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core::io::silent::SilentStruct Class Referenceabstract

#include <SilentStruct.hh>

Inheritance diagram for core::io::silent::SilentStruct:
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Public Member Functions

 SilentStruct (SilentFileOptions const &opts)
 
 ~SilentStruct () override
 
 SilentStruct (SilentStruct const &)
 
SilentStructoperator= (SilentStruct const &)
 
virtual SilentStructOP clone () const =0
 
SilentStructCOP get_self_ptr () const
 self pointers More...
 
SilentStructOP get_self_ptr ()
 
virtual void fill_pose (core::pose::Pose &pose, bool const metapatches=true) const
 
void fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSetCOP residue_set, bool const metapatches=true) const
 non-virtual interface that takes a ResidueTypeSetCOP (instead of a const & to one) and invokes the virtual method that takes the const &. More...
 
virtual void fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set, bool const metapatches=true) const
 Fill a Pose with the conformation information in this SilentStruct and the ResidueTypeSet provided by the caller. This is a virtual method which should be implemented by classes derived from SilentStruct. More...
 
void set_tag_from_pose (const core::pose::Pose &pose)
 Sets the tag from the Pose DataCache. More...
 
void precision (core::Size precision)
 
core::Size precision () const
 
void scoreline_prefix (std::string const &prefix)
 
std::string scoreline_prefix () const
 
virtual void fill_struct (core::pose::Pose const &pose, std::string const &tag="empty_tag")
 opposite of fill_pose – superclass provides functionality used by most SilentStruct types, and is optionally called at the beginning of the subclass's fill_struct method. As of this writing, used only by protein SilentStructs More...
 
void finish_pose (core::pose::Pose &pose) const
 calls optH if command line requests optH. must be called by derived classes. More...
 
virtual Real get_debug_rmsd ()=0
 Do some sort of comparison between the actual RMSD of this silent-struct and the cached coordinates. Used for SilentStruct objects that are rebuild from torsions or other reduced representations of data. More...
 
virtual void print_header (std::ostream &out) const
 print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines: SEQUENCE: <protein sequence>\nSCORE:

More...
 
virtual void print_score_header (std::ostream &out) const
 only print SCORE: header line More...
 
virtual void print_scores (std::ostream &out) const
 print out a SCORE line to the given ozstream. More...
 
virtual void print_conformation (std::ostream &out) const =0
 print the conformation information in SilentStruct to out. More...
 
virtual void print_comments (std::ostream &out) const
 print the comments in this SilentStruct. More...
 
virtual void print_residue_numbers (std::ostream &out) const
 print the resnum in this SilentStruct, if filled. More...
 
virtual void print_submotif_info (std::ostream &out) const
 print the submotif_info in this SilentStruct, if filled. More...
 
virtual Size nres () const
 returns the number of residues contained by this SilentStruct. More...
 
void set_decoy_tag (std::string const &tag)
 set the tag associate with this SilentStruct More...
 
std::string decoy_tag () const
 returns the tag associated with this SilentStruct. More...
 
core::sequence::AnnotatedSequence const & sequence () const
 returns the sequence associated with this SilentStruct. More...
 
void nres (Size nres)
 returns the number of residues in this SilentStruct. More...
 
void decoy_tag (std::string const &tag)
 sets the tag associated with this SilentStruct. More...
 
void sequence (core::sequence::AnnotatedSequence const &sequence)
 sets the sequence for this SilentStruct. More...
 
void silent_energies (utility::vector1< SilentEnergy > const &new_se)
 sets the silent_energies for this SilentStruct. More...
 
void sort_silent_scores ()
 sort all the silent energies by their name. More...
 
bool has_energy (std::string const &scorename) const
 returns true if this SilentStruct has an energy for the given scorename, returns false otherwise. More...
 
core::Real get_energy (std::string const &scorename) const
 Returns the energy associated with the given scorename if this SilentStruct has an energy for that scorename. Otherwise returns 0. More...
 
std::string const & get_string_value (std::string const &scorename) const
 Returns the energy associated with the given scorename if this SilentStruct has an energy for that scorename. Otherwise returns 0. More...
 
