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protocols::hbnet Namespace Reference

Classes

struct  compare_by_x
 
struct  compare_hbond_residues
 
struct  compare_hbond_resnums
 
struct  compare_net_vec
 
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  ConstrainHBondNetworkCreator
 
struct  DecoratedNetworkState
 
class  HBNet
 
class  HBNetCreator
 
class  HBNetScore
 
class  HBNetScoreFilterCreator
 
class  HBNetStapleInterface
 
class  HBNetStapleInterfaceCreator
 
struct  HBondNetStruct
 struct that contains info needed for hbond networks More...
 
struct  HBondResStruct
 struct that represents minimal info for residue in an h-bond network 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

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

Function Documentation

void protocols::hbnet::add_network_resids_to_pose ( core::pose::Pose pose,
utility::vector1< core::Size resids,
std::string  name_of_subset = "HBNet" 
)
PURE_ATTR void protocols::hbnet::add_reslabels_to_pose ( Pose pose,
HBondNetStruct &  i,
std::string  label 
)
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 
)
PURE_ATTR utility::vector1< HBondResStructCOP >::const_iterator protocols::hbnet::find_HBondResStruct ( utility::vector1< HBondResStructCOP > const &  residues,
core::Size  resnum 
)
PURE_ATTR void protocols::hbnet::get_hbond_atom_pairs ( HBondNetStruct &  network,
Pose pose,
bool  bb_exclusion 
)
PURE_ATTR core::Size protocols::hbnet::get_num_edges_for_res ( core::Size const  res,
ObjexxFCL::FArray2D_int &  path_dists 
)
PURE_ATTR core::Size protocols::hbnet::get_num_protein_sc_sc_hbonds ( Pose pose,
HBondNetStruct &  i 
)
PURE_ATTR 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 
)
PURE_ATTR 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 
)
PURE_ATTR bool protocols::hbnet::hbond_exists_in_vector ( utility::vector1< core::scoring::hbonds::HBondCOP > const &  hbond_vec,
core::scoring::hbonds::HBondCOP h2 
)
bool protocols::hbnet::hbond_exists_in_vector ( utility::vector1< HBondCOP > const &  hbond_vec,
HBondCOP h2 
)
PURE_ATTR bool protocols::hbnet::his_tyr_connectivity ( Pose const &  pose,
HBondNetStruct &  i 
)
PURE_ATTR bool protocols::hbnet::network_contains_aa ( char  aa_one_letter,
HBondNetStruct const &  i 
)
PURE_ATTR bool protocols::hbnet::network_contains_aa ( char  aa_one_letter,
utility::vector1< HBondResStructCOP > const &  residues 
)
bool protocols::hbnet::one_network_is_subset_of_other ( utility::vector1< HBondResStructCOP > const &  residues_i,
utility::vector1< HBondResStructCOP > const &  residues_j 
)
CONST_ATTR NODISCARD_ATTR std::string protocols::hbnet::print_headers ( )
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 
)
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 
)
PURE_ATTR std::string protocols::hbnet::print_network ( HBondNetStruct const &  i,
bool  chainid 
)
PURE_ATTR std::string protocols::hbnet::print_network_w_pdb_numbering ( Pose const &  pose,
HBondNetStruct const &  i,
bool  chainid 
)
static basic::Tracer protocols::hbnet::TR ( "protocols.hbnet.HBNetTaskOperations"  )
static
static basic::Tracer protocols::hbnet::TR ( "protocols.hbnet.HBNetStapleInterface"  )
static
static basic::Tracer protocols::hbnet::TR ( "protocols.hbnet.HBNet"  )
static

Variable Documentation

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