#include <ProQ_Energy.hh>

Inheritance diagram for core::energy_methods::ProQ_Energy:

[legend]

Public Types
typedef core::scoring::methods::WholeStructureEnergy	parent

Public Types inherited from core::scoring::methods::WholeStructureEnergy
typedef EnergyMethod	parent

Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::VirtualBase	parent

Public Member Functions
	ProQ_Energy ()
	c-tor More...

	ProQ_Energy (ProQ_Energy const &src)

core::scoring::methods::EnergyMethodOP	clone () const override
	clone More...

void	setup_for_scoring (pose::Pose &pose, core::scoring::ScoreFunction const &scorefxn) const override
	if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing. More...

void	finalize_total_energy (pose::Pose &pose, core::scoring::ScoreFunction const &scorefxn, core::scoring::EnergyMap &totals) const override
	called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call. More...

core::Size	version () const override
	Return the version of the energy method. More...

Distance	atomic_interaction_cutoff () const override
	ProQ_Energy distance cutoff. More...

void	indicate_required_context_graphs (utility::vector1< bool > &) const override
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...

Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy
	WholeStructureEnergy (EnergyMethodCreatorOP)
	Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More...

	~WholeStructureEnergy () override

EnergyMethodType	method_type () const override
	Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...

Public Member Functions inherited from core::scoring::methods::EnergyMethod
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
	if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

virtual void	setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const
	if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More...

virtual void	prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const
	If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const
	Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More...

virtual void	setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const
	Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More...

virtual void	finalize_after_minimizing (pose::Pose &pose) const
	Called after minimization, allowing a derived class to do some teardown steps. More...

virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...

virtual void	finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
	called at the end of derivatives evaluation More...

virtual bool	minimize_in_whole_structure_context (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More...

virtual bool	defines_high_order_terms (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...

virtual bool	has_atomistic_energies () const
	Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method? Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it's not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods. More...

virtual bool	has_atomistic_pairwise_energies () const
	Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method? NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. More...

virtual void	atomistic_energy (core::Size atmno, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const
	Evaluate the (one body) energy associated with a particular atom This may be a "self" energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies() More...

virtual void	atomistic_pair_energy (core::Size atmno1, conformation::Residue const &rsd1, core::Size atomno2, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const
	Evaluate the energy for a particular pair of atoms This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies() More...

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const
	Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More...

ScoreTypes const &	score_types () const
	Returns the score types that this energy method computes. More...

virtual void	show_additional_info (std::ostream &, pose::Pose &, bool) const
	show additional information of the energy method More...

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...

Private Member Functions
void	initialize ()

void	output_local_prediction (pose::Pose &pose, ObjexxFCL::FArray1D< Real > &proq, std::string name) const

void	calculate_feature_vector (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &feature_vector) const

void	calculate_feature_vector_proq2 (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &feature_vector) const

Size	read_profiles_and_entropy (std::string profile, std::string mtxfile)

void	read_zpred (std::string zpredfile)

void	read_mpSA (std::string mpSAfile)

void	read_acc (std::string accfile)

void	read_ss2 (std::string ss2file)

void	atom_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, Size index, int windowsize=21) const

void	res_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, Size index, int windowsize=21) const

void	surf_feature (pose::Pose &pose, utility::vector1< Real > &rsd_sasa_rel, ObjexxFCL::FArray2D< Real > &vec, Size index, int windowsize=21) const

void	gss_sc_feature (pose::Pose &pose, core::scoring::dssp::Dssp &ss, ObjexxFCL::FArray2D< Real > &vec, Size index) const

void	grsa_sc_feature (pose::Pose &pose, utility::vector1< Real > &rsd_sasa_rel, ObjexxFCL::FArray2D< Real > &vec, Size index) const

void	stride_feature (pose::Pose &pose, core::scoring::dssp::Dssp &ss, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=11) const