SilentEnergy const & get_silent_energy (std::string const &scorename) const
 Returns the SilentEnergy associated with this scorename. More...
 
utility::vector1< SilentEnergyget_silent_energies ()
 
void set_valid_energies (utility::vector1< std::string > valid)
 
virtual void clear_energies ()
 Clear all of the energies in the SilentStruct. Doesn't just zero the energies, it entirely removes all knowledge of all energies from this SilentStruct. More...
 
virtual bool init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)=0
 Create a new SilentStruct object from the provided set of lines. This abstract method should be overwritten by derived classes. Returns false if the init_from_lines routine encounters a problem with the lines provided. More...
 
void add_energy (std::string const &scorename, Real value, Real weight=1.0)
 add a score of a given name and value to this SilentStruct. Takes an optional weight that defaults to 1.0. More...
 
void add_string_value (std::string const &scorename, std::string const &value, int const index=-1)
 add a non-floating point score of a given name and value to this SilentStruct. More...
 
void copy_scores (const SilentStruct &src_ss)
 Copy the score information in the given SilentStruct into this SilentStruct. More...
 
void add_comment (std::string name, std::string value)
 add a named comment to this SilentStruct object. Similar to methods for playing with energies, but mapping is string => string rather than string => Real. More...
 
bool has_comment (std::string const &name) const
 
std::string get_comment (std::string const &name) const
 
void comment_from_line (std::string const &line)
 
void comment_from_line (std::string const &line, bool const include_silentfile_comments)
 Creates and adds a comment from an input REMARK line. More...
 
void erase_comment (std::string const &name)
 
void clear_comments ()
 
std::map< std::string, std::string > get_all_comments () const
 
void parse_energies (std::istream &input, utility::vector1< std::string > const &energy_names)
 
void energies_from_pose (core::pose::Pose const &pose)
 Initialize this SilentStruct's energies from the given Pose. This sets energies, energy weights, and the output widths for the energies. More...
 
void energies_into_pose (core::pose::Pose &pose) const
 Put the energy information from this SilentStruct into the pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct. More...
 
virtual ObjexxFCL::FArray2D< Realget_CA_xyz () const =0
 returns the positions of the CA atoms in this ProteinSilentStruct. Useful for RMS calculations. More...
 
utility::vector1< SilentEnergyenergies () const
 Returns the vector of SilentEnergy objects associated with this SilentStruct object. More...
 
EnergyNames energy_names () const
 Returns the EnergyNames that this SilentStruct contains. More...
 
void rename_energies ()
 
bool read_sequence (std::string const &line)
 
void read_score_headers (std::string const &line, utility::vector1< std::string > &enames, SilentFileData &container)
 
std::string one_letter_sequence () const
 strip [...] comment from seqeunce_ and return pure one-letter sequence More...
 
virtual core::Size mem_footprint () const
 
void print_parent_remarks (std::ostream &out) const
 
std::string get_parent_remark (std::string const &name) const
 
bool has_parent_remark (std::string const &name) const
 
void add_parent_remark (std::string const &name, std::string const &value)
 
void get_parent_remark_from_line (std::string const &line)
 
void set_residue_numbers (utility::vector1< int > const &residue_numbers)
 
void set_chains (utility::vector1< char > const &chains)
 
void set_full_model_parameters (core::pose::full_model_info::FullModelParametersCOP setting)
 
core::pose::full_model_info::FullModelParametersCOP full_model_parameters () const
 
void set_segment_IDs (utility::vector1< std::string > const &segids)
 
void fill_struct_with_residue_numbers (pose::Pose const &pose)
 
void fill_other_struct_list (pose::Pose const &pose)
 
void residue_numbers_into_pose (pose::Pose &pose) const
 
void full_model_info_into_pose (pose::Pose &pose) const
 
void figure_out_residue_numbers_from_line (std::istream &line_stream)
 
void figure_out_segment_ids_from_line (std::istream &line_stream)
 
void add_submotif_info_from_line (std::istream &line_stream)
 
void fill_struct_with_submotif_info_list (pose::Pose const &pose)
 
utility::vector1< SilentStructOP > const & other_struct_list () const
 
utility::vector1< SilentStructOP > & nonconst_other_struct_list ()
 
void add_other_struct (SilentStructOP silent_struct)
 
virtual void set_force_bitflip (bool const setting)
 Sets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines. More...
 
virtual bool force_bitflip () const
 Gets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines. More...
 
