#include <RotamerBoltzmannWeight.hh>

Inheritance diagram for protocols::calc_taskop_filters::RotamerBoltzmannWeight:

Public Member Functions
	RotamerBoltzmannWeight ()
	default ctor More...

bool	apply (core::pose::Pose const &pose) const override
	Constructor with a single target residue. 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...

protocols::filters::FilterOP	clone () const override

protocols::filters::FilterOP	fresh_instance () const override

core::Real	compute (core::pose::Pose const &pose) const

	~RotamerBoltzmannWeight () override

core::pack::task::TaskFactoryOP	task_factory () const

void	task_factory (core::pack::task::TaskFactoryOP task_factory)

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...

utility::vector1< core::Size >	first_pass_ala_scan (core::pose::Pose const &pose) const

core::Real	compute_Boltzmann_weight (core::pose::Pose const &pose, core::Size const resi) const

void	rb_jump (core::Size const jump)

core::Size	rb_jump () const

void	sym_dof_names (std::string const &dof_names)

std::string	sym_dof_names () const

void	repacking_radius (core::Real const rad)

core::Real	repacking_radius () const

core::Real	ddG_threshold () const

void	ddG_threshold (core::Real const ddG)

void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)

core::scoring::ScoreFunctionOP	scorefxn () const

core::Real	temperature () const

void	temperature (core::Real const temp)

bool	unbound () const

void	unbound (bool const u)

void	threshold_probability (core::chemical::AA const aa_type, core::Real const probability)

core::Real	threshold_probability (core::chemical::AA const aa_type) const

void	energy_reduction_factor (core::Real const factor)

core::Real	energy_reduction_factor () const

core::Real	interface_interaction_energy (core::pose::Pose const &pose, core::Size const res) const

bool	compute_entropy_reduction () const

void	compute_entropy_reduction (bool const cer)

void	repack (bool const repack)

bool	repack () const

bool	skip_ala_scan () const

void	skip_ala_scan (bool const s)

void	no_modified_ddG (bool const no_ddg)

void	target_residues (std::string const &target_residues_str)

std::string	type () const

void	type (std::string const &s)

bool	write2pdb () const

void	write2pdb (bool const write)

core::Real	compute_modified_ddG (core::pose::Pose const &pose, std::ostream &out) const
	Note that compute( pose ) needs to have been run first. This merely sums over the probabilities. More...

void	write_to_pdb (core::Size const residue, std::string const &residue_name, core::Real const boltzmann_weight) const
	Output per-residue Boltzmann weights to the output pdb file if desired. More...

std::string	name () const override

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 Types
typedef protocols::filters::Filter	parent

Private Member Functions
core::Real	compute_boltz_probability () const

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_

core::Size	rb_jump_

std::string	sym_dof_names_

bool	unbound_

core::scoring::ScoreFunctionOP	scorefxn_

core::Real	temperature_

core::Real	ddG_threshold_

core::Real	repacking_radius_

utility::vector1< core::Real >	threshold_probabilities_per_residue_

core::Real	energy_reduction_factor_

bool	compute_entropy_reduction_

bool	compute_max_

bool	repack_

std::map< core::Size, core::Real >	ddGs_

std::map< core::Size, core::Real >	rotamer_probabilities_

std::string	type_

bool	skip_ala_scan_

bool	skip_report_

bool	fast_calc_

bool	no_modified_ddG_

std::string	target_residues_

bool	write2pdb_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Member Typedef Documentation

◆ parent

typedef protocols::filters::Filter protocols::calc_taskop_filters::RotamerBoltzmannWeight::parent

private

Constructor & Destructor Documentation

◆ RotamerBoltzmannWeight()

protocols::calc_taskop_filters::RotamerBoltzmannWeight::RotamerBoltzmannWeight ( )

default ctor

References core::chemical::num_canonical_aas, and threshold_probabilities_per_residue_.

◆ ~RotamerBoltzmannWeight()

protocols::calc_taskop_filters::RotamerBoltzmannWeight::~RotamerBoltzmannWeight ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::apply ( core::pose::Pose const & pose ) const

overridevirtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

◆ class_name()

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::class_name ( )

static

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeightFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute ( core::pose::Pose const & pose ) const

References core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_phe, core::chemical::aa_trp, core::chemical::aa_tyr, core::select::util::SelectResiduesByLayer::compute(), compute_boltz_probability(), compute_Boltzmann_weight(), protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight(), ddGs_, fast_calc_, first_pass_ala_scan(), core::pose::get_resnum_list_ordered(), core::pose::symmetry::get_sym_aware_jump_num(), core::conformation::Residue::name3(), rb_jump(), repacking_radius(), core::pose::Pose::residue(), core::select::util::SelectResiduesByLayer::restrict_aatypes_for_selection(), rotamer_probabilities_, scorefxn(), protocols::pose_metric_calculators::RotamerBoltzCalculator::set_lazy(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_names(), target_residues_, temperature(), protocols::calc_taskop_filters::TR(), protocols::toolbox::rigid_body::translate(), type_, unbound(), write2pdb(), and write_to_pdb().