void	ss_feature (pose::Pose &pose, core::scoring::dssp::Dssp &ss, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=1) const

void	ss_sc_feature (pose::Pose &pose, core::scoring::dssp::Dssp &ss, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=21) const

void	topology_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index) const

void	zpred_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index) const

void	z_feature (pose::Pose &pose, ObjexxFCL::FArray1D< Real > &Z, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index) const

void	entropy_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=11) const

void	profile_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=3) const

void	rsa_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, utility::vector1< Real > &rsd_sasa_rel, int const pos, Size index, int windowsize=1) const

void	prsa_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=1) const

void	rsa_sc_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, utility::vector1< Real > &rsd_sasa_rel, int const pos, Size index, int windowsize=21) const

void	termini_feature (pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=23) const

Real	crd (pose::Pose &pose, Size i, Size j) const

int	res6 (conformation::Residue const &rsd) const

int	res6 (char const aa) const

int	atom13 (conformation::Residue const &rsd, Size atom_i) const

int	atom13_0 (conformation::Residue const &rsd, Size atom_i) const

char	profile_index_to_aa (int i) const

void	sum_profile (Size k, ObjexxFCL::FArray1D< Real > &vec) const

void	calculateZ (pose::Pose &pose, ObjexxFCL::FArray1D< Real > &Z) const

Private Attributes
core::scoring::ProQPotential const &	potential_

core::scoring::MembraneTopology	topology_

ObjexxFCL::FArray2D< Real >	prob_profile_

ObjexxFCL::FArray2D< Real >	scaled_logodds_profile_

ObjexxFCL::FArray1D< Real >	entropy_

Size	nres_

ObjexxFCL::FArray2D< Real >	ss_pred_

ObjexxFCL::FArray1D< char >	ss1_

ObjexxFCL::FArray1D< Real >	z_pred_

ObjexxFCL::FArray1D< Real >	rsa_pred_

ObjexxFCL::FArray1D< char >	rsa_class_pred_

bool	all_inputs_ProQM_

bool	all_inputs_ProQ2_

Additional Inherited Members
Protected Member Functions inherited from core::scoring::methods::EnergyMethod
void	set_score_types (EnergyMethodCreatorOP creator)
	Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More...

Member Typedef Documentation

◆ parent

typedef core::scoring::methods::WholeStructureEnergy core::energy_methods::ProQ_Energy::parent

Constructor & Destructor Documentation

◆ ProQ_Energy() [1/2]

core::energy_methods::ProQ_Energy::ProQ_Energy ( )

c-tor

References initialize().

◆ ProQ_Energy() [2/2]

core::energy_methods::ProQ_Energy::ProQ_Energy ( ProQ_Energy const & src )

References all_inputs_ProQ2_, all_inputs_ProQM_, entropy_, nres_, prob_profile_, rsa_class_pred_, rsa_pred_, scaled_logodds_profile_, ss1_, ss_pred_, topology_, and z_pred_.

Member Function Documentation

◆ atom13()

int core::energy_methods::ProQ_Energy::atom13	(	conformation::Residue const &	rsd,
		Size	atom_i
	)		const

private

References atom13_0().

Referenced by atom_feature().

◆ atom13_0()

int core::energy_methods::ProQ_Energy::atom13_0	(	conformation::Residue const &	rsd,
		Size	atom_i
	)		const

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::chemical::AtomType::is_virtual(), and core::conformation::Residue::name3().

Referenced by atom13().

◆ atom_feature()

void core::energy_methods::ProQ_Energy::atom_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		Size	index,
		int	windowsize = `21`
	)		const

private

References core::conformation::Residue::atom(), atom13(), core::pose::Pose::energies(), core::conformation::Residue::nheavyatoms(), nres_, core::pose::Pose::residue(), core::scoring::Energies::twelveA_neighbor_graph(), and core::conformation::Atom::xyz().