SilentFileOptions const & options () const
 

Protected Member Functions

void detect_fullatom (core::Size pos, core::Size natoms, bool &fullatom, bool &well_defined)
 @ brief helper to detect fullatom input More...
 
void extract_writeable_cacheable_data (core::pose::Pose const &pose)
 add string serialization of all WriteableCacheableData in as comments. More...
 

Private Types

typedef std::string string
 

Private Member Functions

void update_score ()
 Updates the "score" entry in the silent_energies. More...
 

Private Attributes

bool force_bitflip_
 If true, this forces conversion from big-endian to little-endian (or the converse) when a binary silent structure is initialized from lines (init_from_lines() function). More...
 
Size nres_
 
std::string decoy_tag_
 
core::sequence::AnnotatedSequence sequence_
 
std::map< std::string, std::string > parent_remarks_map_
 
std::map< std::string, std::string > silent_comments_
 
utility::vector1< SilentEnergysilent_energies_
 
utility::vector1< std::string > cache_remarks_
 
utility::vector1< std::string > pdbinfo_labels_
 
utility::vector1< int > residue_numbers_
 
utility::vector1< char > chains_
 
utility::vector1< SilentStructOPother_struct_list_
 
core::pose::full_model_info::FullModelParametersCOP full_model_parameters_
 
utility::vector1< std::string > segment_IDs_
 
utility::vector1< core::pose::full_model_info::SubMotifInfoOPsubmotif_info_list_
 
core::Size precision_
 
std::string scoreline_prefix_
 
SilentFileOptions options_
 

Member Typedef Documentation

◆ string

typedef std::string core::io::silent::SilentStruct::string
private

Constructor & Destructor Documentation

◆ SilentStruct() [1/2]

core::io::silent::SilentStruct::SilentStruct ( SilentFileOptions const &  opts)

◆ ~SilentStruct()

core::io::silent::SilentStruct::~SilentStruct ( )
overridedefault

◆ SilentStruct() [2/2]

core::io::silent::SilentStruct::SilentStruct ( SilentStruct const &  )
default

Member Function Documentation

◆ add_comment()

void core::io::silent::SilentStruct::add_comment ( std::string  name,
std::string  value 
)

add a named comment to this SilentStruct object. Similar to methods for playing with energies, but mapping is string => string rather than string => Real.

References cache_remarks_, pdbinfo_labels_, silent_comments_, and core::io::silent::tr().

Referenced by comment_from_line(), energies_from_pose(), extract_writeable_cacheable_data(), and core::io::silent::ScoreJumpFileSilentStruct::init_from_lines().

◆ add_energy()

void core::io::silent::SilentStruct::add_energy ( std::string const &  scorename,
Real  value,
Real  weight = 1.0 
)

add a score of a given name and value to this SilentStruct. Takes an optional weight that defaults to 1.0.

References protocols::forge::methods::replace(), and silent_energies_.