Referenced by report(), and report_sm().

◆ compute_boltz_probability()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_boltz_probability ( ) const

private

References compute_max_, protocols::mean_field::max(), and rotamer_probabilities_.

Referenced by compute(), and report_sm().

◆ compute_Boltzmann_weight()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight	(	core::pose::Pose const &	pose,
		core::Size const	resi
	)		const

References core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::pack::make_symmetric_PackerTask_by_truncation(), core::pack::pack_rotamers(), rb_jump(), repacking_radius(), core::pose::Pose::replace_residue(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), protocols::filters::Filter::score(), scorefxn(), scorefxn_, core::pose::Pose::size(), temperature(), protocols::calc_taskop_filters::TR(), and unbound().

Referenced by compute().

◆ compute_entropy_reduction() [1/2]

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_entropy_reduction ( ) const

References compute_entropy_reduction_.

Referenced by parse_my_tag().

◆ compute_entropy_reduction() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_entropy_reduction ( bool const cer )

References compute_entropy_reduction_.

◆ compute_modified_ddG()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG	(	core::pose::Pose const &	pose,
		std::ostream &	out
	)		const

Note that compute( pose ) needs to have been run first. This merely sums over the probabilities.

References core::conformation::Residue::aa(), protocols::simple_ddg::DdgFilter::compute(), ddGs_, energy_reduction_factor(), core::conformation::Residue::name3(), no_modified_ddG_, core::conformation::membrane::out, core::pose::Pose::pdb_info(), rb_jump(), repack(), protocols::simple_ddg::DdgFilter::repack(), core::pose::Pose::residue(), rot(), rotamer_probabilities_, scorefxn(), temperature(), and threshold_probability().

Referenced by report(), and report_sm().

◆ ddG_threshold() [1/2]

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::ddG_threshold ( ) const

References ddG_threshold_.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), first_pass_ala_scan(), and parse_my_tag().

◆ ddG_threshold() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::ddG_threshold ( core::Real const ddG )

References ddG_threshold_.

◆ energy_reduction_factor() [1/2]

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::energy_reduction_factor ( ) const

References energy_reduction_factor_.

Referenced by compute_modified_ddG(), and parse_my_tag().

◆ energy_reduction_factor() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::energy_reduction_factor ( core::Real const factor )

References energy_reduction_factor_.

◆ first_pass_ala_scan()

utility::vector1< core::Size > protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan ( core::pose::Pose const & pose ) const

iterate over all packable residues according to the task factory and for each determine whether it contributes to binding at least ddG_threshold R.e.u. (using alanine scanning This list will later be used to do the Boltzmann weight calculations.

References protocols::simple_ddg::DdgFilter::compute(), protocols::simple_ddg::AlaScan::ddG_for_single_residue(), ddG_threshold(), ddGs_, core::conformation::Residue::is_protein(), protocols::simple_ddg::AlaScan::jump(), core::conformation::Residue::name3(), rb_jump(), repack(), protocols::simple_ddg::AlaScan::repack(), protocols::simple_ddg::DdgFilter::repack(), protocols::simple_ddg::AlaScan::repeats(), core::pose::Pose::residue(), scorefxn(), protocols::simple_ddg::AlaScan::scorefxn(), core::pose::Pose::size(), skip_ala_scan(), task_factory(), and protocols::calc_taskop_filters::TR().

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), and compute().

◆ fresh_instance()

protocols::filters::FilterOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ interface_interaction_energy()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy	(	core::pose::Pose const &	pose,
		core::Size const	res
	)		const

References core::conformation::Residue::chain(), core::scoring::EnergyEdge::dot(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::pose::Pose::residue(), scorefxn(), and core::scoring::Energies::weights().

◆ name()

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by protocols::calc_taskop_filters::RotBoltzWeight_subelement_ct_name().

◆ no_modified_ddG()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::no_modified_ddG ( bool const no_ddg )

References no_modified_ddG_.

◆ parse_my_tag()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::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 protocols::cluster::calibur::aa, core::chemical::aa_from_name(), compute_entropy_reduction(), compute_max_, ddG_threshold(), energy_reduction_factor(), fast_calc_, no_modified_ddG_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), rb_jump(), repack(), repacking_radius(), scorefxn(), skip_ala_scan(), skip_report_, sym_dof_names(), target_residues_, task_factory(), temperature(), threshold_probability(), protocols::calc_taskop_filters::TR(), type_, unbound(), and write2pdb().

