –> std::string

provide_citation_info(self: pyrosetta.rosetta.protocols.hbnet.HBNet, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶: C++: protocols::hbnet::HBNet::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::hbnet::HBNet::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

quick_and_dirty_heavy_atom_is_unsat(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, at_id: pyrosetta.rosetta.core.id.AtomID) → bool¶: C++: protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(const class core::pose::Pose &, const class core::id::AtomID) –> bool

quick_and_dirty_network_has_heavy_atom_unsat(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶: C++: protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat(const class core::pose::Pose &, const struct protocols::hbnet::HBondNetStruct &) –> bool

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

res_is_boundary(self: pyrosetta.rosetta.protocols.hbnet.HBNet, res: int) → bool¶: C++: protocols::hbnet::HBNet::res_is_boundary(const unsigned long) const –> bool

res_is_core(self: pyrosetta.rosetta.protocols.hbnet.HBNet, res: int) → bool¶: C++: protocols::hbnet::HBNet::res_is_core(const unsigned long) const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

scale_twobody_energy(self: pyrosetta.rosetta.protocols.hbnet.HBNet, input_twobody_energy: float, : str, : str) → float¶: C++: protocols::hbnet::HBNet::scale_twobody_energy(double, char, char) –> double

search_IG_for_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::search_IG_for_networks(class core::pose::Pose &) –> void

select_best_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → None¶: C++: protocols::hbnet::HBNet::select_best_networks() –> void

set_ala_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::set_ala_pose(class core::pose::Pose &) –> void

set_boundary_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet, boundary_residues: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::hbnet::HBNet::set_boundary_residues(class utility::vector1<bool, class std::allocator<bool> >) –> void

set_core_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet, core_residues: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::hbnet::HBNet::set_core_residues(class utility::vector1<bool, class std::allocator<bool> >) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_extend_existing_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet, extend_existing_networks: bool) → None¶: C++: protocols::hbnet::HBNet::set_extend_existing_networks(bool) –> void

set_find_native(self: pyrosetta.rosetta.protocols.hbnet.HBNet, native: bool) → None¶: C++: protocols::hbnet::HBNet::set_find_native(bool) –> void

set_find_only_native(self: pyrosetta.rosetta.protocols.hbnet.HBNet, only: bool) → None¶: C++: protocols::hbnet::HBNet::set_find_only_native(bool) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_keep_existing_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet, keep_existing_networks: bool) → None¶: C++: protocols::hbnet::HBNet::set_keep_existing_networks(bool) –> void

set_max_networks_size(self: pyrosetta.rosetta.protocols.hbnet.HBNet, max: int) → None¶: C++: protocols::hbnet::HBNet::set_max_networks_size(unsigned long) –> void

set_max_unsat(self: pyrosetta.rosetta.protocols.hbnet.HBNet, max: int) → None¶: C++: protocols::hbnet::HBNet::set_max_unsat(unsigned long) –> void

set_min_networks_size(self: pyrosetta.rosetta.protocols.hbnet.HBNet, min: int) → None¶: C++: protocols::hbnet::HBNet::set_min_networks_size(unsigned long) –> void

set_monte_carlo_branch(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: bool) → None¶

turn on or off the monte carlo branching protocol

C++: protocols::hbnet::HBNet::set_monte_carlo_branch(bool) –> void

set_monte_carlo_seed_must_be_buried(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: bool) → None¶

Only branch from hbonds where at least one residue is buried. Effectively, this results in only finding networks that have at least one buried residue.

C++: protocols::hbnet::HBNet::set_monte_carlo_seed_must_be_buried(bool) –> void

set_monte_carlo_seed_must_be_fully_buried(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: bool) → None¶

Only branch from hbonds where both residues are buried. This results in only finding networks that have at least one buried hbond but this does not prevent having additional exposed hbonds.

C++: protocols::hbnet::HBNet::set_monte_carlo_seed_must_be_fully_buried(bool) –> void

set_monte_carlo_seed_threshold(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: float) → None¶

Maybe you only want to branch from strong hbonds. If this value is -1.2, then only hbonds with a strength of -1.2 or lower will be branched from.

C++: protocols::hbnet::HBNet::set_monte_carlo_seed_threshold(double) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_only_extend_existing(self: pyrosetta.rosetta.protocols.hbnet.HBNet, only_extend_existing: bool) → None¶: C++: protocols::hbnet::HBNet::set_only_extend_existing(bool) –> void

set_orig_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::set_orig_pose(class core::pose::Pose &) –> void

set_score_function(self: pyrosetta.rosetta.protocols.hbnet.HBNet, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::hbnet::HBNet::set_score_function(const class std::shared_ptr<const class core::scoring::ScoreFunction> &) –> void

set_start_res_vec(self: pyrosetta.rosetta.protocols.hbnet.HBNet, start_resnums: pyrosetta.rosetta.std.set_unsigned_long_t) → None¶: C++: protocols::hbnet::HBNet::set_start_res_vec(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) –> void

set_start_resnums(self: pyrosetta.rosetta.protocols.hbnet.HBNet, start_resnums: pyrosetta.rosetta.std.set_unsigned_long_t) → None¶: C++: protocols::hbnet::HBNet::set_start_resnums(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) –> void

set_symm_info(self: pyrosetta.rosetta.protocols.hbnet.HBNet, symminfo: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) → None¶: C++: protocols::hbnet::HBNet::set_symm_info(const class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo> &) –> void

set_symmetry(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::set_symmetry(class core::pose::Pose &) –> void

set_task(self: pyrosetta.rosetta.protocols.hbnet.HBNet, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::hbnet::HBNet::set_task(const class std::shared_ptr<class core::pack::task::PackerTask> &) –> void

set_total_num_mc_runs(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: int) → None¶

set number of monte carlo runs to be divided over all the seed hbonds. A single monte carlo run appears to take roughly 1 ms (very loose estimate).

