protocols::hbnet Namespace Reference

Classes
class	ConstrainHBondNetworkCreator
struct	HBondResStruct
	struct that represents minimal info for residue in an h-bond network More...
struct	compare_hbond_residues
struct	compare_hbond_resnums
struct	HBondNetStruct
	struct that contains info needed for hbond networks More...
struct	compare_net_vec
struct	compare_by_x
struct	DecoratedNetworkState
class	HBNet
class	HBNetCreator
class	HBNetScore
class	HBNetScoreFilterCreator
class	HBNetStapleInterface
class	HBNetStapleInterfaceCreator
class	ConstrainHBondNetwork
	sets allowed residue types to constrain HBNet residues in downstream design; add this Taskop to any design movers downstream of HBNet More...
class	NetworkState
struct	NetworkStateScoreComparator
class	UnsatSelector
	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). More...
class	UnsatSelectorCreator

Typedefs
using	HBNetOP = utility::pointer::shared_ptr< HBNet >
using	HBNetCOP = utility::pointer::shared_ptr< HBNet const >
using	HBondResStructOP = utility::pointer::shared_ptr< HBondResStruct >
using	HBondResStructCOP = utility::pointer::shared_ptr< HBondResStruct const >
using	HBondNetStructOP = utility::pointer::shared_ptr< HBondNetStruct >
using	HBondNetStructCOP = utility::pointer::shared_ptr< HBondNetStruct const >
using	HBNetScoreOP = utility::pointer::shared_ptr< HBNetScore >
using	HBNetScoreCOP = utility::pointer::shared_ptr< HBNetScore const >
using	HBNetStapleInterfaceOP = utility::pointer::shared_ptr< HBNetStapleInterface >
using	HBNetStapleInterfaceCOP = utility::pointer::shared_ptr< HBNetStapleInterface const >
using	ConstrainHBondNetworkOP = utility::pointer::shared_ptr< ConstrainHBondNetwork >
using	ConstrainHBondNetworkCOP = utility::pointer::shared_ptr< ConstrainHBondNetwork const >
typedef utility::pointer::shared_ptr< UnsatSelector >	UnsatSelectorOP
typedef utility::pointer::shared_ptr< UnsatSelector const >	UnsatSelectorCOP

Functions
static basic::Tracer	TR ("protocols.hbnet.HBNet")
bool	one_network_is_subset_of_other (utility::vector1< HBondResStructCOP > const &residues_i, utility::vector1< HBondResStructCOP > const &residues_j)
void	add_network_resids_to_pose (core::pose::Pose &pose, utility::vector1< core::Size > resids, std::string name_of_subset="HBNet")
std::string	print_list_to_string (HBondNetStruct const &network, bool chainid, bool term_w_start, bool term_w_cycle, bool term_w_bb)
std::string	print_list_to_string (Pose const &pose, HBondNetStruct const &network, bool chainid, bool term_w_start, bool term_w_cycle, bool term_w_bb, bool use_pdb_numbering)
std::string	print_network (HBondNetStruct const &i, bool chainid)
std::string	print_network_w_pdb_numbering (Pose const &pose, HBondNetStruct const &i, bool chainid)
std::string	print_headers ()
utility::vector1< HBondResStructCOP >::const_iterator	find_HBondResStruct (utility::vector1< HBondResStructCOP > const &residues, core::Size resnum)
void	get_hbond_atom_pairs (HBondNetStruct &network, Pose &pose, bool bb_exclusion)
bool	hbond_exists_in_vector (utility::vector1< HBondCOP > const &hbond_vec, HBondCOP &h2)
void	add_reslabels_to_pose (Pose &pose, HBondNetStruct &i, std::string label)
Size	get_num_protein_sc_sc_hbonds (Pose &pose, HBondNetStruct &i)
Size	get_num_edges_for_res (core::Size const res, ObjexxFCL::FArray2D_int &path_dists)
void	hbnet_one_body_energies (pose::Pose const &pose, core::pack::rotamer_set::RotamerSet &rotset, core::scoring::ScoreFunction const &sf, utility::vector1< core::PackerEnergy > &energies)
void	hbnet_symm_one_body_energies (pose::Pose const &pose, core::pack::rotamer_set::RotamerSet &rotset, core::scoring::ScoreFunction const &sf, core::pack::task::PackerTask const &task, utility::graph::Graph const &packer_neighbor_graph, utility::vector1< core::PackerEnergy > &energies)
bool	network_contains_aa (char aa_one_letter, HBondNetStruct const &i)
bool	network_contains_aa (char aa_one_letter, utility::vector1< HBondResStructCOP > const &residues)
bool	his_tyr_connectivity (Pose const &pose, HBondNetStruct &i)
bool	edge_satisfies_heavy_unsat_for_node (NetworkState const &current_state, core::scoring::hbonds::graph::HBondNode const *node, core::scoring::hbonds::graph::HBondEdge const *edge)
PURE_ATTR bool	hbond_exists_in_vector (utility::vector1< core::scoring::hbonds::HBondCOP > const &hbond_vec, core::scoring::hbonds::HBondCOP &h2)
static basic::Tracer	TR ("protocols.hbnet.HBNetStapleInterface")
static basic::Tracer	TR ("protocols.hbnet.HBNetTaskOperations")

