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protocols::simple_filters::BuriedUnsatHbondFilter Class Reference

filters based on an upper bound # of buried unsatisfied polar residues More...

#include <BuriedUnsatHbondFilter.hh>

Inheritance diagram for protocols::simple_filters::BuriedUnsatHbondFilter:
Inheritance graph
[legend]

Public Member Functions

 BuriedUnsatHbondFilter ()
 
 BuriedUnsatHbondFilter (core::Size const upper_threshold, core::select::residue_selector::ResidueSelectorOP residue_selector=nullptr, bool const use_legacy_options=false, bool const generous_hbonds=true, bool const use_vasa=true, bool const ignore_surface_res=false, bool const ignore_bb_heavy_unsats=false, bool const use_sc_neighbors=false, bool const only_interface=false, bool const use_ddG_style=false, bool const use_hbnet_behavior=false)
 
 BuriedUnsatHbondFilter (BuriedUnsatHbondFilter const &rval)
 copy constructor More...
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
core::Real compute (core::pose::Pose const &pose) const
 
 ~BuriedUnsatHbondFilter () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
void task_factory (core::pack::task::TaskFactoryOP tf)
 
core::pack::task::TaskFactoryOP task_factory () const
 
std::string name () const override
 
void set_generous_hbonds_ (bool generous_hbonds)
 
void set_use_vsasa (bool use_vsasa)
 
void set_ignore_surface_res (bool ignore_surface_res)
 
void set_ignore_bb_heavy_unsats (bool ignore_bb_heavy_unsats)
 
void set_use_ddG_style (bool use_ddG_style)
 
void set_print_out_info_to_pdb (bool print_out_info_to_pdb)
 
void set_use_reporter_behavior (bool use_reporter_behavior)
 
void set_use_hbnet_behavior (bool use_hbnet_behavior)
 
void set_report_all_unsats (bool report_all_unsats)
 
void set_report_all_heavy_atom_unsats (bool report_all_heavy_atom_unsats)
 
void set_report_sc_heavy_atom_unsats (bool report_sc_heavy_atom_unsats)
 
void set_report_bb_heavy_atom_unsats (bool report_bb_heavy_atom_unsats)
 
void set_report_nonheavy_unsats (bool report_nonheavy_unsats)
 
void set_atomic_depth_deeper_than (bool atomic_depth_deeper_than)
 
void set_atomic_depth_poly_leu (bool atomic_depth_poly_leu)
 
void set_max_hbond_energy (core::Real max_hbond_energy)
 
void set_probe_radius (core::Real probe_radius)
 
void set_burial_cutoff (core::Real burial_cutoff)
 
void set_probe_radius_apo (core::Real probe_radius_apo)
 
void set_burial_cutoff_apo (core::Real burial_cutoff_apo)
 
void set_residue_surface_cutoff (core::Real residue_surface_cutoff)
 
void set_atomic_depth_selection (core::Real atomic_depth_selection)
 
void set_atomic_depth_probe_radius (core::Real atomic_depth_probe_radius)
 
void set_atomic_depth_resolution (core::Real atomic_depth_resolution)
 
void set_atomic_depth_apo_surface (core::Real atomic_depth_apo_surface)
 
void set_upper_threshold (core::Size upper_threshold)
 
void set_jump_num (core::Size jump_num)
 
void set_dalphaball_sasa ()
 
void sym_dof_names (std::string const &sym_dofs)
 
std::string sym_dof_names () const
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorOP residue_selector)
 
void set_use_sc_neighbors (bool use_sc_neighbors)
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual std::string get_type () const
 
std::string get_user_defined_name () const
 
void set_user_defined_name (std::string const &name)
 
virtual void clear ()
 used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

void set_legacy_options ()
 
void update_cutoffs ()
 
core::id::AtomID_Map< boolget_deep_apo_atoms (core::pose::Pose const &pose) const
 

Private Attributes

std::string name_of_sasa_calc_
 
std::string sym_dof_names_
 
bool legacy_options_
 
bool generous_hbonds_
 
bool legacy_counting_
 
bool use_vsasa_
 
bool ignore_surface_res_
 
bool ignore_bb_heavy_unsats_
 
bool use_sc_neighbors_
 
bool only_interface_
 
bool use_ddG_style_
 
bool print_out_info_to_pdb_
 
bool use_reporter_behavior_
 
bool use_hbnet_behavior_
 
bool report_all_unsats_
 
bool report_all_heavy_atom_unsats_
 
bool report_sc_heavy_atom_unsats_
 
bool report_bb_heavy_atom_unsats_
 
bool report_nonheavy_unsats_
 
bool atomic_depth_deeper_than_
 
bool atomic_depth_poly_leu_
 
core::Real max_hbond_energy_
 
core::Real probe_radius_
 
core::Real burial_cutoff_
 
core::Real probe_radius_apo_
 
core::Real burial_cutoff_apo_
 
core::Real residue_surface_cutoff_
 
core::Real atomic_depth_selection_
 
core::Real atomic_depth_probe_radius_
 
core::Real atomic_depth_resolution_
 
core::Real atomic_depth_apo_surface_
 
core::Size upper_threshold_
 
core::Size jump_num_
 
core::select::residue_selector::ResidueSelectorOP residue_selector_
 
core::scoring::ScoreFunctionCOP sfxn_
 
core::pack::task::TaskFactoryOP task_factory_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Detailed Description