C++: protocols::hbnet::HBNet::set_total_num_mc_runs(unsigned long) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_upweight_starting_twobody(self: pyrosetta.rosetta.protocols.hbnet.HBNet, upweight_factor: float) → None¶: C++: protocols::hbnet::HBNet::set_upweight_starting_twobody(double) –> void

setup_packer_task_and_starting_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::setup_packer_task_and_starting_residues(const class core::pose::Pose &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

state_is_starting_aa_type(self: pyrosetta.rosetta.protocols.hbnet.HBNet, : int, : int) → bool¶: C++: protocols::hbnet::HBNet::state_is_starting_aa_type(const unsigned long, const unsigned long) –> bool

symmetric(*args, **kwargs)¶

Overloaded function.

symmetric(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> bool

C++: protocols::hbnet::HBNet::symmetric() const –> bool

symmetric(self: pyrosetta.rosetta.protocols.hbnet.HBNet, is_symmetric_pose: bool) -> None

C++: protocols::hbnet::HBNet::symmetric(const bool) –> void

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.hbnet.HBNet, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::hbnet::HBNet::task_factory(const class std::shared_ptr<class core::pack::task::TaskFactory> &) –> void

task_factory(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::hbnet::HBNet::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

trim_additional_rotamers(self: pyrosetta.rosetta.protocols.hbnet.HBNet, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::trim_additional_rotamers(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_core_and_boundary_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::update_core_and_boundary_residues(const class core::pose::Pose &) –> void

upweight_starting_twobody_energy(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → float¶: C++: protocols::hbnet::HBNet::upweight_starting_twobody_energy() –> double

verbose(*args, **kwargs)¶

Overloaded function.

verbose(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> bool

C++: protocols::hbnet::HBNet::verbose() const –> bool

verbose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, set_verbose: bool) -> None

C++: protocols::hbnet::HBNet::verbose(const bool) –> void

water_clashes(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, water_O: pyrosetta.rosetta.numeric.xyzVector_double_t) → bool¶: C++: protocols::hbnet::HBNet::water_clashes(const class core::pose::Pose &, const class numeric::xyzVector<double>) –> bool

water_oxygen_clashes_with_residue(*args, **kwargs)¶

Overloaded function.

water_oxygen_clashes_with_residue(self: pyrosetta.rosetta.protocols.hbnet.HBNet, water_oxygen: pyrosetta.rosetta.numeric.xyzVector_double_t, resnum: int, rot_state: int) -> bool

C++: protocols::hbnet::HBNet::water_oxygen_clashes_with_residue(const class numeric::xyzVector<double>, const unsigned long, const int) –> bool

water_oxygen_clashes_with_residue(self: pyrosetta.rosetta.protocols.hbnet.HBNet, water_oxygen: pyrosetta.rosetta.numeric.xyzVector_double_t, res: pyrosetta.rosetta.core.conformation.Residue) -> bool

C++: protocols::hbnet::HBNet::water_oxygen_clashes_with_residue(const class numeric::xyzVector<double>, const class core::conformation::Residue &) –> bool

class pyrosetta.rosetta.protocols.hbnet.HBNetCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.hbnet.HBNetCreator, : pyrosetta.rosetta.protocols.hbnet.HBNetCreator) → pyrosetta.rosetta.protocols.hbnet.HBNetCreator¶: C++: protocols::hbnet::HBNetCreator::operator=(const class protocols::hbnet::HBNetCreator &) –> class protocols::hbnet::HBNetCreator &

create_mover(self: pyrosetta.rosetta.protocols.hbnet.HBNetCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::hbnet::HBNetCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.hbnet.HBNetCreator) → str¶: C++: protocols::hbnet::HBNetCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.hbnet.HBNetCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::hbnet::HBNetCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.hbnet.HBNetScore¶

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::hbnet::HBNetScore::apply(const class core::pose::Pose &) const –> bool

clear(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore) → None¶: C++: protocols::hbnet::HBNetScore::clear() –> void

clone(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::hbnet::HBNetScore::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::hbnet::HBNetScore::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_score(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::hbnet::HBNetScore::get_score(class core::pose::Pose &) const –> double

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore) → str¶: C++: protocols::hbnet::HBNetScore::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::hbnet::HBNetScore::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::hbnet::HBNetScore::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNetScore::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

just returns get_score()

C++: protocols::hbnet::HBNetScore::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.hbnet.HBNetScore, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

just returns get_score()

