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:

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_report_heavy_acceptors_and_hpols (bool report_heavy_acceptors_and_hpols)
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)
void	set_is_ligand_residue (bool is_ligand_residue)
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string 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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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< bool >	get_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	report_heavy_acceptors_and_hpols_
bool	atomic_depth_deeper_than_
bool	atomic_depth_poly_leu_
bool	is_ligand_residue_
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

BuriedUnsatHbondFilter() [1/3]

protocols::simple_filters::BuriedUnsatHbondFilter::BuriedUnsatHbondFilter

(

)

References burial_cutoff_, residue_surface_cutoff_, and use_vsasa_.

BuriedUnsatHbondFilter() [2/3]

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
	)

References burial_cutoff_, legacy_options_, residue_surface_cutoff_, and set_legacy_options().

BuriedUnsatHbondFilter() [3/3]

protocols::simple_filters::BuriedUnsatHbondFilter::BuriedUnsatHbondFilter

(

BuriedUnsatHbondFilter const &

rval

)

copy constructor

~BuriedUnsatHbondFilter()

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

overridedefault

Member Function Documentation

apply()

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_.

class_name()

std::string protocols::simple_filters::BuriedUnsatHbondFilter::class_name ( )

static

Referenced by protocols::simple_filters::BuriedUnsatHbondFilterCreator::keyname(), name(), and provide_xml_schema().

clone()

filters::FilterOP protocols::simple_filters::BuriedUnsatHbondFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

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 >::empty(), core::id::AtomID_Map< T >::fill_with(), core::pose::Pose::fold_tree(), generous_hbonds_, core::pose::metrics::EnergyDependentCalculator::get(), get_deep_apo_atoms(), protocols::jd2::JobDistributor::get_instance(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::scoring::get_score_function(), 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(), is_ligand_residue_, core::conformation::symmetry::is_symmetric(), core::conformation::Residue::is_virtual_residue(), 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_heavy_acceptors_and_hpols_, report_nonheavy_unsats_, report_sc_heavy_atom_unsats_, core::pose::Pose::residue(), protocols::rosetta_scripts::residue_packer_states(), residue_selector_, residue_surface_cutoff_, sfxn_, 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(), core::pose::Pose::total_residue(), protocols::rigid::RigidBodyTransMover::trans_axis(), core::pose::Pose::update_residue_neighbors(), use_ddG_style_, use_hbnet_behavior_, use_reporter_behavior_, use_sc_neighbors_, and use_vsasa_.

Referenced by apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), protocols::hbnet::HBNetScore::get_score(), protocols::loop_modeling::utilities::TrajectoryLogger::record_endpoint(), report(), report_sm(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

fresh_instance()

filters::FilterOP protocols::simple_filters::BuriedUnsatHbondFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

get_deep_apo_atoms()

core::id::AtomID_Map< bool > protocols::simple_filters::BuriedUnsatHbondFilter::get_deep_apo_atoms ( core::pose::Pose const &  pose ) const

private

References atomic_depth_apo_surface_, atomic_depth_poly_leu_, atomic_depth_probe_radius_, atomic_depth_resolution_, core::scoring::atomic_depth::atoms_deeper_than(), core::pose::initialize_atomid_map(), jump_num_, core::id::AtomID_Map< T >::n_atom(), core::pose::partition_pose_by_jump(), and core::pose::Pose::size().

Referenced by compute().

name()

std::string protocols::simple_filters::BuriedUnsatHbondFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by compute().

parse_my_tag()

void protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag ( utility::tag::TagCOP  , basic::datacache::DataMap &    )

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References atomic_depth_apo_surface_, atomic_depth_deeper_than_, atomic_depth_poly_leu_, atomic_depth_probe_radius_, atomic_depth_resolution_, atomic_depth_selection_, burial_cutoff_, burial_cutoff_apo_, protocols::simple_filters::buried_unsat_hbond_filter_tracer(), protocols::pack_daemon::error_message, generous_hbonds_, core::select::residue_selector::get_residue_selector(), core::scoring::get_score_function(), core::scoring::get_score_function_name(), ignore_bb_heavy_unsats_, ignore_surface_res_, is_ligand_residue_, jump_num_, legacy_options_, max_hbond_energy_, name_of_sasa_calc_, only_interface_, core::pack::task::parse_task_operations(), print_out_info_to_pdb_, probe_radius_, probe_radius_apo_, report_all_heavy_atom_unsats_, report_all_unsats_, report_bb_heavy_atom_unsats_, report_heavy_acceptors_and_hpols_, report_nonheavy_unsats_, report_sc_heavy_atom_unsats_, residue_selector_, residue_surface_cutoff_, set_legacy_options(), sfxn_, sym_dof_names(), sym_dof_names_, task_factory(), upper_threshold_, use_ddG_style_, use_hbnet_behavior_, use_reporter_behavior_, use_sc_neighbors_, and use_vsasa_.