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ atomic_interaction_cutoff()

Distance core::energy_methods::ProQ_Energy::atomic_interaction_cutoff ( ) const

overridevirtual

ProQ_Energy distance cutoff.

Reimplemented from core::scoring::methods::WholeStructureEnergy.

◆ calculate_feature_vector()

void core::energy_methods::ProQ_Energy::calculate_feature_vector	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	feature_vector
	)		const

private

◆ calculate_feature_vector_proq2()

void core::energy_methods::ProQ_Energy::calculate_feature_vector_proq2	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	feature_vector
	)		const

private

References atom_feature(), core::scoring::calc_per_atom_sasa_sc(), core::pose::Pose::data(), core::scoring::dssp::Dssp::dssp_reduced(), entropy_feature(), grsa_sc_feature(), gss_sc_feature(), nres_, res_feature(), rsa_feature(), rsa_sc_feature(), ss_feature(), ss_sc_feature(), protocols::kinmatch::str(), stride_feature(), surf_feature(), and termini_feature().

Referenced by finalize_total_energy().

◆ calculateZ()

void core::energy_methods::ProQ_Energy::calculateZ	(	pose::Pose &	pose,
		ObjexxFCL::FArray1D< Real > &	Z
	)		const

private

References core::conformation::Residue::atom(), core::conformation::membrane::center, core::sequence::end, core::scoring::MembraneTopology::helix_id(), core::conformation::membrane::normal, nres_, core::pose::Pose::residue(), core::scoring::MembraneTopology::span_begin(), core::scoring::MembraneTopology::span_end(), protocols::loops::start, core::scoring::MembraneTopology::tmhelix(), topology_, and core::conformation::Atom::xyz().

Referenced by calculate_feature_vector().

◆ clone()

core::scoring::methods::EnergyMethodOP core::energy_methods::ProQ_Energy::clone ( ) const

overridevirtual

clone

Implements core::scoring::methods::EnergyMethod.

◆ crd()

Real core::energy_methods::ProQ_Energy::crd	(	pose::Pose &	pose,
		Size	i,
		Size	j
	)		const

private

References core::conformation::Residue::atom(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by res_feature().

◆ entropy_feature()

void core::energy_methods::ProQ_Energy::entropy_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index,
		int	windowsize = `11`
	)		const

private

References entropy_, and nres_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ finalize_total_energy()

void core::energy_methods::ProQ_Energy::finalize_total_energy	(	pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		core::scoring::EnergyMap &	total_energy
	)		const

overridevirtual

called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

called at the end of energy evaluation

Reimplemented from core::scoring::methods::EnergyMethod.

References all_inputs_ProQ2_, all_inputs_ProQM_, calculate_feature_vector(), calculate_feature_vector_proq2(), entropy_, core::scoring::ScoreFunction::get_weight(), nres_, core::scoring::ProQPotential::num_features_proq2(), core::scoring::ProQPotential::num_features_proqm(), output_local_prediction(), potential_, core::scoring::ProQ, core::scoring::ProQM, core::scoring::ProQPotential::score(), core::pose::Pose::size(), and core::energy_methods::TR().

◆ grsa_sc_feature()

void core::energy_methods::ProQ_Energy::grsa_sc_feature	(	pose::Pose &	pose,
		utility::vector1< Real > &	rsd_sasa_rel,
		ObjexxFCL::FArray2D< Real > &	vec,
		Size	index
	)		const

private

References nres_, and rsa_class_pred_.

Referenced by calculate_feature_vector_proq2().

◆ gss_sc_feature()

void core::energy_methods::ProQ_Energy::gss_sc_feature	(	pose::Pose &	pose,
		core::scoring::dssp::Dssp &	ss,
		ObjexxFCL::FArray2D< Real > &	vec,
		Size	index
	)		const

private

References core::scoring::dssp::Dssp::get_dssp_secstruct(), nres_, and ss1_.

Referenced by calculate_feature_vector_proq2().