C++: protocols::hbnet::HBNetScore::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

class pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator¶

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator, : pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator) → pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator¶: C++: protocols::hbnet::HBNetScoreFilterCreator::operator=(const class protocols::hbnet::HBNetScoreFilterCreator &) –> class protocols::hbnet::HBNetScoreFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::hbnet::HBNetScoreFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator) → str¶: C++: protocols::hbnet::HBNetScoreFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::hbnet::HBNetScoreFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface¶

Bases: HBNet

add_start_res(self: pyrosetta.rosetta.protocols.hbnet.HBNet, res: int) → None¶: C++: protocols::hbnet::HBNet::add_start_res(unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

atom_hbonds_to_bridging_water(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, at_id: pyrosetta.rosetta.core.id.AtomID) → bool¶: C++: protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(const class core::pose::Pose &, const class core::id::AtomID) –> bool

static attributes_for_hbnet(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::hbnet::HBNet::attributes_for_hbnet(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::hbnet::HBNetStapleInterface::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

find_native(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::find_native() –> bool

find_unsats(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → None¶: C++: protocols::hbnet::HBNet::find_unsats(const class core::pose::Pose &, struct protocols::hbnet::HBondNetStruct &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::hbnet::HBNetStapleInterface::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_aa_for_state(self: pyrosetta.rosetta.protocols.hbnet.HBNet, res: int, rot: int) → str¶: C++: protocols::hbnet::HBNet::get_aa_for_state(const unsigned long, const unsigned long) const –> char

get_additional_output(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.pose.Pose¶

used by the job distributor and MultiplePoseMover (MPM) to return poses OTF as requested (without need to store in memory)

C++: protocols::hbnet::HBNet::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_ala_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::hbnet::HBNet::get_ala_pose() –> const class core::pose::Pose &

get_boundary_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.utility.vector1_bool¶: C++: protocols::hbnet::HBNet::get_boundary_residues() –> class utility::vector1<bool, class std::allocator<bool> >

get_boundary_selector(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: protocols::hbnet::HBNet::get_boundary_selector() –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_core_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.utility.vector1_bool¶: C++: protocols::hbnet::HBNet::get_core_residues() –> class utility::vector1<bool, class std::allocator<bool> >

get_core_selector(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: protocols::hbnet::HBNet::get_core_selector() –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_extend_existing_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::get_extend_existing_networks() –> bool

get_file_name(self: pyrosetta.rosetta.protocols.hbnet.HBNet, id: int, prefix: str, extension: str) → str¶: C++: protocols::hbnet::HBNet::get_file_name(unsigned long, std::string, std::string) –> std::string

get_helix_id(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, r1: int) → int¶: C++: protocols::hbnet::HBNetStapleInterface::get_helix_id(unsigned long) const –> unsigned long

get_ind_res(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, res_i: int) → int¶: C++: protocols::hbnet::HBNet::get_ind_res(const class core::pose::Pose &, const unsigned long) –> unsigned long

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_keep_existing_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::get_keep_existing_networks() –> bool

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_max_networks_size(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → int¶: C++: protocols::hbnet::HBNet::get_max_networks_size() –> unsigned long

get_max_unsat(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → int¶: C++: protocols::hbnet::HBNet::get_max_unsat() –> unsigned long

get_min_networks_size(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → int¶: C++: protocols::hbnet::HBNet::get_min_networks_size() –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface) → str¶: C++: protocols::hbnet::HBNetStapleInterface::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_native_vec(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t¶: C++: protocols::hbnet::HBNet::get_native_vec() –> class std::vector<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct>, class std::allocator<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct> > > &

get_net_vec(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t¶

return all hbond networks, sorted with best networks at the front, THIS SHOULD RETURN A POINTER (OP)

C++: protocols::hbnet::HBNet::get_net_vec() –> class std::vector<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct>, class std::allocator<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct> > > &

get_network_by_id(self: pyrosetta.rosetta.protocols.hbnet.HBNet, id: int) → pyrosetta.rosetta.protocols.hbnet.HBondNetStruct¶: C++: protocols::hbnet::HBNet::get_network_by_id(unsigned long) –> class std::shared_ptr<struct protocols::hbnet::HBondNetStruct>

get_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t¶: C++: protocols::hbnet::HBNet::get_networks() –> class std::vector<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct>, class std::allocator<class std::shared_ptr<struct protocols::hbnet::HBondNetStruct> > >

get_num_native_rot(*args, **kwargs)¶

Overloaded function.

get_num_native_rot(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t) -> int
get_num_native_rot(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t, sc_rmsd_cut: float) -> int
get_num_native_rot(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t, sc_rmsd_cut: float, super: bool) -> int

return the number of rotamers in a network that are identical in seq or rot to the original input pose:

C++: protocols::hbnet::HBNet::get_num_native_rot(class core::pose::Pose &, 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> > > &, double, bool) –> unsigned long

get_num_native_seq(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t) → int¶: C++: protocols::hbnet::HBNet::get_num_native_seq(class core::pose::Pose &, 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

get_only_extend_existing(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::get_only_extend_existing() –> bool

get_orig_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::hbnet::HBNet::get_orig_pose() –> const class core::pose::Pose &

get_output_vector(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.vector_std_set_unsigned_long_t¶: C++: protocols::hbnet::HBNet::get_output_vector() –> class std::vector<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::allocator<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > > > &

get_packer_graph(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.utility.graph.Graph¶: C++: protocols::hbnet::HBNet::get_packer_graph() –> class std::shared_ptr<class utility::graph::Graph>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_start_res_vec(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::hbnet::HBNet::get_start_res_vec() –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

get_symm_info(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo¶: C++: protocols::hbnet::HBNet::get_symm_info() const –> class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>

get_task(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → pyrosetta.rosetta.core.pack.task.PackerTask¶: C++: protocols::hbnet::HBNet::get_task() const –> class std::shared_ptr<class core::pack::task::PackerTask>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

has_pH_His(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶: C++: protocols::hbnet::HBNetStapleInterface::has_pH_His(const class core::pose::Pose &, struct protocols::hbnet::HBondNetStruct &) –> bool

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

interhelical_contact(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, helix_boundaries: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, r1: int, r2: int, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::hbnet::HBNetStapleInterface::interhelical_contact(const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >, const unsigned long, const unsigned long, const class core::pose::Pose &) –> bool

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

ligand(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → int¶: C++: protocols::hbnet::HBNet::ligand() –> unsigned long

static mover_name() → str¶: C++: protocols::hbnet::HBNetStapleInterface::mover_name() –> std::string

multi_component(*args, **kwargs)¶

Overloaded function.

multi_component(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> bool

C++: protocols::hbnet::HBNet::multi_component() const –> bool

multi_component(self: pyrosetta.rosetta.protocols.hbnet.HBNet, multi_component: bool) -> None

C++: protocols::hbnet::HBNet::multi_component(const bool) –> void

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

net_clash(self: pyrosetta.rosetta.protocols.hbnet.HBNet, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, j: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶

checks if two h-bond networks clash; returns true if they do clash

C++: protocols::hbnet::HBNet::net_clash(const struct protocols::hbnet::HBondNetStruct &, const struct protocols::hbnet::HBondNetStruct &) –> bool

network_meets_final_criteria(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶: C++: protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(const class core::pose::Pose &, struct protocols::hbnet::HBondNetStruct &) –> bool

network_meets_initial_criteria(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶: C++: protocols::hbnet::HBNetStapleInterface::network_meets_initial_criteria(const struct protocols::hbnet::HBondNetStruct &) –> bool

network_spans_all_helices(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶: C++: protocols::hbnet::HBNetStapleInterface::network_spans_all_helices(const struct protocols::hbnet::HBondNetStruct &) const –> bool

num_boundary_res(self: pyrosetta.rosetta.protocols.hbnet.HBNet, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → int¶: C++: protocols::hbnet::HBNet::num_boundary_res(const struct protocols::hbnet::HBondNetStruct &) –> unsigned long

num_core_res(self: pyrosetta.rosetta.protocols.hbnet.HBNet, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → int¶: C++: protocols::hbnet::HBNet::num_core_res(const struct protocols::hbnet::HBondNetStruct &) –> unsigned long

num_helices_w_hbond(*args, **kwargs)¶

Overloaded function.

num_helices_w_hbond(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> int

C++: protocols::hbnet::HBNetStapleInterface::num_helices_w_hbond(const struct protocols::hbnet::HBondNetStruct &) const –> unsigned long

num_helices_w_hbond(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_HBondResStruct_t) -> int

C++: protocols::hbnet::HBNetStapleInterface::num_helices_w_hbond(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> > > &) const –> unsigned long

num_intermolecular_hbonds(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::hbnet::HBNetStapleInterface::num_intermolecular_hbonds(struct protocols::hbnet::HBondNetStruct &, const class core::pose::Pose &) –> unsigned long

only_native(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → bool¶: C++: protocols::hbnet::HBNet::only_native() –> bool

pair_meets_starting_criteria(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, res1: int, rot1: int, res2: int, rot2: int) → bool¶: C++: protocols::hbnet::HBNetStapleInterface::pair_meets_starting_criteria(const unsigned long, const unsigned long, const unsigned long, const unsigned long) –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::hbnet::HBNetStapleInterface::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pdb_numbering(*args, **kwargs)¶

Overloaded function.

pdb_numbering(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> bool

C++: protocols::hbnet::HBNet::pdb_numbering() const –> bool

pdb_numbering(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pdb_numbering: bool) -> None

C++: protocols::hbnet::HBNet::pdb_numbering(const bool) –> void

place_rots_on_pose(*args, **kwargs)¶

Overloaded function.

place_rots_on_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> pyrosetta.rosetta.utility.vector1_unsigned_long
place_rots_on_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, use_pose: bool) -> pyrosetta.rosetta.utility.vector1_unsigned_long

places the rotamers of the provided h-bond network onto the provided pose

C++: protocols::hbnet::HBNet::place_rots_on_pose(class core::pose::Pose &, struct protocols::hbnet::HBondNetStruct &, bool) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

prepare_output(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface) → None¶: C++: protocols::hbnet::HBNetStapleInterface::prepare_output() –> void

print_additional_headers(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface) → str¶: C++: protocols::hbnet::HBNetStapleInterface::print_additional_headers() –> std::string

print_additional_info_for_net(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, pose: pyrosetta.rosetta.core.pose.Pose) → str¶: C++: protocols::hbnet::HBNetStapleInterface::print_additional_info_for_net(struct protocols::hbnet::HBondNetStruct &, const class core::pose::Pose &) –> std::string

provide_citation_info(self: pyrosetta.rosetta.protocols.hbnet.HBNet, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶: C++: protocols::hbnet::HBNet::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::hbnet::HBNetStapleInterface::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

quick_and_dirty_heavy_atom_is_unsat(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, at_id: pyrosetta.rosetta.core.id.AtomID) → bool¶: C++: protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(const class core::pose::Pose &, const class core::id::AtomID) –> bool

quick_and_dirty_network_has_heavy_atom_unsat(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) → bool¶: C++: protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat(const class core::pose::Pose &, const struct protocols::hbnet::HBondNetStruct &) –> bool

