#include <NMerSVMEnergy.hh>

Inheritance diagram for core::scoring::methods::NMerSVMEnergy:

Public Types
typedef ContextIndependentOneBodyEnergy	parent

Public Types inherited from core::scoring::methods::ContextIndependentOneBodyEnergy
typedef OneBodyEnergy	parent

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

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

Public Member Functions
	NMerSVMEnergy ()=delete
	Default constructor is explicitly deleted. Only EnergyMethodOptions constructor is allowed. More...

	NMerSVMEnergy (EnergyMethodOptions const &options)
	EnergyMethodOptions constructor. More...

	NMerSVMEnergy (EnergyMethodOptions const &options, utility::vector1< std::string > const &svm_fnames, utility::vector1< std::string > const &svm_rank_fnames)

	NMerSVMEnergy (core::Size const nmer_length, bool const gate_svm_scores, core::Size const term_length, bool const use_pssm_features, bool const avg_rank_as_energy, core::Real const nmer_svm_scorecut, utility::vector1< std::string > const &svm_fname_vec, utility::vector1< std::string > const &svm_rank_fname_vec, utility::vector1< std::string > const &pssm_fname_vec)

	NMerSVMEnergy (core::Size const nmer_length, bool const gate_svm_scores, core::Size const term_length, bool const use_pssm_features, bool const avg_rank_as_energy, core::Real const nmer_svm_scorecut, utility::vector1< std::string > const &svm_fname_vec, utility::vector1< std::string > const &svm_rank_fname_vec, utility::vector1< std::string > const &pssm_fname_vec, std::string const &aa_matrix)

EnergyMethodOP	clone () const override

virtual bool	operator== (NMerSVMEnergy const &) const

void	residue_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const override
	Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them). More...

bool	minimize_in_whole_structure_context (pose::Pose const &) const override
	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 Real	eval_dof_derivative (id::DOF_ID const &dof_id, id::TorsionID const &tor_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const

void	indicate_required_context_graphs (utility::vector1< bool > &) const override
	context independent; indicates that no context graphs are required More...

void	get_residue_energy_from_sequence (std::string const &, core::Size const &, core::Real &, core::Real &, utility::vector1< core::Real > &, utility::vector1< core::Real > &) const
	the main compute function, rsd_energy_avg is the default return value for residue energy More...

void	get_residue_energy_by_svm (core::pose::Pose const &, core::Size const &, core::Real &, core::Real &, utility::vector1< core::Real > &, utility::vector1< core::Real > &) const
	the main compute function, rsd_energy_avg is the default return value for residue energy More...

void	read_nmer_svm_list (std::string const &)

void	read_nmer_svm (std::string const &)

void	read_nmer_svm_rank_list (std::string const &)
	load svm_ranks from a list file More...

void	read_nmer_svm_rank (std::string const &)
	this is a sorted (ascending) list of precomputed energies of a bunch (100k) of random human peptides More...

void	read_nmer_svm_fname_vector (utility::vector1< std::string > const &)

void	read_nmer_svm_rank_fname_vector (utility::vector1< std::string > const &)

void	read_pssm_features (std::string const )

core::Size	n_svms () const

void	read_aa_encoding_matrix (std::string const &)

void	nmer_length (core::Size const )

core::Size	nmer_length () const

void	term_length (core::Size const )

core::Size	term_length () const

void	use_pssm_features (bool const )

void	avg_rank_as_energy (bool const )

bool	avg_rank_as_energy () const

void	gate_svm_scores (bool const )

void	nmer_svm_scorecut (core::Real const )

utility::vector1 < utility::libsvm::Svm_node_rosettaOP >	get_svm_nodes (utility::vector1< core::Real > const &) const

utility::vector1< core::Real >	encode_aa_string (std::string const &) const

utility::vector1< core::Real >	encode_wtd_avg_aa_string (std::string const &, utility::vector1< core::Real > const &) const

utility::vector1< core::Real >	encode_nmer (std::string const &, core::Size const, core::Size const ) const

void	add_encoded_termini (std::string const &, core::Size const, utility::vector1< core::Real > &) const

void	add_pssm_features (std::string const &, core::Size const, utility::vector1< core::Real > &) const

Public Member Functions inherited from core::scoring::methods::ContextIndependentOneBodyEnergy
	ContextIndependentOneBodyEnergy (EnergyMethodCreatorOP)
	Constructor with an EnergyMethodCreator to inform the parent class which ScoreTypes this EnergyMethod is responsible for computing. More...