Referenced by protocols::rna::denovo::RNA_DeNovoProtocol::add_chem_shift_info(), core::pose::rna::add_number_native_base_pairs(), protocols::mpi_refinement::add_poseinfo_to_ss(), protocols::loophash::MPI_LoopHashRefine::add_structure_to_library(), protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::loophash::MPI_LoopHashRefine_Emperor::add_structures_to_library(), protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator::apply(), protocols::evaluation::SingleValuePoseEvaluator< T >::apply(), protocols::constraints_additional::CombinedConstraintEvaluator::apply(), protocols::constraints_additional::ConstraintEvaluator::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::topology_broker::ConstraintEvaluatorWrapper::apply(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), protocols::comparative_modeling::Align_RotamerEvaluator::apply(), protocols::simple_filters::ContactMapEvaluator::apply(), protocols::simple_filters::JScoreEvaluator::apply(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::simple_filters::StructuralSimilarityEvaluator::apply(), protocols::abinitio::PcaEvaluator::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), protocols::rna::denovo::RNA_DeNovoProtocol::calc_rmsds(), protocols::electron_density::dump_RefinementDB_to_silent(), core::import_pose::PDBSilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), protocols::recces::RECCES_Mover::more_dump_stuff(), protocols::stepwise::modeler::rna::output_data(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::rna::denovo::RNA_DeNovoProtocol::output_silent_struct(), protocols::stepwise::legacy::modeler::protein::output_silent_struct(), parse_energies(), and protocols::electron_density::DockPDBIntoDensityMover::score_and_dump_natives().

◆ add_other_struct()

void core::io::silent::SilentStruct::add_other_struct ( SilentStructOP  silent_struct)

◆ add_parent_remark()

void core::io::silent::SilentStruct::add_parent_remark ( std::string const &  name,
std::string const &  value 
)

◆ add_string_value()

void core::io::silent::SilentStruct::add_string_value ( std::string const &  scorename,
std::string const &  value,
int const  index = -1 
)

◆ add_submotif_info_from_line()

void core::io::silent::SilentStruct::add_submotif_info_from_line ( std::istream &  line_stream)

◆ clear_comments()

void core::io::silent::SilentStruct::clear_comments ( )

References silent_comments_.

◆ clear_energies()

virtual void core::io::silent::SilentStruct::clear_energies ( )
inlinevirtual

Clear all of the energies in the SilentStruct. Doesn't just zero the energies, it entirely removes all knowledge of all energies from this SilentStruct.

References silent_energies_.

Referenced by protocols::electron_density::dump_RefinementDB_to_silent(), energies_from_pose(), and protocols::electron_density::DockPDBIntoDensityMover::score_and_dump_natives().

◆ clone()

virtual SilentStructOP core::io::silent::SilentStruct::clone ( ) const
pure virtual

◆ comment_from_line() [1/2]

void core::io::silent::SilentStruct::comment_from_line ( std::string const &  line)

◆ comment_from_line() [2/2]

void core::io::silent::SilentStruct::comment_from_line ( std::string const &  line,
bool const  include_silentfile_comments 
)

Creates and adds a comment from an input REMARK line.

Parameters
[in]lineInput comment line, of the format "REMARK key value [value]*"
[in]include_silentfile_commentsIf true, 'REMARK XXX SILENTFILE' lines will be added to comments.

References add_comment(), core::io::silent::tr(), and protocols::hybridization::val.

◆ copy_scores()

void core::io::silent::SilentStruct::copy_scores ( const SilentStruct src_ss)

Copy the score information in the given SilentStruct into this SilentStruct.

References protocols::forge::methods::replace(), and silent_energies_.

◆ decoy_tag() [1/2]

std::string core::io::silent::SilentStruct::decoy_tag ( ) const
inline

returns the tag associated with this SilentStruct.

References decoy_tag_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), protocols::evaluation::PoseEvaluator::apply(), core::io::silent::BinarySilentStruct::BinarySilentStruct(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::ScoreFileSilentStruct::fill_struct(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), fill_struct(), core::import_pose::PDBSilentStruct::fill_struct(), protocols::mpi_refinement::MPI_Refinement::format_silent_struct(), core::import_pose::PDBSilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::io::silent::BinarySilentStruct::init_from_lines(), parse_energies(), core::import_pose::PDBSilentStruct::PDBSilentStruct(), core::io::silent::BinarySilentStruct::print_conformation(), core::io::silent::RNA_SilentStruct::print_conformation(), core::io::silent::ScoreJumpFileSilentStruct::print_conformation(), print_residue_numbers(), print_score_header(), print_scores(), print_submotif_info(), core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template(), core::io::silent::RigidBodySilentStruct::RigidBodySilentStruct(), core::io::silent::RNA_SilentStruct::RNA_SilentStruct(), core::io::silent::ScoreFileSilentStruct::ScoreFileSilentStruct(), core::io::silent::ScoreJumpFileSilentStruct::ScoreJumpFileSilentStruct(), and set_tag_from_pose().