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

res_is_boundary(self: pyrosetta.rosetta.protocols.hbnet.HBNet, res: int) → bool¶: C++: protocols::hbnet::HBNet::res_is_boundary(const unsigned long) const –> bool

res_is_core(self: pyrosetta.rosetta.protocols.hbnet.HBNet, res: int) → bool¶: C++: protocols::hbnet::HBNet::res_is_core(const unsigned long) const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

residues_are_interface_pairs(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, res1: int, res2: int) → bool¶: C++: protocols::hbnet::HBNetStapleInterface::residues_are_interface_pairs(const unsigned long, const unsigned long) –> bool

same_helix(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, helix_boundaries: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, r1: int, r2: int) → bool¶: C++: protocols::hbnet::HBNetStapleInterface::same_helix(const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >, const unsigned long, const unsigned long) –> bool

scale_twobody_energy(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, input_twobody_energy: float, res1: str, res2: str) → float¶: C++: protocols::hbnet::HBNetStapleInterface::scale_twobody_energy(double, char, char) –> double

search_IG_for_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::search_IG_for_networks(class core::pose::Pose &) –> void

select_best_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → None¶: C++: protocols::hbnet::HBNet::select_best_networks() –> void

set_ala_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::set_ala_pose(class core::pose::Pose &) –> void

set_boundary_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet, boundary_residues: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::hbnet::HBNet::set_boundary_residues(class utility::vector1<bool, class std::allocator<bool> >) –> void

set_core_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet, core_residues: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::hbnet::HBNet::set_core_residues(class utility::vector1<bool, class std::allocator<bool> >) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_extend_existing_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet, extend_existing_networks: bool) → None¶: C++: protocols::hbnet::HBNet::set_extend_existing_networks(bool) –> void

set_find_native(self: pyrosetta.rosetta.protocols.hbnet.HBNet, native: bool) → None¶: C++: protocols::hbnet::HBNet::set_find_native(bool) –> void

set_find_only_native(self: pyrosetta.rosetta.protocols.hbnet.HBNet, only: bool) → None¶: C++: protocols::hbnet::HBNet::set_find_only_native(bool) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_keep_existing_networks(self: pyrosetta.rosetta.protocols.hbnet.HBNet, keep_existing_networks: bool) → None¶: C++: protocols::hbnet::HBNet::set_keep_existing_networks(bool) –> void

set_max_networks_size(self: pyrosetta.rosetta.protocols.hbnet.HBNet, max: int) → None¶: C++: protocols::hbnet::HBNet::set_max_networks_size(unsigned long) –> void

set_max_unsat(self: pyrosetta.rosetta.protocols.hbnet.HBNet, max: int) → None¶: C++: protocols::hbnet::HBNet::set_max_unsat(unsigned long) –> void

set_min_networks_size(self: pyrosetta.rosetta.protocols.hbnet.HBNet, min: int) → None¶: C++: protocols::hbnet::HBNet::set_min_networks_size(unsigned long) –> void

set_monte_carlo_branch(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: bool) → None¶

turn on or off the monte carlo branching protocol

C++: protocols::hbnet::HBNet::set_monte_carlo_branch(bool) –> void

set_monte_carlo_seed_must_be_buried(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: bool) → None¶

Only branch from hbonds where at least one residue is buried. Effectively, this results in only finding networks that have at least one buried residue.

C++: protocols::hbnet::HBNet::set_monte_carlo_seed_must_be_buried(bool) –> void

set_monte_carlo_seed_must_be_fully_buried(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: bool) → None¶

Only branch from hbonds where both residues are buried. This results in only finding networks that have at least one buried hbond but this does not prevent having additional exposed hbonds.

C++: protocols::hbnet::HBNet::set_monte_carlo_seed_must_be_fully_buried(bool) –> void

set_monte_carlo_seed_threshold(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: float) → None¶

Maybe you only want to branch from strong hbonds. If this value is -1.2, then only hbonds with a strength of -1.2 or lower will be branched from.