◆ indicate_required_context_graphs()

void core::energy_methods::ProQ_Energy::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required ) const

inlineoverridevirtual

Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

Implements core::scoring::methods::EnergyMethod.

◆ initialize()

void core::energy_methods::ProQ_Energy::initialize ( )

private

References all_inputs_ProQ2_, all_inputs_ProQM_, entropy_, core::scoring::MembraneTopology::initialize(), nres_, read_acc(), read_mpSA(), read_profiles_and_entropy(), read_ss2(), read_zpred(), topology_, and core::energy_methods::TR().

Referenced by ProQ_Energy().

◆ output_local_prediction()

void core::energy_methods::ProQ_Energy::output_local_prediction	(	pose::Pose &	pose,
		ObjexxFCL::FArray1D< Real > &	proq,
		std::string	name
	)		const

private

References core::pose::Pose::data(), nres_, and protocols::kinmatch::str().

Referenced by finalize_total_energy().

◆ profile_feature()

void core::energy_methods::ProQ_Energy::profile_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index,
		int	windowsize = `3`
	)		const

private

References nres_, and scaled_logodds_profile_.

Referenced by calculate_feature_vector().

◆ profile_index_to_aa()

char core::energy_methods::ProQ_Energy::profile_index_to_aa ( int i ) const

private

References core::chemical::oneletter_code_from_aa().

Referenced by res_feature(), and sum_profile().

◆ prsa_feature()

void core::energy_methods::ProQ_Energy::prsa_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index,
		int	windowsize = `1`
	)		const

private

References nres_, and rsa_pred_.

Referenced by calculate_feature_vector().

◆ read_acc()

void core::energy_methods::ProQ_Energy::read_acc ( std::string accfile )

private

References nres_, and rsa_class_pred_.

Referenced by initialize().

◆ read_mpSA()

void core::energy_methods::ProQ_Energy::read_mpSA ( std::string mpSAfile )

private

References nres_, rsa_class_pred_, and rsa_pred_.

Referenced by initialize().

◆ read_profiles_and_entropy()

Size core::energy_methods::ProQ_Energy::read_profiles_and_entropy	(	std::string	profile,
		std::string	mtxfile
	)

private

References entropy_, nres_, prob_profile_, scaled_logodds_profile_, and core::energy_methods::TR().

Referenced by initialize().

◆ read_ss2()

void core::energy_methods::ProQ_Energy::read_ss2 ( std::string ss2file )

private

References nres_, ss1_, and ss_pred_.

Referenced by initialize().

◆ read_zpred()

void core::energy_methods::ProQ_Energy::read_zpred ( std::string zpredfile )

private

References nres_, and z_pred_.

Referenced by initialize().

◆ res6() [1/2]

int core::energy_methods::ProQ_Energy::res6 ( char const aa ) const

private

References protocols::cluster::calibur::aa.

◆ res6() [2/2]

int core::energy_methods::ProQ_Energy::res6 ( conformation::Residue const & rsd ) const

private

References protocols::cluster::calibur::aa, and core::conformation::Residue::name1().

Referenced by res_feature(), and sum_profile().

◆ res_feature()

void core::energy_methods::ProQ_Energy::res_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		Size	index,
		int	windowsize = `21`
	)		const

private

References crd(), core::pose::Pose::energies(), core::chemical::first_l_aa, nres_, core::chemical::num_canonical_aas, prob_profile_, profile_index_to_aa(), res6(), core::pose::Pose::residue(), and core::scoring::Energies::twelveA_neighbor_graph().