◆ decoy_tag() [2/2]

void core::io::silent::SilentStruct::decoy_tag ( std::string const &  tag)
inline

sets the tag associated with this SilentStruct.

References decoy_tag_.

◆ detect_fullatom()

void core::io::silent::SilentStruct::detect_fullatom ( core::Size  pos,
core::Size  natoms,
bool &  fullatom,
bool &  well_defined 
)
protected

◆ energies()

utility::vector1< SilentEnergy > core::io::silent::SilentStruct::energies ( ) const
inline

Returns the vector of SilentEnergy objects associated with this SilentStruct object.

References silent_energies_.

Referenced by energies_into_pose(), and energy_names().

◆ energies_from_pose()

void core::io::silent::SilentStruct::energies_from_pose ( core::pose::Pose const &  pose)

◆ energies_into_pose()

void core::io::silent::SilentStruct::energies_into_pose ( core::pose::Pose pose) const

◆ energy_names()

EnergyNames core::io::silent::SilentStruct::energy_names ( ) const

◆ erase_comment()

void core::io::silent::SilentStruct::erase_comment ( std::string const &  name)

References silent_comments_.

◆ extract_writeable_cacheable_data()

void core::io::silent::SilentStruct::extract_writeable_cacheable_data ( core::pose::Pose const &  pose)
protected

add string serialization of all WriteableCacheableData in as comments.

Parameters
posea pose containing a datacache with WriteableCacheableData.

References add_comment(), and core::pose::Pose::data().

Referenced by fill_struct().

◆ figure_out_residue_numbers_from_line()

void core::io::silent::SilentStruct::figure_out_residue_numbers_from_line ( std::istream &  line_stream)

◆ figure_out_segment_ids_from_line()

void core::io::silent::SilentStruct::figure_out_segment_ids_from_line ( std::istream &  line_stream)

◆ fill_other_struct_list()

void core::io::silent::SilentStruct::fill_other_struct_list ( pose::Pose const &  pose)

◆ fill_pose() [1/3]

void core::io::silent::SilentStruct::fill_pose ( core::pose::Pose pose,
bool const  metapatches = true 
) const
virtual

◆ fill_pose() [2/3]

void core::io::silent::SilentStruct::fill_pose ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  residue_set,
bool const  metapatches = true 
) const
virtual

Fill a Pose with the conformation information in this SilentStruct and the ResidueTypeSet provided by the caller. This is a virtual method which should be implemented by classes derived from SilentStruct.

Fill a Pose with the conformation information in this SilentStruct and the ResidueTypeSet provided by the caller. This is a virtual method which must be implemented by classes derived from SilentStruct.

Reimplemented in core::io::silent::ScoreJumpFileSilentStruct, core::io::silent::ScoreFileSilentStruct, core::io::silent::RNA_SilentStruct, core::io::silent::RigidBodySilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, and core::import_pose::PDBSilentStruct.

References core::io::silent::tr().

◆ fill_pose() [3/3]

void core::io::silent::SilentStruct::fill_pose ( core::pose::Pose pose,
core::chemical::ResidueTypeSetCOP  residue_set,
bool const  metapatches = true 
) const

non-virtual interface that takes a ResidueTypeSetCOP (instead of a const & to one) and invokes the virtual method that takes the const &.

Fill a Pose with the conformation information in this SilentStruct and the ResidueTypeSetCOP provided by the caller.

References fill_pose().

◆ fill_struct()

void core::io::silent::SilentStruct::fill_struct ( core::pose::Pose const &  pose,
std::string const &  tag = "empty_tag" 
)
virtual

◆ fill_struct_with_residue_numbers()

void core::io::silent::SilentStruct::fill_struct_with_residue_numbers ( pose::Pose const &  pose)

◆ fill_struct_with_submotif_info_list()

void core::io::silent::SilentStruct::fill_struct_with_submotif_info_list ( pose::Pose const &  pose)

◆ finish_pose()

void core::io::silent::SilentStruct::finish_pose ( core::pose::Pose pose) const

◆ force_bitflip()

virtual bool core::io::silent::SilentStruct::force_bitflip ( ) const
inlinevirtual

Gets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines.