EnergyMethodType	method_type () const override
	Returns the ci_1b element of the EnergyMethodType enumeration; this method should NOT be overridden by derived classes. More...

Public Member Functions inherited from core::scoring::methods::OneBodyEnergy
	OneBodyEnergy (EnergyMethodCreatorOP)
	Constructor with an EnergyMethodCreator to inform the EnergyMethod parent which ScoreTypes this EnergyMethod is responsible for computing. More...

	~OneBodyEnergy () override

virtual bool	defines_score_for_residue (conformation::Residue const &) const
	During minimization, energy methods are allowed to decide that they say nothing about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return "true" for all residues. More...

virtual bool	use_extended_residue_energy_interface () const
	Rely on the extended version of the residue_energy function during score-function evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return 'true' for the extended version. The default method implemented in this class returns 'false'. More...

virtual void	residue_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap &emap) const
	Evaluate the one-body energies for a particular residue, in the context of a given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns "true". Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...

virtual void	setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &, kinematics::MinimizerMapBase const &, basic::datacache::BasicDataCache &, ResSingleMinimizationData &) const
	Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...

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

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const
	Do any setup work should the coordinates of this residue, who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. More...

virtual bool	requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More...

virtual void	setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &res_data_cache) const
	Do any setup work necessary before evaluating the derivatives for this residue. More...

virtual void	eval_residue_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const
	Evaluate the derivative for an atom in a residue in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. DEPRECATED – too slow. More...

virtual bool	defines_dof_derivatives (pose::Pose const &p) const
	Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More...

virtual utility::vector1 < id::PartialAtomID >	atoms_with_dof_derivatives (conformation::Residue const &res, pose::Pose const &pose) const
	For a particular residue, list which atoms go into defining the DOF derivatives, including any atoms on adjacent residues. The Pose is provided for context, but there is no requirement that res be a member of that Pose. More...

virtual Real	eval_residue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const
	Evaluate the DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. 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 void	setup_for_scoring (pose::Pose &, ScoreFunction const &) const
	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...

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	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...

virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) 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...

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	read_nmer_svms_from_options (EnergyMethodOptions const &options)

void	initialize_from_options (EnergyMethodOptions const &options)

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

Private Attributes
utility::vector1 < utility::libsvm::Svm_rosettaCOP >	all_nmer_svms_

utility::vector1 < utility::vector1< core::Real > >	all_nmer_svms_ranks_

std::map< char, utility::vector1< core::Real > >	aa_encoder_

core::Size	nmer_length_

core::Size	nmer_cterm_

core::Size	term_length_

bool	gate_svm_scores_

bool	use_pssm_features_

bool	avg_rank_as_energy_

core::Real	nmer_svm_scorecut_

core::scoring::methods::NMerPSSMEnergy	nmer_pssm_

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 ContextIndependentOneBodyEnergy core::scoring::methods::NMerSVMEnergy::parent

Constructor & Destructor Documentation

core::scoring::methods::NMerSVMEnergy::NMerSVMEnergy ( )

delete

Default constructor is explicitly deleted. Only EnergyMethodOptions constructor is allowed.

core::scoring::methods::NMerSVMEnergy::NMerSVMEnergy ( EnergyMethodOptions const & options )

EnergyMethodOptions constructor.

