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BuriedUnsatPolarsFinder Class Reference
Inheritance diagram for BuriedUnsatPolarsFinder:
Inheritance graph
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Public Member Functions

 BuriedUnsatPolarsFinder ()
 
virtual ~BuriedUnsatPolarsFinder ()
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 
 BuriedUnsatPolarsFinder ()
 
virtual ~BuriedUnsatPolarsFinder ()
 
virtual void apply (pose::Pose &pose)
 
void generous_hbond () const
 
void bunsats_thorough_check (pose::Pose const &pose, id::AtomID_Map< bool > &bunsat_thorough_atomid_map) const
 
bool single_bunsat_thorough_check (pose::Pose const &pose, id::AtomID const &bunsat_candidate_atom_id) const
 
bool bunsat_donor_nbr_residue_check (pose::Pose const &pose, id::AtomID const &bunsat_candidate_atom_id, Residue const &bunsat_rsd, Vector const &bunsat_xyz, Size const test_resi) const
 
bool bunsat_acc_nbr_residue_check (pose::Pose const &pose, id::AtomID const &bunsat_candidate_atom_id, Residue const &bunsat_rsd, Vector const &bunsat_xyz, Size const &test_resi) const
 
bool metal_check (Residue const &test_rsd, Vector const &bunsat_xyz, Vector const &test_xyz) const
 
bool AHD_and_dist_check ()
 
bool adjacent_bbbb_check (Size const &bunsat_resi, std::string const &bunsat_atom_name, Size const &test_resi, std::string const &test_atom_name) const
 
bool self_scsc (Residue const &bunsat_rsd, Size const &bunsat_resi, Size const &bunsat_atom_num, Residue const &test_rsd, Size const &test_resi, Size const &test_atom_num) const
 
bool sulphur_bond_check (Residue const &test_rsd, Size const &test_atom_num, Vector const &bunsat_xyz, Vector const &test_xyz) const
 
bool don_geom_check (core::pose::Pose const &pose, Residue const &bunsat_rsd, Size const &bunsat_atom_num, Vector const &bunsat_xyz, Vector const &test_xyz) const
 
bool acc_geom_check (core::pose::Pose const &pose, Vector const &bunsat_xyz, Residue const &test_rsd, Size const &test_atom_num, Vector const &test_xyz) const
 
virtual std::string get_name () const
 
 BuriedUnsatPolarsFinder ()
 
virtual ~BuriedUnsatPolarsFinder ()
 
virtual void apply (pose::Pose &pose)
 
virtual std::string get_name () const
 

Constructor & Destructor Documentation

◆ BuriedUnsatPolarsFinder() [1/3]

BuriedUnsatPolarsFinder::BuriedUnsatPolarsFinder ( )
inline

◆ ~BuriedUnsatPolarsFinder() [1/3]

virtual BuriedUnsatPolarsFinder::~BuriedUnsatPolarsFinder ( )
inlinevirtual

◆ BuriedUnsatPolarsFinder() [2/3]

BuriedUnsatPolarsFinder::BuriedUnsatPolarsFinder ( )
inline

◆ ~BuriedUnsatPolarsFinder() [2/3]

virtual BuriedUnsatPolarsFinder::~BuriedUnsatPolarsFinder ( )
inlinevirtual

◆ BuriedUnsatPolarsFinder() [3/3]

BuriedUnsatPolarsFinder::BuriedUnsatPolarsFinder ( )
inline

◆ ~BuriedUnsatPolarsFinder() [3/3]

virtual BuriedUnsatPolarsFinder::~BuriedUnsatPolarsFinder ( )
inlinevirtual

Member Function Documentation

◆ acc_geom_check()

bool BuriedUnsatPolarsFinder::acc_geom_check ( core::pose::Pose const &  pose,
Vector const &  bunsat_xyz,
Residue const &  test_rsd,
Size const &  test_atom_num,
Vector const &  test_xyz 
) const
inline

References AHD_cutoff, numeric::angle_of(), numeric::conversions::degrees(), dist(), dist_cutoff, numeric::xyzVector< T >::distance(), hydroxyl_dist_cutoff, and basic::options::option.

◆ adjacent_bbbb_check()

bool BuriedUnsatPolarsFinder::adjacent_bbbb_check ( Size const &  bunsat_resi,
std::string const &  bunsat_atom_name,
Size const &  test_resi,
std::string const &  test_atom_name 
) const
inline

References ObjexxFCL::abs().