filters based on an upper bound # of buried unsatisfied polar residues

Constructor & Destructor Documentation

protocols::simple_filters::BuriedUnsatHbondFilter::BuriedUnsatHbondFilter ( )
protocols::simple_filters::BuriedUnsatHbondFilter::BuriedUnsatHbondFilter ( core::Size const  upper_threshold,
core::select::residue_selector::ResidueSelectorOP  residue_selector = nullptr,
bool const  use_legacy_options = false,
bool const  generous_hbonds = true,
bool const  use_vasa = true,
bool const  ignore_surface_res = false,
bool const  ignore_bb_heavy_unsats = false,
bool const  use_sc_neighbors = false,
bool const  only_interface = false,
bool const  use_ddG_style = false,
bool const  use_hbnet_behavior = false 
)
protocols::simple_filters::BuriedUnsatHbondFilter::BuriedUnsatHbondFilter ( BuriedUnsatHbondFilter const &  rval)

copy constructor

protocols::simple_filters::BuriedUnsatHbondFilter::~BuriedUnsatHbondFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::BuriedUnsatHbondFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References protocols::simple_filters::buried_unsat_hbond_filter_tracer(), compute(), and upper_threshold_.

std::string protocols::simple_filters::BuriedUnsatHbondFilter::class_name ( )
static
filters::FilterOP protocols::simple_filters::BuriedUnsatHbondFilter::clone ( ) const
inlineoverridevirtual
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::compute ( core::pose::Pose const &  pose) const

References core::pose::motif::a(), protocols::rigid::RigidBodyTransMover::apply(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_is_polar_hydrogen(), core::conformation::Residue::atom_name(), atomic_depth_apo_surface_, atomic_depth_deeper_than_, atomic_depth_poly_leu_, atomic_depth_probe_radius_, atomic_depth_resolution_, atomic_depth_selection_, core::scoring::atomic_depth::atoms_deeper_than(), burial_cutoff_, burial_cutoff_apo_, protocols::simple_filters::buried_unsat_hbond_filter_tracer(), core::pose::Pose::conformation(), core::id::AtomID_Map< T >::fill_with(), generous_hbonds_, core::pose::metrics::EnergyDependentCalculator::get(), get_deep_apo_atoms(), protocols::jd2::JobDistributor::get_instance(), core::pose::symmetry::get_sym_aware_jump_num(), protocols::filters::Filter::get_user_defined_name(), ignore_bb_heavy_unsats_, ignore_surface_res_, core::pose::initialize_atomid_map(), core::conformation::symmetry::is_symmetric(), jump_num_, legacy_counting_, legacy_options_, max_hbond_energy_, core::id::AtomID_Map< T >::n_atom(), name(), core::conformation::Residue::name3(), name_of_sasa_calc_, core::conformation::Residue::nheavyatoms(), core::pose::Pose::num_chains(), core::pose::Pose::num_jump(), only_interface_, print_out_info_to_pdb_, probe_radius_, probe_radius_apo_, report_all_heavy_atom_unsats_, report_all_unsats_, report_bb_heavy_atom_unsats_, report_nonheavy_unsats_, report_sc_heavy_atom_unsats_, core::pose::Pose::residue(), protocols::rosetta_scripts::residue_packer_states(), residue_selector_, residue_surface_cutoff_, core::id::AtomID_Map< T >::size(), core::pose::Pose::size(), protocols::rigid::RigidBodyTransMover::step_size(), protocols::kinmatch::str(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_names(), core::pose::symmetry::sym_dof_names(), sym_dof_names_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), task_factory(), core::id::to_string(), protocols::rigid::RigidBodyTransMover::trans_axis(), use_ddG_style_, use_hbnet_behavior_, use_reporter_behavior_, use_sc_neighbors_, and use_vsasa_.

Referenced by apply(), protocols::hbnet::HBNetScore::get_score(), protocols::loop_modeling::utilities::TrajectoryLogger::record_endpoint(), report(), and report_sm().

filters::FilterOP protocols::simple_filters::BuriedUnsatHbondFilter::fresh_instance ( ) const
inlineoverridevirtual
core::id::AtomID_Map< bool > protocols::simple_filters::BuriedUnsatHbondFilter::get_deep_apo_atoms ( core::pose::Pose const &  pose) const
private
std::string protocols::simple_filters::BuriedUnsatHbondFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by compute().

void protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::simple_filters::BuriedUnsatHbondFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_filters::BuriedUnsatHbondFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_apo_surface ( core::Real  atomic_depth_apo_surface)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_deeper_than ( bool  atomic_depth_deeper_than)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_poly_leu ( bool  atomic_depth_poly_leu)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_probe_radius ( core::Real  atomic_depth_probe_radius)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_resolution ( core::Real  atomic_depth_resolution)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_selection ( core::Real  atomic_depth_selection)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_burial_cutoff ( core::Real  burial_cutoff)
inline