Variables
static core::Real const	MIN_HB_E_CUTOFF = { -0.1 }
static core::Real const	SC_RMSD_CUTOFF = { 0.5 }

Typedef Documentation

ConstrainHBondNetworkCOP

using protocols::hbnet::ConstrainHBondNetworkCOP = typedef utility::pointer::shared_ptr< ConstrainHBondNetwork const >

ConstrainHBondNetworkOP

using protocols::hbnet::ConstrainHBondNetworkOP = typedef utility::pointer::shared_ptr< ConstrainHBondNetwork >

HBNetCOP

using protocols::hbnet::HBNetCOP = typedef utility::pointer::shared_ptr< HBNet const >

HBNetOP

using protocols::hbnet::HBNetOP = typedef utility::pointer::shared_ptr< HBNet >

HBNetScoreCOP

using protocols::hbnet::HBNetScoreCOP = typedef utility::pointer::shared_ptr< HBNetScore const >

HBNetScoreOP

using protocols::hbnet::HBNetScoreOP = typedef utility::pointer::shared_ptr< HBNetScore >

HBNetStapleInterfaceCOP

using protocols::hbnet::HBNetStapleInterfaceCOP = typedef utility::pointer::shared_ptr< HBNetStapleInterface const >

HBNetStapleInterfaceOP

using protocols::hbnet::HBNetStapleInterfaceOP = typedef utility::pointer::shared_ptr< HBNetStapleInterface >

HBondNetStructCOP

using protocols::hbnet::HBondNetStructCOP = typedef utility::pointer::shared_ptr< HBondNetStruct const >

HBondNetStructOP

using protocols::hbnet::HBondNetStructOP = typedef utility::pointer::shared_ptr< HBondNetStruct >

HBondResStructCOP

using protocols::hbnet::HBondResStructCOP = typedef utility::pointer::shared_ptr< HBondResStruct const >

HBondResStructOP

using protocols::hbnet::HBondResStructOP = typedef utility::pointer::shared_ptr< HBondResStruct >

UnsatSelectorCOP

typedef utility::pointer::shared_ptr< UnsatSelector const > protocols::hbnet::UnsatSelectorCOP

UnsatSelectorOP

typedef utility::pointer::shared_ptr< UnsatSelector > protocols::hbnet::UnsatSelectorOP

Function Documentation

add_network_resids_to_pose()

void protocols::hbnet::add_network_resids_to_pose	(	core::pose::Pose &	pose,
		utility::vector1< core::Size >	resids,
		std::string	name_of_subset = "HBNet"
	)

References protocols::residue_selectors::StoreResidueSubsetMover::apply(), core::select::resids(), protocols::residue_selectors::StoreResidueSubsetMover::set_subset(), and core::pose::Pose::size().