provide_xml_schema()

void protocols::simple_filters::BuriedUnsatHbondFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::scoring::attributes_for_get_score_function_name(), core::select::residue_selector::attributes_for_parse_residue_selector(), core::pack::task::attributes_for_parse_task_operations(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_filters::BuriedUnsatHbondFilterCreator::provide_xml_schema().

report()

void protocols::simple_filters::BuriedUnsatHbondFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

report_sm()

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().

set_atomic_depth_apo_surface()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_apo_surface ( core::Real  atomic_depth_apo_surface )

inline

References atomic_depth_apo_surface_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

set_atomic_depth_deeper_than()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_deeper_than ( bool  atomic_depth_deeper_than )

inline

References atomic_depth_deeper_than_.

set_atomic_depth_poly_leu()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_poly_leu ( bool  atomic_depth_poly_leu )

inline

References atomic_depth_poly_leu_.

set_atomic_depth_probe_radius()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_probe_radius ( core::Real  atomic_depth_probe_radius )

inline

References atomic_depth_probe_radius_.

set_atomic_depth_resolution()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_resolution ( core::Real  atomic_depth_resolution )

inline

References atomic_depth_resolution_.

set_atomic_depth_selection()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_selection ( core::Real  atomic_depth_selection )

inline

References atomic_depth_selection_.

set_burial_cutoff()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_burial_cutoff ( core::Real  burial_cutoff )

inline

References burial_cutoff_.

set_burial_cutoff_apo()

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

inline

References burial_cutoff_apo_.

set_dalphaball_sasa()

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

inline

References name_of_sasa_calc_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

set_generous_hbonds_()

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

inline

References generous_hbonds_.

set_ignore_bb_heavy_unsats()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_ignore_bb_heavy_unsats ( bool  ignore_bb_heavy_unsats )

inline

References ignore_bb_heavy_unsats_.

set_ignore_surface_res()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_ignore_surface_res ( bool  ignore_surface_res )

inline

References ignore_surface_res_.

set_is_ligand_residue()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_is_ligand_residue ( bool  is_ligand_residue )

inline

References is_ligand_residue_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

set_jump_num()

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

inline

References jump_num_.

set_legacy_options()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_legacy_options ( )

inlineprivate

References generous_hbonds_, ignore_bb_heavy_unsats_, ignore_surface_res_, legacy_counting_, only_interface_, use_ddG_style_, use_hbnet_behavior_, use_reporter_behavior_, use_sc_neighbors_, and use_vsasa_.

Referenced by BuriedUnsatHbondFilter(), and parse_my_tag().

set_max_hbond_energy()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_max_hbond_energy ( core::Real  max_hbond_energy )

inline

References max_hbond_energy_.

set_print_out_info_to_pdb()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_print_out_info_to_pdb ( bool  print_out_info_to_pdb )

inline

References print_out_info_to_pdb_.

set_probe_radius()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_probe_radius ( core::Real  probe_radius )

inline

References probe_radius_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

set_probe_radius_apo()

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

inline

References probe_radius_apo_.

set_report_all_heavy_atom_unsats()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_all_heavy_atom_unsats ( bool  report_all_heavy_atom_unsats )

inline

References report_all_heavy_atom_unsats_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

set_report_all_unsats()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_all_unsats ( bool  report_all_unsats )

inline

References report_all_unsats_.

set_report_bb_heavy_atom_unsats()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_bb_heavy_atom_unsats ( bool  report_bb_heavy_atom_unsats )

inline

References report_bb_heavy_atom_unsats_.

Referenced by protocols::loop_modeling::utilities::TrajectoryLogger::record_endpoint().

set_report_heavy_acceptors_and_hpols()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_heavy_acceptors_and_hpols ( bool  report_heavy_acceptors_and_hpols )

inline

References report_heavy_acceptors_and_hpols_.

set_report_nonheavy_unsats()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_nonheavy_unsats ( bool  report_nonheavy_unsats )

inline

References report_nonheavy_unsats_.

set_report_sc_heavy_atom_unsats()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_report_sc_heavy_atom_unsats ( bool  report_sc_heavy_atom_unsats )

inline

References report_sc_heavy_atom_unsats_.