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ rsa_feature()

void core::energy_methods::ProQ_Energy::rsa_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		utility::vector1< Real > &	rsd_sasa_rel,
		int const	pos,
		Size	index,
		int	windowsize = `1`
	)		const

private

References nres_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ rsa_sc_feature()

void core::energy_methods::ProQ_Energy::rsa_sc_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		utility::vector1< Real > &	rsd_sasa_rel,
		int const	pos,
		Size	index,
		int	windowsize = `21`
	)		const

private

References nres_, and rsa_class_pred_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ setup_for_scoring()

void core::energy_methods::ProQ_Energy::setup_for_scoring	(	pose::Pose &	,
		core::scoring::ScoreFunction const &
	)		const

overridevirtual

if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

Reimplemented from core::scoring::methods::EnergyMethod.

References potential_, core::scoring::ProQPotential::setup_for_scoring(), and core::pose::Pose::update_residue_neighbors().

◆ ss_feature()

void core::energy_methods::ProQ_Energy::ss_feature	(	pose::Pose &	pose,
		core::scoring::dssp::Dssp &	ss,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index,
		int	windowsize = `1`
	)		const

private

References core::scoring::dssp::Dssp::get_dssp_secstruct(), nres_, and ss_pred_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ ss_sc_feature()

void core::energy_methods::ProQ_Energy::ss_sc_feature	(	pose::Pose &	pose,
		core::scoring::dssp::Dssp &	ss,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index,
		int	windowsize = `21`
	)		const

private

References core::scoring::dssp::Dssp::get_dssp_secstruct(), nres_, and ss1_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ stride_feature()

void core::energy_methods::ProQ_Energy::stride_feature	(	pose::Pose &	pose,
		core::scoring::dssp::Dssp &	ss,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index,
		int	windowsize = `11`
	)		const

private

References core::scoring::dssp::Dssp::get_dssp_secstruct(), and nres_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ sum_profile()

void core::energy_methods::ProQ_Energy::sum_profile	(	Size	k,
		ObjexxFCL::FArray1D< Real > &	vec
	)		const

private

References core::chemical::first_l_aa, core::chemical::num_canonical_aas, prob_profile_, profile_index_to_aa(), and res6().

Referenced by surf_feature().

◆ surf_feature()

void core::energy_methods::ProQ_Energy::surf_feature	(	pose::Pose &	pose,
		utility::vector1< Real > &	rsd_sasa_rel,
		ObjexxFCL::FArray2D< Real > &	vec,
		Size	index,
		int	windowsize = `21`
	)		const

private

References nres_, protocols::loops::start, and sum_profile().

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ termini_feature()

void core::energy_methods::ProQ_Energy::termini_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index,
		int	windowsize = `23`
	)		const

private

References nres_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

◆ topology_feature()

void core::energy_methods::ProQ_Energy::topology_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index
	)		const

private

References nres_, core::scoring::MembraneTopology::tmregion(), and topology_.

Referenced by calculate_feature_vector().

◆ version()

core::Size core::energy_methods::ProQ_Energy::version ( ) const

overridevirtual

Return the version of the energy method.

Implements core::scoring::methods::EnergyMethod.

◆ z_feature()

void core::energy_methods::ProQ_Energy::z_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray1D< Real > &	Z,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index
	)		const

private

References nres_.

Referenced by calculate_feature_vector().

◆ zpred_feature()

void core::energy_methods::ProQ_Energy::zpred_feature	(	pose::Pose &	pose,
		ObjexxFCL::FArray2D< Real > &	vec,
		int const	pos,
		Size	index
	)		const

private

References nres_, and z_pred_.

Referenced by calculate_feature_vector().

Member Data Documentation

◆ all_inputs_ProQ2_

bool core::energy_methods::ProQ_Energy::all_inputs_ProQ2_

private

Referenced by finalize_total_energy(), initialize(), and ProQ_Energy().

◆ all_inputs_ProQM_

bool core::energy_methods::ProQ_Energy::all_inputs_ProQM_

private

Referenced by finalize_total_energy(), initialize(), and ProQ_Energy().

◆ entropy_

ObjexxFCL::FArray1D< Real > core::energy_methods::ProQ_Energy::entropy_

private

Referenced by entropy_feature(), finalize_total_energy(), initialize(), ProQ_Energy(), and read_profiles_and_entropy().