Referenced by protocols::hbnet::HBNet::place_rots_on_pose().

add_reslabels_to_pose()

PURE_ATTR void protocols::hbnet::add_reslabels_to_pose	(	Pose &	pose,
		HBondNetStruct &	i,
		std::string	label
	)

References core::pose::Pose::pdb_info(), and protocols::hbnet::HBondNetStruct::residues.

edge_satisfies_heavy_unsat_for_node()

PURE_ATTR bool protocols::hbnet::edge_satisfies_heavy_unsat_for_node	(	NetworkState const &	current_state,
		core::scoring::hbonds::graph::HBondNode const *	node,
		core::scoring::hbonds::graph::HBondEdge const *	edge
	)

References core::scoring::hbonds::graph::AtomInfoSet::contains(), protocols::hbnet::NetworkState::get_unsats_for_mres(), core::scoring::hbond, core::scoring::hbonds::graph::HBondEdge::hbonds(), and core::scoring::hbonds::graph::HBondNode::moltenres().

Referenced by protocols::hbnet::HBNet::get_next_node().

find_HBondResStruct()

PURE_ATTR utility::vector1< HBondResStructCOP >::const_iterator protocols::hbnet::find_HBondResStruct	(	utility::vector1< HBondResStructCOP > const &	residues,
		core::Size	resnum
	)

Referenced by protocols::hbnet::HBNet::merge_2_branched_networks(), protocols::hbnet::HBNet::minimize_network(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), and protocols::hbnet::HBNet::store_network().

get_hbond_atom_pairs()

PURE_ATTR void protocols::hbnet::get_hbond_atom_pairs	(	HBondNetStruct &	network,
		Pose &	pose,
		bool	bb_exclusion
	)

References core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check(), core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), core::scoring::hbonds::HBondOptions::exclude_intra_res_protein(), core::scoring::hbonds::fill_hbond_set(), hbond_exists_in_vector(), core::scoring::hbonds::HBondSet::hbond_options(), protocols::hbnet::HBondNetStruct::hbond_set, protocols::hbnet::HBondNetStruct::hbond_vec, protocols::hbnet::HBondNetStruct::residues, protocols::hbnet::HBondNetStruct::total_hbonds, and core::scoring::hbonds::HBondOptions::use_hb_env_dep().

Referenced by protocols::hbnet::HBNet::get_native_networks(), protocols::hbnet::HBNet::output_networks(), and protocols::hbnet::HBNet::select_best_networks().

get_num_edges_for_res()

PURE_ATTR core::Size protocols::hbnet::get_num_edges_for_res	(	core::Size const	res,
		ObjexxFCL::FArray2D_int &	path_dists
	)

get_num_protein_sc_sc_hbonds()

PURE_ATTR core::Size protocols::hbnet::get_num_protein_sc_sc_hbonds	(	Pose &	pose,
		HBondNetStruct &	i
	)

References protocols::hbnet::HBondNetStruct::hbond_vec, core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

hbnet_one_body_energies()

void protocols::hbnet::hbnet_one_body_energies	(	pose::Pose const &	pose,
		core::pack::rotamer_set::RotamerSet &	rotset,
		core::scoring::ScoreFunction const &	sf,
		utility::vector1< core::PackerEnergy > &	energies
	)

References core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_1b(), core::pack::rotamer_set::RotamerSet::num_rotamers(), core::pack::rotamer_set::RotamerSet::rotamer(), and core::scoring::ScoreFunction::weights().

hbnet_symm_one_body_energies()

void protocols::hbnet::hbnet_symm_one_body_energies	(	pose::Pose const &	pose,
		core::pack::rotamer_set::RotamerSet &	rotset,
		core::scoring::ScoreFunction const &	sf,
		core::pack::task::PackerTask const &	task,
		utility::graph::Graph const &	packer_neighbor_graph,
		utility::vector1< core::PackerEnergy > &	energies
	)

References core::pose::Pose::conformation(), core::conformation::Residue::copy_residue_connections_from(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_1b(), core::scoring::ScoreFunction::evaluate_rotamer_pair_energies(), core::pose::symmetry::is_symmetric(), core::pack::rotamer_set::RotamerSet::num_rotamers(), core::conformation::Residue::orient_onto_residue(), core::pack::task::PackerTask::pack_residue(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), rot(), core::pack::rotamer_set::RotamerSet::rotamer(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::scoring::ScoreFunction::weights().