References force_bitflip_.

Referenced by core::io::silent::BinarySilentStruct::init_from_lines().

◆ full_model_info_into_pose()

void core::io::silent::SilentStruct::full_model_info_into_pose ( pose::Pose pose) const

◆ full_model_parameters()

core::pose::full_model_info::FullModelParametersCOP core::io::silent::SilentStruct::full_model_parameters ( ) const
inline

◆ get_all_comments()

std::map< std::string, std::string > core::io::silent::SilentStruct::get_all_comments ( ) const

References silent_comments_.

Referenced by energies_into_pose().

◆ get_CA_xyz()

virtual ObjexxFCL::FArray2D< Real > core::io::silent::SilentStruct::get_CA_xyz ( ) const
pure virtual

◆ get_comment()

std::string core::io::silent::SilentStruct::get_comment ( std::string const &  name) const

References silent_comments_.

◆ get_debug_rmsd()

virtual Real core::io::silent::SilentStruct::get_debug_rmsd ( )
pure virtual

Do some sort of comparison between the actual RMSD of this silent-struct and the cached coordinates. Used for SilentStruct objects that are rebuild from torsions or other reduced representations of data.

Implemented in core::io::silent::ScoreJumpFileSilentStruct, core::io::silent::ScoreFileSilentStruct, core::io::silent::RNA_SilentStruct, core::io::silent::RigidBodySilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, and core::import_pose::PDBSilentStruct.

◆ get_energy()

core::Real core::io::silent::SilentStruct::get_energy ( std::string const &  scorename) const

◆ get_parent_remark()

std::string core::io::silent::SilentStruct::get_parent_remark ( std::string const &  name) const

References parent_remarks_map_.

◆ get_parent_remark_from_line()

void core::io::silent::SilentStruct::get_parent_remark_from_line ( std::string const &  line)

◆ get_self_ptr() [1/2]

SilentStructOP core::io::silent::SilentStruct::get_self_ptr ( )
inline

◆ get_self_ptr() [2/2]

SilentStructCOP core::io::silent::SilentStruct::get_self_ptr ( ) const
inline

◆ get_silent_energies()

utility::vector1< SilentEnergy > core::io::silent::SilentStruct::get_silent_energies ( )
inline

References silent_energies_.

◆ get_silent_energy()

SilentEnergy const & core::io::silent::SilentStruct::get_silent_energy ( std::string const &  scorename) const

Returns the SilentEnergy associated with this scorename.

References has_energy(), and silent_energies_.

Referenced by get_energy(), get_string_value(), and set_valid_energies().

◆ get_string_value()

std::string const & core::io::silent::SilentStruct::get_string_value ( std::string const &  scorename) const

Returns the energy associated with the given scorename if this SilentStruct has an energy for that scorename. Otherwise returns 0.

References protocols::viewer::empty_string(), get_silent_energy(), has_energy(), and core::io::silent::SilentEnergy::string_value().

Referenced by protocols::loophash::MPI_LoopHashRefine::format_silent_struct().

◆ has_comment()

bool core::io::silent::SilentStruct::has_comment ( std::string const &  name) const

References silent_comments_.

◆ has_energy()

bool core::io::silent::SilentStruct::has_energy ( std::string const &  scorename) const

◆ has_parent_remark()

bool core::io::silent::SilentStruct::has_parent_remark ( std::string const &  name) const

References parent_remarks_map_.

◆ init_from_lines()

virtual bool core::io::silent::SilentStruct::init_from_lines ( utility::vector1< std::string > const &  lines,
SilentFileData container 
)
pure virtual

Create a new SilentStruct object from the provided set of lines. This abstract method should be overwritten by derived classes. Returns false if the init_from_lines routine encounters a problem with the lines provided.