Referenced by protocols::loop_modeling::utilities::TrajectoryLogger::record_endpoint().

set_residue_selector()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_residue_selector ( core::select::residue_selector::ResidueSelectorOP  residue_selector )

inline

References residue_selector_.

set_residue_surface_cutoff()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_residue_surface_cutoff ( core::Real  residue_surface_cutoff )

inline

References residue_surface_cutoff_.

set_upper_threshold()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_upper_threshold ( core::Size  upper_threshold )

inline

References upper_threshold_.

set_use_ddG_style()

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

inline

References use_ddG_style_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().

set_use_hbnet_behavior()

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

inline

References use_hbnet_behavior_.

set_use_reporter_behavior()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_use_reporter_behavior ( bool  use_reporter_behavior )

inline

References use_reporter_behavior_.

set_use_sc_neighbors()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_use_sc_neighbors ( bool  use_sc_neighbors )

inline

References update_cutoffs(), and use_sc_neighbors_.

set_use_vsasa()

void protocols::simple_filters::BuriedUnsatHbondFilter::set_use_vsasa ( bool  use_vsasa )

inline

References use_vsasa_.

sym_dof_names() [1/2]

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

inline

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

sym_dof_names() [2/2]

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

inline

References sym_dof_names_.

task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::simple_filters::BuriedUnsatHbondFilter::task_factory

(

)

const

References task_factory_.

Referenced by compute(), and parse_my_tag().

task_factory() [2/2]

void protocols::simple_filters::BuriedUnsatHbondFilter::task_factory

(

core::pack::task::TaskFactoryOP

tf

)

References task_factory_.

update_cutoffs()

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

inlineprivate

References burial_cutoff_, residue_surface_cutoff_, and use_sc_neighbors_.

Referenced by set_use_sc_neighbors().

Member Data Documentation

atomic_depth_apo_surface_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_apo_surface_

private

Referenced by compute(), get_deep_apo_atoms(), parse_my_tag(), and set_atomic_depth_apo_surface().

atomic_depth_deeper_than_

bool protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_deeper_than_

private

Referenced by compute(), parse_my_tag(), and set_atomic_depth_deeper_than().

atomic_depth_poly_leu_

bool protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_poly_leu_

private

Referenced by compute(), get_deep_apo_atoms(), parse_my_tag(), and set_atomic_depth_poly_leu().

atomic_depth_probe_radius_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_probe_radius_

private

Referenced by compute(), get_deep_apo_atoms(), parse_my_tag(), and set_atomic_depth_probe_radius().

atomic_depth_resolution_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_resolution_

private

Referenced by compute(), get_deep_apo_atoms(), parse_my_tag(), and set_atomic_depth_resolution().

atomic_depth_selection_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::atomic_depth_selection_

private

Referenced by compute(), parse_my_tag(), and set_atomic_depth_selection().

burial_cutoff_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::burial_cutoff_

private

Referenced by BuriedUnsatHbondFilter(), compute(), parse_my_tag(), set_burial_cutoff(), and update_cutoffs().

burial_cutoff_apo_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::burial_cutoff_apo_

private

Referenced by compute(), parse_my_tag(), and set_burial_cutoff_apo().

generous_hbonds_

bool protocols::simple_filters::BuriedUnsatHbondFilter::generous_hbonds_

private

Referenced by compute(), parse_my_tag(), set_generous_hbonds_(), and set_legacy_options().

ignore_bb_heavy_unsats_

bool protocols::simple_filters::BuriedUnsatHbondFilter::ignore_bb_heavy_unsats_

private

Referenced by compute(), parse_my_tag(), set_ignore_bb_heavy_unsats(), and set_legacy_options().

ignore_surface_res_

bool protocols::simple_filters::BuriedUnsatHbondFilter::ignore_surface_res_

private

Referenced by compute(), parse_my_tag(), set_ignore_surface_res(), and set_legacy_options().

is_ligand_residue_

bool protocols::simple_filters::BuriedUnsatHbondFilter::is_ligand_residue_

private

Referenced by compute(), parse_my_tag(), and set_is_ligand_residue().

jump_num_

core::Size protocols::simple_filters::BuriedUnsatHbondFilter::jump_num_

mutableprivate

Referenced by compute(), get_deep_apo_atoms(), parse_my_tag(), and set_jump_num().

legacy_counting_

bool protocols::simple_filters::BuriedUnsatHbondFilter::legacy_counting_

private

Referenced by compute(), and set_legacy_options().

legacy_options_

bool protocols::simple_filters::BuriedUnsatHbondFilter::legacy_options_

private

Referenced by BuriedUnsatHbondFilter(), compute(), and parse_my_tag().

max_hbond_energy_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::max_hbond_energy_

private

Referenced by compute(), parse_my_tag(), and set_max_hbond_energy().

name_of_sasa_calc_

std::string protocols::simple_filters::BuriedUnsatHbondFilter::name_of_sasa_calc_

private

Referenced by compute(), parse_my_tag(), and set_dalphaball_sasa().