◆ AHD_and_dist_check()

bool BuriedUnsatPolarsFinder::AHD_and_dist_check ( )
inline

◆ apply() [1/3]

virtual void BuriedUnsatPolarsFinder::apply ( core::pose::Pose &  pose)
inlinevirtual

References predPRE::chain, lactamize::filename, pyrosetta.distributed.io::get_score_function(), create_a3b_hbs::i, beta_nonlocal::pose, rosetta_resnum, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, TR, and basic::MetricValue< T >::value().

Referenced by pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), and pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ apply() [2/3]

virtual void BuriedUnsatPolarsFinder::apply ( pose::Pose &  pose)
inlinevirtual

References lactamize::filename, generous_hbond_settings, pyrosetta.distributed.io::get_score_function(), basic::options::option, beta_nonlocal::pose, res, sasa_cutoff, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::TR, use_regular_sasa_calc, use_varsoldist_sasa_calc, and basic::MetricValue< T >::value().

Referenced by pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), and pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ apply() [3/3]

virtual void BuriedUnsatPolarsFinder::apply ( pose::Pose &  pose)
inlinevirtual

References lactamize::filename, pyrosetta.distributed.io::get_score_function(), beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::TR.

Referenced by pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), and pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ bunsat_acc_nbr_residue_check()

bool BuriedUnsatPolarsFinder::bunsat_acc_nbr_residue_check ( pose::Pose const &  pose,
id::AtomID const &  bunsat_candidate_atom_id,
Residue const &  bunsat_rsd,
Vector const &  bunsat_xyz,
Size const &  test_resi 
) const
inline

References beta_nonlocal::pose.

◆ bunsat_donor_nbr_residue_check()

bool BuriedUnsatPolarsFinder::bunsat_donor_nbr_residue_check ( pose::Pose const &  pose,
id::AtomID const &  bunsat_candidate_atom_id,
Residue const &  bunsat_rsd,
Vector const &  bunsat_xyz,
Size const  test_resi 
) const
inline

References beta_nonlocal::pose.

◆ bunsats_thorough_check()

void BuriedUnsatPolarsFinder::bunsats_thorough_check ( pose::Pose const &  pose,
id::AtomID_Map< bool > &  bunsat_thorough_atomid_map 
) const
inline

References beta_nonlocal::pose, and res.

◆ don_geom_check()

bool BuriedUnsatPolarsFinder::don_geom_check ( core::pose::Pose const &  pose,
Residue const &  bunsat_rsd,
Size const &  bunsat_atom_num,
Vector const &  bunsat_xyz,
Vector const &  test_xyz 
) const
inline

References AHD_cutoff, numeric::angle_of(), numeric::conversions::degrees(), dist(), dist_cutoff, numeric::xyzVector< T >::distance(), and basic::options::option.

◆ generous_hbond()

void BuriedUnsatPolarsFinder::generous_hbond ( ) const
inline

References pyrosetta.distributed.io::get_score_function(), and oop_conformations::scorefxn.

◆ get_name() [1/3]

virtual std::string BuriedUnsatPolarsFinder::get_name ( ) const
inlinevirtual

◆ get_name() [2/3]

virtual std::string BuriedUnsatPolarsFinder::get_name ( ) const
inlinevirtual

◆ get_name() [3/3]

virtual std::string BuriedUnsatPolarsFinder::get_name ( ) const
inlinevirtual

◆ metal_check()

bool BuriedUnsatPolarsFinder::metal_check ( Residue const &  test_rsd,
Vector const &  bunsat_xyz,
Vector const &  test_xyz 
) const
inline

References numeric::xyzVector< T >::distance(), metal_dist_cutoff, and basic::options::option.

◆ self_scsc()

bool BuriedUnsatPolarsFinder::self_scsc ( Residue const &  bunsat_rsd,
Size const &  bunsat_resi,
Size const &  bunsat_atom_num,
Residue const &  test_rsd,
Size const &  test_resi,
Size const &  test_atom_num 
) const
inline

◆ single_bunsat_thorough_check()

bool BuriedUnsatPolarsFinder::single_bunsat_thorough_check ( pose::Pose const &  pose,
id::AtomID const &  bunsat_candidate_atom_id 
) const
inline

References dist_cutoff, basic::options::OptionKeys::frags::contacts::neighbors, and beta_nonlocal::pose.

◆ sulphur_bond_check()

bool BuriedUnsatPolarsFinder::sulphur_bond_check ( Residue const &  test_rsd,
Size const &  test_atom_num,
Vector const &  bunsat_xyz,
Vector const &  test_xyz 
) const
inline

References numeric::xyzVector< T >::distance(), basic::options::option, and sulphur_dist_cutoff.

The documentation for this class was generated from the following files:
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