◆ nres_

Size core::energy_methods::ProQ_Energy::nres_

private

◆ potential_

core::scoring::ProQPotential const& core::energy_methods::ProQ_Energy::potential_

private

Referenced by finalize_total_energy(), and setup_for_scoring().

◆ prob_profile_

ObjexxFCL::FArray2D< Real > core::energy_methods::ProQ_Energy::prob_profile_

private

Referenced by ProQ_Energy(), read_profiles_and_entropy(), res_feature(), and sum_profile().

◆ rsa_class_pred_

ObjexxFCL::FArray1D< char > core::energy_methods::ProQ_Energy::rsa_class_pred_

private

Referenced by grsa_sc_feature(), ProQ_Energy(), read_acc(), read_mpSA(), and rsa_sc_feature().

◆ rsa_pred_

ObjexxFCL::FArray1D< Real > core::energy_methods::ProQ_Energy::rsa_pred_

private

Referenced by ProQ_Energy(), prsa_feature(), and read_mpSA().

◆ scaled_logodds_profile_

ObjexxFCL::FArray2D< Real > core::energy_methods::ProQ_Energy::scaled_logodds_profile_

private

Referenced by profile_feature(), ProQ_Energy(), and read_profiles_and_entropy().

◆ ss1_

ObjexxFCL::FArray1D< char > core::energy_methods::ProQ_Energy::ss1_

private

Referenced by gss_sc_feature(), ProQ_Energy(), read_ss2(), and ss_sc_feature().

◆ ss_pred_

ObjexxFCL::FArray2D< Real > core::energy_methods::ProQ_Energy::ss_pred_

private

Referenced by ProQ_Energy(), read_ss2(), and ss_feature().

◆ topology_

core::scoring::MembraneTopology core::energy_methods::ProQ_Energy::topology_

private

Referenced by calculateZ(), initialize(), ProQ_Energy(), and topology_feature().

◆ z_pred_

ObjexxFCL::FArray1D< Real > core::energy_methods::ProQ_Energy::z_pred_

private

Referenced by ProQ_Energy(), read_zpred(), and zpred_feature().

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

src/core/energy_methods/ProQ_Energy.hh
src/core/energy_methods/ProQ_Energy.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ ProQ_Energy() [1/2]

◆ ProQ_Energy() [2/2]

Member Function Documentation

◆ atom13()

◆ atom13_0()

◆ atom_feature()

◆ atomic_interaction_cutoff()

◆ calculate_feature_vector()

◆ calculate_feature_vector_proq2()

◆ calculateZ()

◆ clone()

◆ crd()

◆ entropy_feature()

◆ finalize_total_energy()

◆ grsa_sc_feature()

◆ gss_sc_feature()

◆ indicate_required_context_graphs()

◆ initialize()

◆ output_local_prediction()

◆ profile_feature()

◆ profile_index_to_aa()

◆ prsa_feature()

◆ read_acc()

◆ read_mpSA()

◆ read_profiles_and_entropy()

◆ read_ss2()

◆ read_zpred()

◆ res6() [1/2]

◆ res6() [2/2]

◆ res_feature()

◆ rsa_feature()

◆ rsa_sc_feature()

◆ setup_for_scoring()

◆ ss_feature()

◆ ss_sc_feature()

◆ stride_feature()

◆ sum_profile()

◆ surf_feature()

◆ termini_feature()

◆ topology_feature()

◆ version()

◆ z_feature()

◆ zpred_feature()

Member Data Documentation

◆ all_inputs_ProQ2_

◆ all_inputs_ProQM_

◆ entropy_

◆ nres_

◆ potential_

◆ prob_profile_

◆ rsa_class_pred_

◆ rsa_pred_

◆ scaled_logodds_profile_

◆ ss1_

◆ ss_pred_

◆ topology_

◆ z_pred_