C++: protocols::hbnet::HBNet::set_monte_carlo_seed_threshold(double) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_only_extend_existing(self: pyrosetta.rosetta.protocols.hbnet.HBNet, only_extend_existing: bool) → None¶: C++: protocols::hbnet::HBNet::set_only_extend_existing(bool) –> void

set_orig_pose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::set_orig_pose(class core::pose::Pose &) –> void

set_score_function(self: pyrosetta.rosetta.protocols.hbnet.HBNet, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::hbnet::HBNet::set_score_function(const class std::shared_ptr<const class core::scoring::ScoreFunction> &) –> void

set_start_res_vec(self: pyrosetta.rosetta.protocols.hbnet.HBNet, start_resnums: pyrosetta.rosetta.std.set_unsigned_long_t) → None¶: C++: protocols::hbnet::HBNet::set_start_res_vec(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) –> void

set_start_resnums(self: pyrosetta.rosetta.protocols.hbnet.HBNet, start_resnums: pyrosetta.rosetta.std.set_unsigned_long_t) → None¶: C++: protocols::hbnet::HBNet::set_start_resnums(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) –> void

set_symm_info(self: pyrosetta.rosetta.protocols.hbnet.HBNet, symminfo: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) → None¶: C++: protocols::hbnet::HBNet::set_symm_info(const class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo> &) –> void

set_symmetry(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::set_symmetry(class core::pose::Pose &) –> void

set_task(self: pyrosetta.rosetta.protocols.hbnet.HBNet, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::hbnet::HBNet::set_task(const class std::shared_ptr<class core::pack::task::PackerTask> &) –> void

set_total_num_mc_runs(self: pyrosetta.rosetta.protocols.hbnet.HBNet, setting: int) → None¶

set number of monte carlo runs to be divided over all the seed hbonds. A single monte carlo run appears to take roughly 1 ms (very loose estimate).

C++: protocols::hbnet::HBNet::set_total_num_mc_runs(unsigned long) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_upweight_starting_twobody(self: pyrosetta.rosetta.protocols.hbnet.HBNet, upweight_factor: float) → None¶: C++: protocols::hbnet::HBNet::set_upweight_starting_twobody(double) –> void

setup_packer_task_and_starting_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues(const class core::pose::Pose &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

state_is_starting_aa_type(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface, res: int, rot_id: int) → bool¶: C++: protocols::hbnet::HBNetStapleInterface::state_is_starting_aa_type(const unsigned long, const unsigned long) –> bool

symmetric(*args, **kwargs)¶

Overloaded function.

symmetric(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> bool

C++: protocols::hbnet::HBNet::symmetric() const –> bool

symmetric(self: pyrosetta.rosetta.protocols.hbnet.HBNet, is_symmetric_pose: bool) -> None

C++: protocols::hbnet::HBNet::symmetric(const bool) –> void

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.hbnet.HBNet, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::hbnet::HBNet::task_factory(const class std::shared_ptr<class core::pack::task::TaskFactory> &) –> void

task_factory(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::hbnet::HBNet::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

trim_additional_rotamers(self: pyrosetta.rosetta.protocols.hbnet.HBNet, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::trim_additional_rotamers(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_core_and_boundary_residues(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::hbnet::HBNet::update_core_and_boundary_residues(const class core::pose::Pose &) –> void

upweight_starting_twobody_energy(self: pyrosetta.rosetta.protocols.hbnet.HBNet) → float¶: C++: protocols::hbnet::HBNet::upweight_starting_twobody_energy() –> double

verbose(*args, **kwargs)¶

Overloaded function.

verbose(self: pyrosetta.rosetta.protocols.hbnet.HBNet) -> bool

C++: protocols::hbnet::HBNet::verbose() const –> bool

verbose(self: pyrosetta.rosetta.protocols.hbnet.HBNet, set_verbose: bool) -> None

C++: protocols::hbnet::HBNet::verbose(const bool) –> void

water_clashes(self: pyrosetta.rosetta.protocols.hbnet.HBNet, pose: pyrosetta.rosetta.core.pose.Pose, water_O: pyrosetta.rosetta.numeric.xyzVector_double_t) → bool¶: C++: protocols::hbnet::HBNet::water_clashes(const class core::pose::Pose &, const class numeric::xyzVector<double>) –> bool

water_oxygen_clashes_with_residue(*args, **kwargs)¶

Overloaded function.

water_oxygen_clashes_with_residue(self: pyrosetta.rosetta.protocols.hbnet.HBNet, water_oxygen: pyrosetta.rosetta.numeric.xyzVector_double_t, resnum: int, rot_state: int) -> bool

C++: protocols::hbnet::HBNet::water_oxygen_clashes_with_residue(const class numeric::xyzVector<double>, const unsigned long, const int) –> bool

water_oxygen_clashes_with_residue(self: pyrosetta.rosetta.protocols.hbnet.HBNet, water_oxygen: pyrosetta.rosetta.numeric.xyzVector_double_t, res: pyrosetta.rosetta.core.conformation.Residue) -> bool

C++: protocols::hbnet::HBNet::water_oxygen_clashes_with_residue(const class numeric::xyzVector<double>, const class core::conformation::Residue &) –> bool

class pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator, : pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator) → pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator¶: C++: protocols::hbnet::HBNetStapleInterfaceCreator::operator=(const class protocols::hbnet::HBNetStapleInterfaceCreator &) –> class protocols::hbnet::HBNetStapleInterfaceCreator &

create_mover(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::hbnet::HBNetStapleInterfaceCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator) → str¶: C++: protocols::hbnet::HBNetStapleInterfaceCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::hbnet::HBNetStapleInterfaceCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.hbnet.HBondNetStruct¶