References initialize_from_options(), and read_nmer_svms_from_options().

core::scoring::methods::NMerSVMEnergy::NMerSVMEnergy	(	EnergyMethodOptions const &	options,
		utility::vector1< std::string > const &	svm_fnames,
		utility::vector1< std::string > const &	svm_rank_fnames
	)

References all_nmer_svms_, all_nmer_svms_ranks_, initialize_from_options(), read_nmer_svm(), and read_nmer_svm_rank().

core::scoring::methods::NMerSVMEnergy::NMerSVMEnergy	(	core::Size const	nmer_length,
		bool const	gate_svm_scores,
		core::Size const	term_length,
		bool const	use_pssm_features,
		bool const	avg_rank_as_energy,
		core::Real const	nmer_svm_scorecut,
		utility::vector1< std::string > const &	svm_fname_vec,
		utility::vector1< std::string > const &	svm_rank_fname_vec,
		utility::vector1< std::string > const &	pssm_fname_vec
	)

References avg_rank_as_energy(), core::scoring::methods::NMerPSSMEnergy::gate_pssm_scores(), gate_svm_scores(), core::scoring::methods::NMerPSSMEnergy::nmer_length(), nmer_length(), nmer_pssm_, core::scoring::methods::NMerPSSMEnergy::nmer_pssm_scorecut(), nmer_svm_scorecut(), read_aa_encoding_matrix(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_fname_vector(), read_nmer_svm_fname_vector(), read_nmer_svm_rank_fname_vector(), term_length(), and use_pssm_features().

core::scoring::methods::NMerSVMEnergy::NMerSVMEnergy	(	core::Size const	nmer_length,
		bool const	gate_svm_scores,
		core::Size const	term_length,
		bool const	use_pssm_features,
		bool const	avg_rank_as_energy,
		core::Real const	nmer_svm_scorecut,
		utility::vector1< std::string > const &	svm_fname_vec,
		utility::vector1< std::string > const &	svm_rank_fname_vec,
		utility::vector1< std::string > const &	pssm_fname_vec,
		std::string const &	aa_matrix
	)

References avg_rank_as_energy(), core::scoring::methods::NMerPSSMEnergy::gate_pssm_scores(), gate_svm_scores(), core::scoring::methods::NMerPSSMEnergy::nmer_length(), nmer_length(), nmer_pssm_, core::scoring::methods::NMerPSSMEnergy::nmer_pssm_scorecut(), nmer_svm_scorecut(), read_aa_encoding_matrix(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_fname_vector(), read_nmer_svm_fname_vector(), read_nmer_svm_rank_fname_vector(), term_length(), and use_pssm_features().

Member Function Documentation

void core::scoring::methods::NMerSVMEnergy::add_encoded_termini	(	std::string const &	chain_sequence,
		core::Size const	chain_seqpos,
		utility::vector1< core::Real > &	feature_vals
	)		const

References encode_wtd_avg_aa_string(), nmer_length_, and term_length_.

Referenced by encode_nmer().

void core::scoring::methods::NMerSVMEnergy::add_pssm_features	(	std::string const &	seq,
		core::Size const	isvm,
		utility::vector1< core::Real > &	feature_vals
	)		const

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::scoring::methods::NMerPSSMEnergy::n_pssms(), n_svms(), nmer_pssm_, core::scoring::methods::NMerPSSMEnergy::pssm_energy_at_frame_seqpos(), and core::id::to_string().

Referenced by encode_nmer().

void core::scoring::methods::NMerSVMEnergy::avg_rank_as_energy ( bool const avg_rank_as_energy )

bool core::scoring::methods::NMerSVMEnergy::avg_rank_as_energy ( ) const

Referenced by initialize_from_options(), and NMerSVMEnergy().

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

overridevirtual

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

vector1< Real > core::scoring::methods::NMerSVMEnergy::encode_aa_string ( std::string const & seq ) const

References protocols::cluster::calibur::aa, and aa_encoder_.