Referenced by protocols::hbnet::HBNet::run().

hbond_exists_in_vector() [1/2]

PURE_ATTR bool protocols::hbnet::hbond_exists_in_vector	(	utility::vector1< core::scoring::hbonds::HBondCOP > const &	hbond_vec,
		core::scoring::hbonds::HBondCOP &	h2
	)

References protocols::antibody::h1, and protocols::antibody::h2.

Referenced by protocols::hbnet::UnsatSelector::compute(), and get_hbond_atom_pairs().

hbond_exists_in_vector() [2/2]

bool protocols::hbnet::hbond_exists_in_vector	(	utility::vector1< HBondCOP > const &	hbond_vec,
		HBondCOP &	h2
	)

References protocols::antibody::h1, and protocols::antibody::h2.

Referenced by protocols::hbnet::UnsatSelector::compute(), and get_hbond_atom_pairs().

his_tyr_connectivity()

PURE_ATTR bool protocols::hbnet::his_tyr_connectivity	(	Pose const &	pose,
		HBondNetStruct &	i
	)

References protocols::hbnet::HBondNetStruct::hbond_vec, core::conformation::Residue::name1(), and core::pose::Pose::residue().

Referenced by protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria().

network_contains_aa() [1/2]

PURE_ATTR bool protocols::hbnet::network_contains_aa	(	char	aa_one_letter,
		HBondNetStruct const &	i
	)

References protocols::hbnet::HBondNetStruct::residues.

Referenced by protocols::hbnet::HBNetStapleInterface::has_pH_His(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), and protocols::hbnet::HBNetStapleInterface::prepare_output().

network_contains_aa() [2/2]

PURE_ATTR bool protocols::hbnet::network_contains_aa	(	char	aa_one_letter,
		utility::vector1< HBondResStructCOP > const &	residues
	)

one_network_is_subset_of_other()

bool protocols::hbnet::one_network_is_subset_of_other	(	utility::vector1< HBondResStructCOP > const &	residues_i,
		utility::vector1< HBondResStructCOP > const &	residues_j
	)

Referenced by protocols::hbnet::HBNet::monte_carlo_net_clash().

print_headers()

CONST_ATTR NODISCARD_ATTR std::string protocols::hbnet::print_headers

(

)

Referenced by protocols::hbnet::HBNet::apply(), protocols::hbnet::HBNet::get_additional_output(), protocols::hbnet::HBNet::output_networks(), protocols::hbnet::HBNet::set_constraints(), and protocols::hbnet::HBNet::write_network_pdb().

print_list_to_string() [1/2]

PURE_ATTR std::string protocols::hbnet::print_list_to_string	(	HBondNetStruct const &	network,
		bool	chainid,
		bool	term_w_start,
		bool	term_w_cycle,
		bool	term_w_bb
	)

References protocols::hbnet::HBondNetStruct::asymm_residues, and protocols::hbnet::HBondNetStruct::residues.

Referenced by protocols::hbnet::HBNet::branch_overlapping_networks(), print_network(), print_network_w_pdb_numbering(), protocols::hbnet::HBNet::remove_replicate_networks(), and protocols::hbnet::HBNet::select_best_networks().

print_list_to_string() [2/2]

PURE_ATTR std::string protocols::hbnet::print_list_to_string	(	Pose const &	pose,
		HBondNetStruct const &	network,
		bool	chainid,
		bool	term_w_start,
		bool	term_w_cycle,
		bool	term_w_bb,
		bool	use_pdb_numbering
	)

References protocols::hbnet::HBondNetStruct::asymm_residues, core::pose::Pose::pdb_info(), protocols::hbnet::HBondNetStruct::residues, protocols::analysis::total, and core::pose::Pose::total_residue().