Bases: pybind11_object

struct that contains info needed for hbond networks

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

Assigment operator, needed as copy constructor is specified

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

property asymm_residues¶

property cst_file_written¶

property hbond_set¶

property hbond_vec¶

property id¶

property is_extended¶

property is_native¶

property lig_num_unsatisfied¶

property lig_state_list¶

property net_indices¶

property network_pdb_written¶

property num_boundary_residues¶

property num_core_residues¶

property num_heavy_unsat¶

property num_intermolecular_hbs¶

property num_unsat_Hpol¶

property outstring¶

property percent_hbond_capacity¶

property pml_file_written¶

property residues¶

property rotamers¶

property score¶

property scored¶

property sort_by_percent_hbond_capacity¶

property sort_first_by_tot_unsat¶

property term_w_bb¶

property term_w_cycle¶

property term_w_start¶

property total_hbonds¶

property total_polar_atoms¶

property unsat_Hpols¶

property unsat_accs¶

class pyrosetta.rosetta.protocols.hbnet.HBondResStruct¶

Bases: pybind11_object

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

property aa¶

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 &

property chainid¶

property is_ligand¶

property is_protein¶

property is_solvent¶

property resnum¶

property rot_index¶

class pyrosetta.rosetta.protocols.hbnet.NetworkState¶

Bases: pybind11_object

add_edge(self: pyrosetta.rosetta.protocols.hbnet.NetworkState, edge: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge) → None¶: C++: protocols::hbnet::NetworkState::add_edge(const class core::scoring::hbonds::graph::HBondEdge *) –> void

add_node(self: pyrosetta.rosetta.protocols.hbnet.NetworkState, node: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → None¶: C++: protocols::hbnet::NetworkState::add_node(const class core::scoring::hbonds::graph::HBondNode *) –> void

add_polar_atoms(self: pyrosetta.rosetta.protocols.hbnet.NetworkState, node: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → None¶

NetworkState keeps track of polar atoms that need to be satisfied.: This function allows NetworkState to copy the vector of polar atoms from the HBondNode

C++: protocols::hbnet::NetworkState::add_polar_atoms(const class core::scoring::hbonds::graph::HBondNode *) –> void

append_twobody_energy(self: pyrosetta.rosetta.protocols.hbnet.NetworkState, setting: float) → None¶: C++: protocols::hbnet::NetworkState::append_twobody_energy(double) –> void

edges(self: pyrosetta.rosetta.protocols.hbnet.NetworkState) → pyrosetta.rosetta.utility.vector1_const_core_scoring_hbonds_graph_HBondEdge_*¶: C++: protocols::hbnet::NetworkState::edges() –> class utility::vector1<const class core::scoring::hbonds::graph::HBondEdge *, class std::allocator<const class core::scoring::hbonds::graph::HBondEdge *> > &

full_twobody_energy(*args, **kwargs)¶

Overloaded function.

full_twobody_energy(self: pyrosetta.rosetta.protocols.hbnet.NetworkState) -> float

C++: protocols::hbnet::NetworkState::full_twobody_energy() const –> double

full_twobody_energy(self: pyrosetta.rosetta.protocols.hbnet.NetworkState, setting: float) -> None

C++: protocols::hbnet::NetworkState::full_twobody_energy(double) –> void

get_unsats_for_mres(self: pyrosetta.rosetta.protocols.hbnet.NetworkState, mres: int) → pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet¶

get vector of AtomInfos for atoms that are unsatisfied

C++: protocols::hbnet::NetworkState::get_unsats_for_mres(unsigned int) –> class core::scoring::hbonds::graph::AtomInfoSet *

monte_carlo_seed(self: pyrosetta.rosetta.protocols.hbnet.NetworkState) → pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge¶: C++: protocols::hbnet::NetworkState::monte_carlo_seed() const –> const class core::scoring::hbonds::graph::HBondEdge *

mres_has_heavy_unsats(self: pyrosetta.rosetta.protocols.hbnet.NetworkState, mres: int) → bool¶

are there any heavy (not hydrogen) buried unsats at this molten residue position that are not participating in network hbonds?

C++: protocols::hbnet::NetworkState::mres_has_heavy_unsats(unsigned int) const –> bool

mres_has_unsats(self: pyrosetta.rosetta.protocols.hbnet.NetworkState, mres: int) → bool¶

are there any buried unsats at this molten residue position that are not participating in network hbonds?

C++: protocols::hbnet::NetworkState::mres_has_unsats(unsigned int) const –> bool

nodes(self: pyrosetta.rosetta.protocols.hbnet.NetworkState) → pyrosetta.rosetta.utility.vector1_const_core_scoring_hbonds_graph_HBondNode_*¶: C++: protocols::hbnet::NetworkState::nodes() –> class utility::vector1<const class core::scoring::hbonds::graph::HBondNode *, class std::allocator<const class core::scoring::hbonds::graph::HBondNode *> > &

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.protocols.hbnet.NetworkState) -> float

This holds whatever metric is used for sorting (getter)

C++: protocols::hbnet::NetworkState::score() const –> double

score(self: pyrosetta.rosetta.protocols.hbnet.NetworkState, setting: float) -> None

This holds whatever metric is used for sorting (setter)