only_interface_

bool protocols::simple_filters::BuriedUnsatHbondFilter::only_interface_

private

Referenced by compute(), parse_my_tag(), and set_legacy_options().

print_out_info_to_pdb_

bool protocols::simple_filters::BuriedUnsatHbondFilter::print_out_info_to_pdb_

private

Referenced by compute(), parse_my_tag(), and set_print_out_info_to_pdb().

probe_radius_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::probe_radius_

private

Referenced by compute(), parse_my_tag(), and set_probe_radius().

probe_radius_apo_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::probe_radius_apo_

private

Referenced by compute(), parse_my_tag(), and set_probe_radius_apo().

report_all_heavy_atom_unsats_

bool protocols::simple_filters::BuriedUnsatHbondFilter::report_all_heavy_atom_unsats_

private

Referenced by compute(), parse_my_tag(), and set_report_all_heavy_atom_unsats().

report_all_unsats_

bool protocols::simple_filters::BuriedUnsatHbondFilter::report_all_unsats_

private

Referenced by compute(), parse_my_tag(), and set_report_all_unsats().

report_bb_heavy_atom_unsats_

bool protocols::simple_filters::BuriedUnsatHbondFilter::report_bb_heavy_atom_unsats_

private

Referenced by compute(), parse_my_tag(), and set_report_bb_heavy_atom_unsats().

report_heavy_acceptors_and_hpols_

bool protocols::simple_filters::BuriedUnsatHbondFilter::report_heavy_acceptors_and_hpols_

private

Referenced by compute(), parse_my_tag(), and set_report_heavy_acceptors_and_hpols().

report_nonheavy_unsats_

bool protocols::simple_filters::BuriedUnsatHbondFilter::report_nonheavy_unsats_

private

Referenced by compute(), parse_my_tag(), and set_report_nonheavy_unsats().

report_sc_heavy_atom_unsats_

bool protocols::simple_filters::BuriedUnsatHbondFilter::report_sc_heavy_atom_unsats_

private

Referenced by compute(), parse_my_tag(), and set_report_sc_heavy_atom_unsats().

residue_selector_

core::select::residue_selector::ResidueSelectorOP protocols::simple_filters::BuriedUnsatHbondFilter::residue_selector_

private

Referenced by compute(), parse_my_tag(), and set_residue_selector().

residue_surface_cutoff_

core::Real protocols::simple_filters::BuriedUnsatHbondFilter::residue_surface_cutoff_

private

Referenced by BuriedUnsatHbondFilter(), compute(), parse_my_tag(), set_residue_surface_cutoff(), and update_cutoffs().

sfxn_

core::scoring::ScoreFunctionCOP protocols::simple_filters::BuriedUnsatHbondFilter::sfxn_

mutableprivate

Referenced by compute(), and parse_my_tag().

sym_dof_names_

std::string protocols::simple_filters::BuriedUnsatHbondFilter::sym_dof_names_

private

Referenced by compute(), parse_my_tag(), and sym_dof_names().

task_factory_

core::pack::task::TaskFactoryOP protocols::simple_filters::BuriedUnsatHbondFilter::task_factory_

private

Referenced by task_factory().

upper_threshold_

core::Size protocols::simple_filters::BuriedUnsatHbondFilter::upper_threshold_

private

Referenced by apply(), parse_my_tag(), and set_upper_threshold().

use_ddG_style_

bool protocols::simple_filters::BuriedUnsatHbondFilter::use_ddG_style_

private

Referenced by compute(), parse_my_tag(), set_legacy_options(), and set_use_ddG_style().

use_hbnet_behavior_

bool protocols::simple_filters::BuriedUnsatHbondFilter::use_hbnet_behavior_

private

Referenced by compute(), parse_my_tag(), set_legacy_options(), and set_use_hbnet_behavior().

use_reporter_behavior_

bool protocols::simple_filters::BuriedUnsatHbondFilter::use_reporter_behavior_

private

Referenced by compute(), parse_my_tag(), set_legacy_options(), and set_use_reporter_behavior().

use_sc_neighbors_

bool protocols::simple_filters::BuriedUnsatHbondFilter::use_sc_neighbors_

private

Referenced by compute(), parse_my_tag(), set_legacy_options(), set_use_sc_neighbors(), and update_cutoffs().

use_vsasa_

bool protocols::simple_filters::BuriedUnsatHbondFilter::use_vsasa_

private

Referenced by BuriedUnsatHbondFilter(), compute(), parse_my_tag(), set_legacy_options(), and set_use_vsasa().

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

• src/protocols/simple_filters/BuriedUnsatHbondFilter.hh
• src/protocols/simple_filters/BuriedUnsatHbondFilter.cc