Referenced by encode_nmer(), and encode_wtd_avg_aa_string().

vector1< Real > core::scoring::methods::NMerSVMEnergy::encode_nmer	(	std::string const &	chain_sequence,
		core::Size const	chain_seqpos,
		core::Size const	isvm
	)		const

References add_encoded_termini(), add_pssm_features(), encode_aa_string(), nmer_length_, term_length_, and use_pssm_features_.

Referenced by get_residue_energy_from_sequence().

vector1< Real > core::scoring::methods::NMerSVMEnergy::encode_wtd_avg_aa_string	(	std::string const &	seq,
		utility::vector1< core::Real > const &	wts
	)		const

References protocols::cluster::calibur::aa, and encode_aa_string().

Referenced by add_encoded_termini().

Real core::scoring::methods::NMerSVMEnergy::eval_dof_derivative	(	id::DOF_ID const &	dof_id,
		id::TorsionID const &	tor_id,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights
	)		const

virtual

void core::scoring::methods::NMerSVMEnergy::gate_svm_scores ( bool const gate_svm_scores )

Referenced by initialize_from_options(), NMerSVMEnergy(), and protocols::simple_filters::NMerSVMEnergyFilter::parse_my_tag().

void core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm	(	core::pose::Pose const &	pose,
		core::Size const &	seqpos,
		core::Real &	rsd_energy_avg,
		core::Real &	rsd_rank_avg,
		utility::vector1< core::Real > &	rsd_svm_energies,
		utility::vector1< core::Real > &	rsd_svm_ranks
	)		const

the main compute function, rsd_energy_avg is the default return value for residue energy

optionally return normalized rank avg value instead

References core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::chain_sequence(), core::pose::Pose::conformation(), get_residue_energy_from_sequence(), and nmer_length_.

Referenced by protocols::simple_filters::NMerSVMEnergyFilter::compute(), and residue_energy().

void core::scoring::methods::NMerSVMEnergy::get_residue_energy_from_sequence	(	std::string const &	peptide,
		core::Size const &	chain_p1_seq_pos,
		core::Real &	rsd_energy_avg,
		core::Real &	rsd_rank_avg,
		utility::vector1< core::Real > &	rsd_svm_energies,
		utility::vector1< core::Real > &	rsd_svm_ranks
	)		const

the main compute function, rsd_energy_avg is the default return value for residue energy

optionally return normalized rank avg value instead

References all_nmer_svms_, all_nmer_svms_ranks_, avg_rank_as_energy_, encode_nmer(), gate_svm_scores_, get_svm_nodes(), n_svms(), and nmer_svm_scorecut_.

Referenced by get_residue_energy_by_svm().

vector1< Svm_node_rosettaOP > core::scoring::methods::NMerSVMEnergy::get_svm_nodes ( utility::vector1< core::Real > const & feature_vals ) const

Referenced by get_residue_energy_from_sequence().

void core::scoring::methods::NMerSVMEnergy::indicate_required_context_graphs ( utility::vector1< bool > & ) const

overridevirtual

context independent; indicates that no context graphs are required

NMerSVMEnergy is context independent; indicates that no context graphs are required.

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

void core::scoring::methods::NMerSVMEnergy::initialize_from_options ( EnergyMethodOptions const & options )

private

This function triggers reads from disk the first time only, and then data are cached globally in the ScoringManager. This is fully threadsafe. –VKM

Referenced by NMerSVMEnergy().

bool core::scoring::methods::NMerSVMEnergy::minimize_in_whole_structure_context ( pose::Pose const & ) const

inlineoverridevirtual

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.

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

Size core::scoring::methods::NMerSVMEnergy::n_svms ( ) const

Referenced by add_pssm_features(), protocols::simple_filters::NMerSVMEnergyFilter::compute(), get_residue_energy_from_sequence(), and residue_energy().

void core::scoring::methods::NMerSVMEnergy::nmer_length ( core::Size const nmer_length )

Referenced by protocols::simple_filters::NMerSVMEnergyFilter::compute(), and protocols::simple_filters::NMerSVMEnergyFilter::parse_my_tag().