Implemented in core::io::silent::ScoreJumpFileSilentStruct, core::io::silent::ScoreFileSilentStruct, core::io::silent::RNA_SilentStruct, core::io::silent::RigidBodySilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, and core::import_pose::PDBSilentStruct.

◆ mem_footprint()

virtual core::Size core::io::silent::SilentStruct::mem_footprint ( ) const
inlinevirtual

◆ nonconst_other_struct_list()

utility::vector1< SilentStructOP >& core::io::silent::SilentStruct::nonconst_other_struct_list ( )
inline

◆ nres() [1/2]

virtual Size core::io::silent::SilentStruct::nres ( ) const
inlinevirtual

◆ nres() [2/2]

void core::io::silent::SilentStruct::nres ( Size  nres)
inline

returns the number of residues in this SilentStruct.

References nres(), and nres_.

◆ one_letter_sequence()

std::string core::io::silent::SilentStruct::one_letter_sequence ( ) const

◆ operator=()

SilentStruct & core::io::silent::SilentStruct::operator= ( SilentStruct const &  )
default

◆ options()

SilentFileOptions const & core::io::silent::SilentStruct::options ( ) const

◆ other_struct_list()

utility::vector1< SilentStructOP > const& core::io::silent::SilentStruct::other_struct_list ( ) const
inline

◆ parse_energies()

void core::io::silent::SilentStruct::parse_energies ( std::istream &  input,
utility::vector1< std::string > const &  energy_names 
)

◆ precision() [1/2]

core::Size core::io::silent::SilentStruct::precision ( ) const

References precision_.

Referenced by precision(), and print_scores().

◆ precision() [2/2]

void core::io::silent::SilentStruct::precision ( core::Size  precision)

References precision(), and precision_.

◆ print_comments()

void core::io::silent::SilentStruct::print_comments ( std::ostream &  out) const
virtual

◆ print_conformation()

virtual void core::io::silent::SilentStruct::print_conformation ( std::ostream &  out) const
pure virtual

◆ print_header()

void core::io::silent::SilentStruct::print_header ( std::ostream &  out) const
virtual

◆ print_parent_remarks()

void core::io::silent::SilentStruct::print_parent_remarks ( std::ostream &  out) const

◆ print_residue_numbers()

void core::io::silent::SilentStruct::print_residue_numbers ( std::ostream &  out) const
virtual

◆ print_score_header()

void core::io::silent::SilentStruct::print_score_header ( std::ostream &  out) const
virtual

◆ print_scores()

void core::io::silent::SilentStruct::print_scores ( std::ostream &  out) const
virtual

◆ print_submotif_info()

void core::io::silent::SilentStruct::print_submotif_info ( std::ostream &  out) const
virtual

◆ read_score_headers()

void core::io::silent::SilentStruct::read_score_headers ( std::string const &  line,
utility::vector1< std::string > &  enames,
SilentFileData container 
)

◆ read_sequence()

bool core::io::silent::SilentStruct::read_sequence ( std::string const &  line)

◆ rename_energies()

void core::io::silent::SilentStruct::rename_energies ( )

◆ residue_numbers_into_pose()

void core::io::silent::SilentStruct::residue_numbers_into_pose ( pose::Pose pose) const

◆ scoreline_prefix() [1/2]

std::string core::io::silent::SilentStruct::scoreline_prefix ( ) const

◆ scoreline_prefix() [2/2]

void core::io::silent::SilentStruct::scoreline_prefix ( std::string const &  prefix)

References scoreline_prefix_.

◆ sequence() [1/2]

core::sequence::AnnotatedSequence const& core::io::silent::SilentStruct::sequence ( ) const
inline

◆ sequence() [2/2]

void core::io::silent::SilentStruct::sequence ( core::sequence::AnnotatedSequence const &  sequence)
inline

sets the sequence for this SilentStruct.

References sequence(), and sequence_.