◆ provide_xml_schema()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), class_name(), protocols::filters::complex_type_name_for_filter(), and protocols::calc_taskop_filters::RotBoltzWeight_subelement_ct_name().

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeightFilterCreator::provide_xml_schema().

◆ rb_jump() [1/2]

core::Size protocols::calc_taskop_filters::RotamerBoltzmannWeight::rb_jump ( ) const

References rb_jump_.

Referenced by compute(), compute_Boltzmann_weight(), compute_modified_ddG(), first_pass_ala_scan(), and parse_my_tag().

◆ rb_jump() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::rb_jump ( core::Size const jump )

References rb_jump_.

◆ repack() [1/2]

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::repack ( ) const

References repack_.

Referenced by compute_modified_ddG(), first_pass_ala_scan(), parse_my_tag(), and repack().

◆ repack() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::repack ( bool const repack )

References repack(), and repack_.

◆ repacking_radius() [1/2]

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::repacking_radius ( ) const

References repacking_radius_.

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

◆ repacking_radius() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::repacking_radius ( core::Real const rad )

References repacking_radius_.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply().

◆ report()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), compute_modified_ddG(), core::conformation::Residue::name3(), no_modified_ddG_, core::conformation::membrane::out, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), rot(), rotamer_probabilities_, skip_report_, and type_.

◆ report_sm()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::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(), compute_boltz_probability(), compute_modified_ddG(), no_modified_ddG_, and protocols::calc_taskop_filters::TR().

◆ scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::scorefxn ( ) const

References scorefxn_.

Referenced by compute(), compute_Boltzmann_weight(), compute_modified_ddG(), first_pass_ala_scan(), interface_interaction_energy(), parse_my_tag(), and scorefxn().

◆ scorefxn() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

References scorefxn(), and scorefxn_.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply().

◆ skip_ala_scan() [1/2]

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::skip_ala_scan ( ) const

References skip_ala_scan_.

Referenced by first_pass_ala_scan(), and parse_my_tag().

◆ skip_ala_scan() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::skip_ala_scan ( bool const s )

References skip_ala_scan_.

◆ sym_dof_names() [1/2]

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::sym_dof_names ( ) const

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

◆ sym_dof_names() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::sym_dof_names ( std::string const & dof_names )

References sym_dof_names_.

◆ target_residues()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::target_residues ( std::string const & target_residues_str )

References target_residues_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::task_factory ( ) const

References task_factory_.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), first_pass_ala_scan(), parse_my_tag(), and task_factory().

◆ task_factory() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::task_factory ( core::pack::task::TaskFactoryOP task_factory )

References task_factory(), and task_factory_.

◆ temperature() [1/2]

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::temperature ( ) const

References temperature_.

Referenced by compute(), compute_Boltzmann_weight(), compute_modified_ddG(), and parse_my_tag().

◆ temperature() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::temperature ( core::Real const temp )

References temperature_.

◆ threshold_probability() [1/2]

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::threshold_probability ( core::chemical::AA const aa_type ) const

References threshold_probabilities_per_residue_.

◆ threshold_probability() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::threshold_probability	(	core::chemical::AA const	aa_type,
		core::Real const	probability
	)

References protocols::simple_moves::bb_sampler::probability, and threshold_probabilities_per_residue_.

Referenced by compute_modified_ddG(), and parse_my_tag().

◆ type() [1/2]

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::type ( ) const

References type_.

◆ type() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::type ( std::string const & s )

References type_.

◆ unbound() [1/2]

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::unbound ( ) const

References unbound_.

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

◆ unbound() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::unbound ( bool const u )

References protocols::hybridization::u, and unbound_.

◆ write2pdb() [1/2]

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::write2pdb ( ) const

References write2pdb_.

Referenced by compute(), and parse_my_tag().

◆ write2pdb() [2/2]

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::write2pdb ( bool const write )

References write2pdb_.

◆ write_to_pdb()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::write_to_pdb	(	core::Size const	residue,
		std::string const &	residue_name,
		core::Real const	boltzmann_weight
	)		const

Output per-residue Boltzmann weights to the output pdb file if desired.

References protocols::jd2::add_string_to_current_job(), and protocols::filters::Filter::get_user_defined_name().

Referenced by compute().

Member Data Documentation

◆ compute_entropy_reduction_

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_entropy_reduction_

private

Referenced by compute_entropy_reduction().

◆ compute_max_

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_max_

private

Referenced by compute_boltz_probability(), and parse_my_tag().

◆ ddG_threshold_

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::ddG_threshold_

private

Referenced by ddG_threshold().

