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core::scoring::methods::NMerSVMEnergy Class Reference

#include <NMerSVMEnergy.hh>

Inheritance diagram for core::scoring::methods::NMerSVMEnergy:
Inheritance graph
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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::Realencode_aa_string (std::string const &) const
 
utility::vector1< core::Realencode_wtd_avg_aa_string (std::string const &, utility::vector1< core::Real > const &) const
 
utility::vector1< core::Realencode_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 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 bool energy_method_provides_citation_info () const
 Does this energy method provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool energy_method_is_unpublished () const
 Does this energy method indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

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

Member Function Documentation

void core::scoring::methods::NMerSVMEnergy::add_encoded_termini ( std::string const &  ,
core::Size  const,
utility::vector1< core::Real > &   
) const
void core::scoring::methods::NMerSVMEnergy::add_pssm_features ( std::string const &  ,
core::Size  const,
utility::vector1< core::Real > &   
) const
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
EnergyMethodOP core::scoring::methods::NMerSVMEnergy::clone ( ) const
overridevirtual
vector1< Real > core::scoring::methods::NMerSVMEnergy::encode_aa_string ( std::string const &  seq) const
vector1< Real > core::scoring::methods::NMerSVMEnergy::encode_nmer ( std::string const &  ,
core::Size  const,
core::Size  const 
) const
vector1< Real > core::scoring::methods::NMerSVMEnergy::encode_wtd_avg_aa_string ( std::string const &  ,
utility::vector1< core::Real > const &   
) const
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)
void core::scoring::methods::NMerSVMEnergy::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
void core::scoring::methods::NMerSVMEnergy::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

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 &  ) const
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
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
void core::scoring::methods::NMerSVMEnergy::nmer_length ( core::Size  const)
Size core::scoring::methods::NMerSVMEnergy::nmer_length ( ) const
void core::scoring::methods::NMerSVMEnergy::nmer_svm_scorecut ( core::Real  const)
bool core::scoring::methods::NMerSVMEnergy::operator== ( NMerSVMEnergy const &  other) const
virtual
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)
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)
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
void core::scoring::methods::NMerSVMEnergy::read_pssm_features ( std::string const  filename)
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)
Size core::scoring::methods::NMerSVMEnergy::term_length ( ) const
void core::scoring::methods::NMerSVMEnergy::use_pssm_features ( bool const  use_pssm_features)
core::Size core::scoring::methods::NMerSVMEnergy::version ( ) const
overrideprivatevirtual

Return the version of the energy method.

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

Member Data Documentation

std::map< char, utility::vector1< core::Real > > core::scoring::methods::NMerSVMEnergy::aa_encoder_
private
utility::vector1< utility::libsvm::Svm_rosettaCOP > core::scoring::methods::NMerSVMEnergy::all_nmer_svms_
private
utility::vector1< utility::vector1< core::Real > > core::scoring::methods::NMerSVMEnergy::all_nmer_svms_ranks_
private
bool core::scoring::methods::NMerSVMEnergy::avg_rank_as_energy_
private
bool core::scoring::methods::NMerSVMEnergy::gate_svm_scores_
private
core::Size core::scoring::methods::NMerSVMEnergy::nmer_cterm_
private

Referenced by operator==().

core::Size core::scoring::methods::NMerSVMEnergy::nmer_length_
private
core::scoring::methods::NMerPSSMEnergy core::scoring::methods::NMerSVMEnergy::nmer_pssm_
private
core::Real core::scoring::methods::NMerSVMEnergy::nmer_svm_scorecut_
private
core::Size core::scoring::methods::NMerSVMEnergy::term_length_
private
bool core::scoring::methods::NMerSVMEnergy::use_pssm_features_
private

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