Size core::scoring::methods::NMerSVMEnergy::nmer_length ( ) const

Referenced by initialize_from_options(), and NMerSVMEnergy().

void core::scoring::methods::NMerSVMEnergy::nmer_svm_scorecut ( core::Real const nmer_svm_scorecut )

Referenced by initialize_from_options(), NMerSVMEnergy(), and protocols::simple_filters::NMerSVMEnergyFilter::parse_my_tag().

bool core::scoring::methods::NMerSVMEnergy::operator== ( NMerSVMEnergy const & other ) const

virtual

References aa_encoder_, all_nmer_svms_, all_nmer_svms_ranks_, avg_rank_as_energy_, gate_svm_scores_, nmer_cterm_, nmer_length_, nmer_pssm_, nmer_svm_scorecut_, term_length_, and use_pssm_features_.

void core::scoring::methods::NMerSVMEnergy::read_aa_encoding_matrix ( std::string const & fname )

References aa_encoder_.

Referenced by initialize_from_options(), and NMerSVMEnergy().

void core::scoring::methods::NMerSVMEnergy::read_nmer_svm ( std::string const & svm_fname )

References all_nmer_svms_, and core::scoring::nmer_svm.

Referenced by NMerSVMEnergy(), protocols::simple_filters::NMerSVMEnergyFilter::parse_my_tag(), read_nmer_svm_fname_vector(), read_nmer_svm_list(), and read_nmer_svms_from_options().

void core::scoring::methods::NMerSVMEnergy::read_nmer_svm_fname_vector ( utility::vector1< std::string > const & svm_fname_vec )

References read_nmer_svm().

Referenced by NMerSVMEnergy().

void core::scoring::methods::NMerSVMEnergy::read_nmer_svm_list ( std::string const & svm_list_fname )

References all_nmer_svms_, read_nmer_svm(), protocols::sparta::split(), and core::scoring::methods::TR().

Referenced by protocols::simple_filters::NMerSVMEnergyFilter::parse_my_tag(), and read_nmer_svms_from_options().

void core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank ( std::string const & svm_rank_fname )

this is a sorted (ascending) list of precomputed energies of a bunch (100k) of random human peptides

...used to give a ile rank score, useful for comparing diff MHC alelle predictions

References all_nmer_svms_ranks_.

Referenced by NMerSVMEnergy(), read_nmer_svm_rank_fname_vector(), read_nmer_svm_rank_list(), and read_nmer_svms_from_options().

void core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank_fname_vector ( utility::vector1< std::string > const & svm_rank_fname_vec )

References read_nmer_svm_rank().

Referenced by NMerSVMEnergy().

void core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank_list ( std::string const & svm_rank_list_fname )

load svm_ranks from a list file

References read_nmer_svm_rank(), protocols::sparta::split(), and core::scoring::methods::TR().

Referenced by read_nmer_svms_from_options().

void core::scoring::methods::NMerSVMEnergy::read_nmer_svms_from_options ( EnergyMethodOptions const & options )

private

This function triggers reads from disk the first time only, and then data are cached globally in the ScoringManager. This is fully threadsafe. –VKM

Referenced by NMerSVMEnergy().

void core::scoring::methods::NMerSVMEnergy::read_pssm_features ( std::string const filename )

References core::scoring::methods::NMerPSSMEnergy::nmer_length(), nmer_length_, nmer_pssm_, core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(), and use_pssm_features_.

void core::scoring::methods::NMerSVMEnergy::residue_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		EnergyMap &	emap
	)		const

overridevirtual

Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them).

Implements core::scoring::methods::ContextIndependentOneBodyEnergy.

References all_nmer_svms_, avg_rank_as_energy_, get_residue_energy_by_svm(), n_svms(), core::scoring::nmer_svm, and core::conformation::Residue::seqpos().

void core::scoring::methods::NMerSVMEnergy::term_length ( core::Size const term_length )