◆ ddGs_

std::map< core::Size, core::Real > protocols::calc_taskop_filters::RotamerBoltzmannWeight::ddGs_

mutableprivate

the following are mutable b/c they only sum up data in the filter. They do not affect how the filter is run (so the filter will remain logically constant, despite these variables) Mutability here allows the variables to be changed even in const methods.

Referenced by compute(), compute_modified_ddG(), and first_pass_ala_scan().

◆ energy_reduction_factor_

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::energy_reduction_factor_

private

Referenced by energy_reduction_factor().

◆ fast_calc_

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::fast_calc_

private

Referenced by compute(), and parse_my_tag().

◆ no_modified_ddG_

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::no_modified_ddG_

private

Referenced by compute_modified_ddG(), no_modified_ddG(), parse_my_tag(), report(), and report_sm().

◆ rb_jump_

core::Size protocols::calc_taskop_filters::RotamerBoltzmannWeight::rb_jump_

private

Referenced by rb_jump().

◆ repack_

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::repack_

private

Referenced by repack().

◆ repacking_radius_

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::repacking_radius_

private

Referenced by repacking_radius().

◆ rotamer_probabilities_

std::map< core::Size, core::Real > protocols::calc_taskop_filters::RotamerBoltzmannWeight::rotamer_probabilities_

mutableprivate

Referenced by compute(), compute_boltz_probability(), compute_modified_ddG(), and report().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::scorefxn_

private

Referenced by compute_Boltzmann_weight(), and scorefxn().

◆ skip_ala_scan_

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::skip_ala_scan_

private

Referenced by skip_ala_scan().

◆ skip_report_

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::skip_report_

private

Referenced by parse_my_tag(), and report().

◆ sym_dof_names_

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::sym_dof_names_

private

Referenced by sym_dof_names().

◆ target_residues_

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::target_residues_

private

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

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::task_factory_

private

Referenced by task_factory().

◆ temperature_

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::temperature_

private

Referenced by temperature().

◆ threshold_probabilities_per_residue_

utility::vector1< core::Real > protocols::calc_taskop_filters::RotamerBoltzmannWeight::threshold_probabilities_per_residue_

private

Referenced by RotamerBoltzmannWeight(), and threshold_probability().

◆ type_

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::type_

private

Referenced by compute(), parse_my_tag(), report(), and type().

◆ unbound_

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::unbound_

private

Referenced by unbound().

◆ write2pdb_

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::write2pdb_

private

Referenced by write2pdb().

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

src/protocols/calc_taskop_filters/RotamerBoltzmannWeight.hh
src/protocols/calc_taskop_filters/RotamerBoltzmannWeight.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ RotamerBoltzmannWeight()

◆ ~RotamerBoltzmannWeight()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ compute_boltz_probability()

◆ compute_Boltzmann_weight()

◆ compute_entropy_reduction() [1/2]

◆ compute_entropy_reduction() [2/2]

◆ compute_modified_ddG()

◆ ddG_threshold() [1/2]

◆ ddG_threshold() [2/2]

◆ energy_reduction_factor() [1/2]

◆ energy_reduction_factor() [2/2]

◆ first_pass_ala_scan()

◆ fresh_instance()

◆ interface_interaction_energy()

◆ name()

◆ no_modified_ddG()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ rb_jump() [1/2]

◆ rb_jump() [2/2]

◆ repack() [1/2]

◆ repack() [2/2]

◆ repacking_radius() [1/2]

◆ repacking_radius() [2/2]

◆ report()

◆ report_sm()

◆ scorefxn() [1/2]

◆ scorefxn() [2/2]

◆ skip_ala_scan() [1/2]

◆ skip_ala_scan() [2/2]

◆ sym_dof_names() [1/2]

◆ sym_dof_names() [2/2]

◆ target_residues()

◆ task_factory() [1/2]

◆ task_factory() [2/2]

◆ temperature() [1/2]

◆ temperature() [2/2]

◆ threshold_probability() [1/2]

◆ threshold_probability() [2/2]

◆ type() [1/2]

◆ type() [2/2]

◆ unbound() [1/2]

◆ unbound() [2/2]

◆ write2pdb() [1/2]

◆ write2pdb() [2/2]

◆ write_to_pdb()

Member Data Documentation

◆ compute_entropy_reduction_

◆ compute_max_

◆ ddG_threshold_

◆ ddGs_

◆ energy_reduction_factor_

◆ fast_calc_

◆ no_modified_ddG_

◆ rb_jump_

◆ repack_

◆ repacking_radius_

◆ rotamer_probabilities_

◆ scorefxn_

◆ skip_ala_scan_

◆ skip_report_

◆ sym_dof_names_

◆ target_residues_

◆ task_factory_

◆ temperature_

◆ threshold_probabilities_per_residue_