C++: protocols::hbnet::NetworkState::score(double) –> void

class pyrosetta.rosetta.protocols.hbnet.NetworkStateScoreComparator¶

Bases: pybind11_object

static compare(a: pyrosetta.rosetta.protocols.hbnet.NetworkState, b: pyrosetta.rosetta.protocols.hbnet.NetworkState) → bool¶: C++: protocols::hbnet::NetworkStateScoreComparator::compare(const class protocols::hbnet::NetworkState &, const class protocols::hbnet::NetworkState &) –> bool

class pyrosetta.rosetta.protocols.hbnet.UnsatSelector¶

Bases: ResidueSelector

A ResidueSelector that selects alpha-amino acids that are either in the positive phi or negative phi region of Ramachandran space (depending on user preferences).

apply(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: protocols::hbnet::UnsatSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector, : pyrosetta.rosetta.protocols.hbnet.UnsatSelector) → pyrosetta.rosetta.protocols.hbnet.UnsatSelector¶: C++: protocols::hbnet::UnsatSelector::operator=(const class protocols::hbnet::UnsatSelector &) –> class protocols::hbnet::UnsatSelector &

static class_name() → str¶

Get the mover class name.

C++: protocols::hbnet::UnsatSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone function.

Copy this object and return owning pointer to the copy (created on the heap).

C++: protocols::hbnet::UnsatSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

consider_mainchain_only(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector) → bool¶

Get whether we only consider mainchain hydrogen bond: donors and acceptors.

C++: protocols::hbnet::UnsatSelector::consider_mainchain_only() const –> bool

get_name(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector) → str¶

Get the mover class name.

C++: protocols::hbnet::UnsatSelector::get_name() const –> std::string

hbond_energy_cutoff(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector) → float¶

Get the threshold for considering something to be a: hydrogen bond.

C++: protocols::hbnet::UnsatSelector::hbond_energy_cutoff() const –> const double &

legacy(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector) → bool¶

Get the legacy preference

C++: protocols::hbnet::UnsatSelector::legacy() const –> bool

mode(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector) → bool¶

Get the maximum allowed number of instances of an oversaturated: hydrogen bond acceptor.

C++: protocols::hbnet::UnsatSelector::mode() const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

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

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶

Provide XSD information, allowing automatic evaluation of bad XML.

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

scorefxn(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector) → pyrosetta.rosetta.core.scoring.ScoreFunction¶

Get the scorefunction.

C++: protocols::hbnet::UnsatSelector::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_consider_mainchain_only(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector, input_setting: bool) → None¶

Set whether we only consider mainchain hydrogen bond: donors and acceptors.

C++: protocols::hbnet::UnsatSelector::set_consider_mainchain_only(const bool) –> void

set_hbond_energy_cutoff(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector, input_value: float) → None¶

Set the threshold for considering something to be a: hydrogen bond.

C++: protocols::hbnet::UnsatSelector::set_hbond_energy_cutoff(const double &) –> void

set_legacy(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector, input_setting: bool) → None¶

Set whether legacy option should be used

C++: protocols::hbnet::UnsatSelector::set_legacy(const bool) –> void

set_mode(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector, input_setting: bool) → None¶

Set the maximum allowed number of instances of an oversaturated: hydrogen bond acceptor.

C++: protocols::hbnet::UnsatSelector::set_mode(const bool) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelector, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Set the scorefunction.

Clones the input.

C++: protocols::hbnet::UnsatSelector::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

class pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator, : pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator) → pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator¶: C++: protocols::hbnet::UnsatSelectorCreator::operator=(const class protocols::hbnet::UnsatSelectorCreator &) –> class protocols::hbnet::UnsatSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: protocols::hbnet::UnsatSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator) → str¶: C++: protocols::hbnet::UnsatSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::hbnet::UnsatSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

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

Overloaded function.

add_reslabels_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> None
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 &, std::string) –> void

class pyrosetta.rosetta.protocols.hbnet.compare_by_x¶: Bases: pybind11_object

class pyrosetta.rosetta.protocols.hbnet.compare_hbond_residues¶: Bases: pybind11_object

class pyrosetta.rosetta.protocols.hbnet.compare_hbond_resnums¶: Bases: pybind11_object

class pyrosetta.rosetta.protocols.hbnet.compare_net_vec¶: Bases: pybind11_object

pyrosetta.rosetta.protocols.hbnet.edge_satisfies_heavy_unsat_for_node(current_state: protocols::hbnet::NetworkState, node: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, edge: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge) → bool¶: C++: protocols::hbnet::edge_satisfies_heavy_unsat_for_node(const class protocols::hbnet::NetworkState &, const class core::scoring::hbonds::graph::HBondNode *, const class core::scoring::hbonds::graph::HBondEdge *) –> bool

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

Overloaded function.

get_hbond_atom_pairs(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, pose: pyrosetta.rosetta.core.pose.Pose) -> None
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: pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t) → 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.

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

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.

print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> str
print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool) -> str
print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool) -> str
print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool, term_w_cycle: bool) -> str
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

print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> str
print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool) -> str
print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct, chainid: bool, term_w_start: bool) -> str
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
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
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.

print_network(i: pyrosetta.rosetta.protocols.hbnet.HBondNetStruct) -> str
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