print_network()

PURE_ATTR std::string protocols::hbnet::print_network	(	HBondNetStruct const &	i,
		bool	chainid
	)

References protocols::hbnet::HBondNetStruct::asymm_residues, protocols::hbnet::HBondNetStruct::id, protocols::hbnet::HBondNetStruct::is_extended, protocols::hbnet::HBondNetStruct::is_native, protocols::hbnet::HBondNetStruct::num_unsat_Hpol, protocols::hbnet::HBondNetStruct::percent_hbond_capacity, print_list_to_string(), protocols::hbnet::HBondNetStruct::residues, protocols::hbnet::HBondNetStruct::score, protocols::hbnet::HBondNetStruct::term_w_bb, protocols::hbnet::HBondNetStruct::term_w_cycle, protocols::hbnet::HBondNetStruct::term_w_start, and protocols::hbnet::HBondNetStruct::total_hbonds.

Referenced by protocols::hbnet::HBNet::output_networks().

print_network_w_pdb_numbering()

PURE_ATTR std::string protocols::hbnet::print_network_w_pdb_numbering	(	Pose const &	pose,
		HBondNetStruct const &	i,
		bool	chainid
	)

References protocols::hbnet::HBondNetStruct::asymm_residues, protocols::hbnet::HBondNetStruct::id, protocols::hbnet::HBondNetStruct::is_extended, protocols::hbnet::HBondNetStruct::is_native, protocols::hbnet::HBondNetStruct::num_unsat_Hpol, protocols::hbnet::HBondNetStruct::percent_hbond_capacity, print_list_to_string(), protocols::hbnet::HBondNetStruct::residues, protocols::hbnet::HBondNetStruct::score, protocols::hbnet::HBondNetStruct::term_w_bb, protocols::hbnet::HBondNetStruct::term_w_cycle, protocols::hbnet::HBondNetStruct::term_w_start, and protocols::hbnet::HBondNetStruct::total_hbonds.

Referenced by protocols::hbnet::HBNet::output_networks().

TR() [1/3]

static basic::Tracer protocols::hbnet::TR ( "protocols.hbnet.HBNet"  )

static

Referenced by protocols::hbnet::HBNet::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::hbnet::HBNet::branch_overlapping_networks(), protocols::hbnet::HBNet::create_ptask(), protocols::hbnet::HBNet::estimate_saturation(), protocols::hbnet::HBNet::find_unsats(), protocols::hbnet::HBNet::get_additional_output(), protocols::hbnet::HBNetStapleInterface::has_pH_His(), protocols::hbnet::HBNet::MC_branch_overlapping_networks(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::hbnet::HBNet::output_networks(), protocols::hbnet::HBNet::parse_my_tag(), protocols::hbnet::HBNetStapleInterface::prepare_output(), protocols::hbnet::HBNet::remove_replicate_networks(), protocols::hbnet::HBNet::run(), protocols::hbnet::HBNet::search_IG_for_networks(), protocols::hbnet::HBNet::select_best_networks(), protocols::hbnet::HBNet::set_symmetry(), protocols::hbnet::HBNet::setup(), and protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

TR() [2/3]

static basic::Tracer protocols::hbnet::TR ( "protocols.hbnet.HBNetStapleInterface"  )

static

TR() [3/3]

static basic::Tracer protocols::hbnet::TR ( "protocols.hbnet.HBNetTaskOperations"  )

static

Variable Documentation

MIN_HB_E_CUTOFF

core::Real const protocols::hbnet::MIN_HB_E_CUTOFF = { -0.1 }

static

Referenced by protocols::hbnet::HBNet::score_network_on_pose().

SC_RMSD_CUTOFF

core::Real const protocols::hbnet::SC_RMSD_CUTOFF = { 0.5 }

static

Referenced by protocols::hbnet::HBNet::monte_carlo_net_clash(), protocols::hbnet::HBNet::net_clash(), and protocols::hbnet::HBNet::network_already_stored().