◆ set_chains()

void core::io::silent::SilentStruct::set_chains ( utility::vector1< char > const &  chains)
inline

◆ set_decoy_tag()

void core::io::silent::SilentStruct::set_decoy_tag ( std::string const &  tag)
inline

◆ set_force_bitflip()

virtual void core::io::silent::SilentStruct::set_force_bitflip ( bool const  setting)
inlinevirtual

Sets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines.

References force_bitflip_.

◆ set_full_model_parameters()

void core::io::silent::SilentStruct::set_full_model_parameters ( core::pose::full_model_info::FullModelParametersCOP  setting)
inline

◆ set_residue_numbers()

void core::io::silent::SilentStruct::set_residue_numbers ( utility::vector1< int > const &  residue_numbers)
inline

◆ set_segment_IDs()

void core::io::silent::SilentStruct::set_segment_IDs ( utility::vector1< std::string > const &  segids)
inline

◆ set_tag_from_pose()

void core::io::silent::SilentStruct::set_tag_from_pose ( const core::pose::Pose pose)

◆ set_valid_energies()

void core::io::silent::SilentStruct::set_valid_energies ( utility::vector1< std::string >  valid)

◆ silent_energies()

void core::io::silent::SilentStruct::silent_energies ( utility::vector1< SilentEnergy > const &  new_se)
inline

sets the silent_energies for this SilentStruct.

References silent_energies_.

Referenced by set_valid_energies().

◆ sort_silent_scores()

void core::io::silent::SilentStruct::sort_silent_scores ( )

sort all the silent energies by their name.

References silent_energies_, and core::io::silent::SilentEnergy_sort_by_name().

◆ update_score()

void core::io::silent::SilentStruct::update_score ( )
private

Updates the "score" entry in the silent_energies.

References protocols::hybridization::score, and silent_energies_.

Referenced by energies_from_pose().

Member Data Documentation

◆ cache_remarks_

utility::vector1< std::string > core::io::silent::SilentStruct::cache_remarks_
private

◆ chains_

utility::vector1< char > core::io::silent::SilentStruct::chains_
private

◆ decoy_tag_

std::string core::io::silent::SilentStruct::decoy_tag_
private

◆ force_bitflip_

bool core::io::silent::SilentStruct::force_bitflip_
private

If true, this forces conversion from big-endian to little-endian (or the converse) when a binary silent structure is initialized from lines (init_from_lines() function).

Referenced by force_bitflip(), and set_force_bitflip().

◆ full_model_parameters_

core::pose::full_model_info::FullModelParametersCOP core::io::silent::SilentStruct::full_model_parameters_
private

◆ nres_

Size core::io::silent::SilentStruct::nres_
private

◆ options_

SilentFileOptions core::io::silent::SilentStruct::options_
private

◆ other_struct_list_

utility::vector1< SilentStructOP > core::io::silent::SilentStruct::other_struct_list_
private

◆ parent_remarks_map_

std::map< std::string, std::string > core::io::silent::SilentStruct::parent_remarks_map_
private

◆ pdbinfo_labels_

utility::vector1< std::string > core::io::silent::SilentStruct::pdbinfo_labels_
private

◆ precision_

core::Size core::io::silent::SilentStruct::precision_
private

Referenced by precision().

◆ residue_numbers_

utility::vector1< int > core::io::silent::SilentStruct::residue_numbers_
private

◆ scoreline_prefix_

std::string core::io::silent::SilentStruct::scoreline_prefix_
private

Referenced by scoreline_prefix().

◆ segment_IDs_

utility::vector1< std::string > core::io::silent::SilentStruct::segment_IDs_
private

◆ sequence_

core::sequence::AnnotatedSequence core::io::silent::SilentStruct::sequence_
private

Referenced by sequence().

◆ silent_comments_

std::map< std::string, std::string > core::io::silent::SilentStruct::silent_comments_
private

◆ silent_energies_

utility::vector1< SilentEnergy > core::io::silent::SilentStruct::silent_energies_
private

◆ submotif_info_list_

utility::vector1< core::pose::full_model_info::SubMotifInfoOP > core::io::silent::SilentStruct::submotif_info_list_
mutableprivate

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