#include <ProQ_Energy.hh>

Public Types
typedef WholeStructureEnergy	parent

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

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

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

	ProQ_Energy (ProQ_Energy const &src)

virtual EnergyMethodOP	clone () const
	clone More...

virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &scorefxn) const

virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &scorefxn, EnergyMap &totals) const
	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...

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

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

virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	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...

virtual	~WholeStructureEnergy ()

EnergyMethodType	method_type () const
	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...

	EnergyMethod (EnergyMethod const &src)
	Copy constructor copies over the score types of the source. More...

virtual	~EnergyMethod ()

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const

virtual void	prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	ensure this function gets called. The default behavior is to do nothing. 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	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 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...

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, 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, dssp::Dssp &ss, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=11) const

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

void	ss_sc_feature (pose::Pose &pose, 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
ProQPotential const &	potential_

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

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

Constructor & Destructor Documentation

core::scoring::methods::ProQ_Energy::ProQ_Energy ( )

c-tor

References initialize().

Referenced by clone().

core::scoring::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

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

private

References atom13_0().

Referenced by atom_feature().

int core::scoring::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().

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

private

References atom13(), core::graph::Node::const_edge_list_end(), numeric::xyzVector< class >::distance_squared(), core::pose::Pose::energies(), core::graph::Edge::get_node(), l, nres, nres_, basic::options::option, basic::options::OptionKeys::ProQ::prof_bug, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

Distance core::scoring::methods::ProQ_Energy::atomic_interaction_cutoff ( ) const

virtual

ProQ_Energy distance cutoff.

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

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

private

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

private

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

private

References core::conformation::Residue::atom(), core::conformation::membrane::center, numeric::xyzVector< class >::dot(), core::sequence::end, core::scoring::MembraneTopology::helix_id(), basic::options::OptionKeys::ProQ::membrane, core::conformation::membrane::normal, numeric::xyzVector< class >::normalize(), nres_, basic::options::option, core::pose::Pose::residue(), core::scoring::MembraneTopology::span_begin(), core::scoring::MembraneTopology::span_end(), start, core::scoring::MembraneTopology::tmhelix(), topology_, core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by calculate_feature_vector().

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

virtual

clone

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

References ProQ_Energy().

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

private

References numeric::xyzVector< class >::distance_squared(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by res_feature().

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

private

References entropy_, nres, and nres_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

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

virtual

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(), basic::options::OptionKeys::ProQ::normalize, nres, nres_, core::scoring::ProQPotential::num_features_proq2(), core::scoring::ProQPotential::num_features_proqm(), basic::options::option, basic::options::OptionKeys::ProQ::output_local_prediction, output_local_prediction(), potential_, core::scoring::ProQ, core::scoring::ProQM, core::scoring::ProQPotential::score(), core::pose::Pose::total_residue(), and core::scoring::methods::TR.

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

private

References match, nres, nres_, and rsa_class_pred_.

Referenced by calculate_feature_vector_proq2().

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

private

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

Referenced by calculate_feature_vector_proq2().

virtual void core::scoring::methods::ProQ_Energy::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required ) const

inlinevirtual

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.

void core::scoring::methods::ProQ_Energy::initialize ( )

private

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

private

References utility::io::ozstream::close(), core::pose::Pose::data(), exit, basic::datacache::BasicDataCache::get(), utility::io::ozstream::good(), gz, basic::datacache::BasicDataCache::has(), nres_, basic::options::option, output, basic::options::OptionKeys::ProQ::prefix, tag, and basic::options::OptionKeys::ProQ::use_gzip.

Referenced by finalize_total_energy().

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

private

References nres, nres_, and scaled_logodds_profile_.

Referenced by calculate_feature_vector().

char core::scoring::methods::ProQ_Energy::profile_index_to_aa ( int i ) const

private

Referenced by res_feature(), and sum_profile().

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

private

References nres, nres_, and rsa_pred_.

Referenced by calculate_feature_vector().

void core::scoring::methods::ProQ_Energy::read_acc ( std::string accfile )

private

References utility::io::izstream::fail(), getline(), l, nres_, utility::io::izstream::open(), rsa_class_pred_, runtime_assert, and utility_exit_with_message.

Referenced by initialize().

void core::scoring::methods::ProQ_Energy::read_mpSA ( std::string mpSAfile )

private

References utility::io::izstream::fail(), getline(), l, nres_, utility::io::izstream::open(), rsa_class_pred_, rsa_pred_, and utility_exit_with_message.

Referenced by initialize().

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

private

References utility::io::izstream::close(), entropy_, utility::io::izstream::fail(), getline(), l, nres, nres_, utility::io::izstream::open(), prob_profile_, scaled_logodds_profile_, core::scoring::methods::TR, and utility_exit_with_message.

Referenced by initialize().

void core::scoring::methods::ProQ_Energy::read_ss2 ( std::string ss2file )

private

References utility::io::izstream::fail(), utility::io::izstream::get(), getline(), l, nres_, utility::io::izstream::open(), ss1_, ss_pred_, and utility_exit_with_message.

Referenced by initialize().

void core::scoring::methods::ProQ_Energy::read_zpred ( std::string zpredfile )

private

References utility::io::izstream::fail(), getline(), l, nres_, utility::io::izstream::open(), utility_exit_with_message, and z_pred_.

Referenced by initialize().

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

private

References core::conformation::Residue::name1().

Referenced by res_feature(), and sum_profile().

int core::scoring::methods::ProQ_Energy::res6 ( char const aa ) const

private

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

private

References core::graph::Node::const_edge_list_end(), crd(), core::pose::Pose::energies(), core::graph::Edge::get_node(), l, nres, nres_, basic::options::option, prob_profile_, basic::options::OptionKeys::ProQ::prof_bug, profile_index_to_aa(), res6(), and core::pose::Pose::residue().

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

void core::scoring::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, and nres_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

void core::scoring::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, nres_, and rsa_class_pred_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

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

virtual

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

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

void core::scoring::methods::ProQ_Energy::ss_feature	(	pose::Pose &	pose,
		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, nres_, ss_pred_, and ss_type.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

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

private

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

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

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

private

References core::pack::dunbrack::c, core::scoring::dssp::Dssp::get_dssp_secstruct(), nres, and nres_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

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

private

References prob_profile_, profile_index_to_aa(), and res6().

Referenced by surf_feature().

void core::scoring::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, nres_, start, and sum_profile().

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

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

private

References nres, and nres_.

Referenced by calculate_feature_vector(), and calculate_feature_vector_proq2().

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

private

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

Referenced by calculate_feature_vector().

core::Size core::scoring::methods::ProQ_Energy::version ( ) const

virtual

Return the version of the energy method.

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

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