References burial_cutoff_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_burial_cutoff_apo ( core::Real  burial_cutoff_apo)
inline

References burial_cutoff_apo_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_dalphaball_sasa ( )
inline

References name_of_sasa_calc_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_generous_hbonds_ ( bool  generous_hbonds)
inline

References generous_hbonds_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_ignore_bb_heavy_unsats ( bool  ignore_bb_heavy_unsats)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_ignore_surface_res ( bool  ignore_surface_res)
inline

References ignore_surface_res_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_jump_num ( core::Size  jump_num)
inline

References jump_num_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_legacy_options ( )
inlineprivate
void protocols::simple_filters::BuriedUnsatHbondFilter::set_max_hbond_energy ( core::Real  max_hbond_energy)
inline

References max_hbond_energy_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_print_out_info_to_pdb ( bool  print_out_info_to_pdb)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_probe_radius ( core::Real  probe_radius)
inline

References probe_radius_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_probe_radius_apo ( core::Real  probe_radius_apo)
inline

References probe_radius_apo_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_all_heavy_atom_unsats ( bool  report_all_heavy_atom_unsats)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_all_unsats ( bool  report_all_unsats)
inline

References report_all_unsats_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_bb_heavy_atom_unsats ( bool  report_bb_heavy_atom_unsats)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_nonheavy_unsats ( bool  report_nonheavy_unsats)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_sc_heavy_atom_unsats ( bool  report_sc_heavy_atom_unsats)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_residue_selector ( core::select::residue_selector::ResidueSelectorOP  residue_selector)
inline

References residue_selector_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_residue_surface_cutoff ( core::Real  residue_surface_cutoff)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_upper_threshold ( core::Size  upper_threshold)
inline

References upper_threshold_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_use_ddG_style ( bool  use_ddG_style)
inline

References use_ddG_style_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_use_hbnet_behavior ( bool  use_hbnet_behavior)
inline

References use_hbnet_behavior_.

void protocols::simple_filters::BuriedUnsatHbondFilter::set_use_reporter_behavior ( bool  use_reporter_behavior)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_use_sc_neighbors ( bool  use_sc_neighbors)
inline
void protocols::simple_filters::BuriedUnsatHbondFilter::set_use_vsasa ( bool  use_vsasa)
inline

References use_vsasa_.

void protocols::simple_filters::BuriedUnsatHbondFilter::sym_dof_names ( std::string const &  sym_dofs)
inline

References sym_dof_names_.

std::string protocols::simple_filters::BuriedUnsatHbondFilter::sym_dof_names ( ) const
inline

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::BuriedUnsatHbondFilter::task_factory ( core::pack::task::TaskFactoryOP  tf)

References task_factory_.

core::pack::task::TaskFactoryOP protocols::simple_filters::BuriedUnsatHbondFilter::task_factory ( ) const

References task_factory_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::BuriedUnsatHbondFilter::update_cutoffs ( )
inlineprivate

Member Data Documentation

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_apo_surface_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_deeper_than_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_poly_leu_
private
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_probe_radius_
private
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_resolution_
private
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_selection_
private
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::burial_cutoff_
private
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::burial_cutoff_apo_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::generous_hbonds_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::ignore_bb_heavy_unsats_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::ignore_surface_res_
private
core::Size protocols::simple_filters::BuriedUnsatHbondFilter::jump_num_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::legacy_counting_
private

Referenced by compute(), and set_legacy_options().

bool protocols::simple_filters::BuriedUnsatHbondFilter::legacy_options_
private
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::max_hbond_energy_
private
std::string protocols::simple_filters::BuriedUnsatHbondFilter::name_of_sasa_calc_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::only_interface_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::print_out_info_to_pdb_
private
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::probe_radius_
private
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::probe_radius_apo_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::report_all_heavy_atom_unsats_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::report_all_unsats_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::report_bb_heavy_atom_unsats_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::report_nonheavy_unsats_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::report_sc_heavy_atom_unsats_
private
core::select::residue_selector::ResidueSelectorOP protocols::simple_filters::BuriedUnsatHbondFilter::residue_selector_
private
core::Real protocols::simple_filters::BuriedUnsatHbondFilter::residue_surface_cutoff_
private
core::scoring::ScoreFunctionCOP protocols::simple_filters::BuriedUnsatHbondFilter::sfxn_
private
std::string protocols::simple_filters::BuriedUnsatHbondFilter::sym_dof_names_
private
core::pack::task::TaskFactoryOP protocols::simple_filters::BuriedUnsatHbondFilter::task_factory_
private

Referenced by task_factory().

core::Size protocols::simple_filters::BuriedUnsatHbondFilter::upper_threshold_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::use_ddG_style_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::use_hbnet_behavior_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::use_reporter_behavior_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::use_sc_neighbors_
private
bool protocols::simple_filters::BuriedUnsatHbondFilter::use_vsasa_
private

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