Rosetta 3.4
Public Member Functions | Protected Member Functions
core::io::silent::SilentStruct Class Reference

#include <SilentStruct.hh>

Inheritance diagram for core::io::silent::SilentStruct:
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List of all members.

Public Member Functions

 SilentStruct ()
 ~SilentStruct ()
 SilentStruct (SilentStruct const &)
SilentStructoperator= (SilentStruct const &)
virtual SilentStructOP clone () const =0
virtual void fill_pose (core::pose::Pose &pose) const
virtual void fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set) 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.
void set_tag_from_pose (const core::pose::Pose &pose)
 Sets the tag from the Pose DataCache.
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 tag="empty_tag")=0
 opposite of fill_pose
void finish_pose (core::pose::Pose &pose) const
 calls optH if command line requests optH. must be called by derived classes.
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.
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>="">: <list of score-types>.
virtual void print_score_header (std::ostream &out) const
 only print SCORE: header line
virtual void print_scores (std::ostream &out) const
 print out a SCORE line to the given ozstream.
virtual void print_conformation (std::ostream &out) const =0
 print the conformation information in SilentStruct to out.
virtual void print_comments (std::ostream &out) const
 print the comments in this SilentStruct.
virtual Size nres () const
 returns the number of residues contained by this SilentStruct.
void set_decoy_tag (std::string const &tag)
 set the tag associate with this SilentStruct
std::string decoy_tag () const
 returns the tag associated with this SilentStruct.
core::sequence::AnnotatedSequence
const & 
sequence () const
 returns the sequence associated with this SilentStruct.
void nres (Size nres)
 returns the number of residues in this SilentStruct.
void decoy_tag (std::string const &tag)
 sets the tag associated with this SilentStruct.
void sequence (core::sequence::AnnotatedSequence const &sequence)
 sets the sequence for this SilentStruct.
void silent_energies (utility::vector1< SilentEnergy > const &new_se)
 sets the silent_energies for this SilentStruct.
void sort_silent_scores ()
 sort all the silent energies by their name.
bool has_energy (std::string const scorename) const
 returns true if this SilentStruct has an energy for the given scorename, returns false otherwise.
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.
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.
SilentEnergy const & get_silent_energy (std::string const &scorename) const
 Returns the SilentEnergy associated with this scorename.
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.
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.
void add_energy (std::string 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.
void add_string_value (std::string scorename, std::string const &value)
 add a non-floating point score of a given name and value to this SilentStruct.
void copy_scores (const SilentStruct &src_ss)
 Copy the score information in the given SilentStruct into this SilentStruct.
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.
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 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.
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.
virtual ObjexxFCL::FArray2D< Realget_CA_xyz () const =0
 returns the positions of the CA atoms in this ProteinSilentStruct. Useful for RMS calculations.
utility::vector1< SilentEnergyenergies () const
 Returns the vector of SilentEnergy objects associated with this SilentStruct object.
EnergyNames energy_names () const
 Returns the EnergyNames that this SilentStruct contains.
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
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)

Protected Member Functions

void detect_fullatom (core::Size pos, core::Size natoms, bool &fullatom, bool &well_defined)
 @ brief helper to detect fullatom input

Constructor & Destructor Documentation

core::io::silent::SilentStruct::SilentStruct ( )
core::io::silent::SilentStruct::~SilentStruct ( )
core::io::silent::SilentStruct::SilentStruct ( SilentStruct const &  src)

Member Function Documentation

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.

Referenced by comment_from_line(), energies_from_pose(), energies_into_pose(), and core::io::silent::BinaryProteinSilentStruct::init_from_lines().

void core::io::silent::SilentStruct::add_energy ( std::string  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 core::sequence::end, and protocols::forge::methods::replace().

Referenced by 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::simple_filters::StructuralSimilarityEvaluator::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::simple_filters::JScoreEvaluator::apply(), protocols::simple_filters::ContactMapEvaluator::apply(), protocols::evaluation::SingleValuePoseEvaluator< T >::apply(), protocols::constraints_additional::ConstraintEvaluator::apply(), protocols::constraints_additional::CombinedConstraintEvaluator::apply(), protocols::comparative_modeling::Align_RotamerEvaluator::apply(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator::apply(), protocols::abinitio::PcaEvaluator::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), protocols::swa::RigidBodySampler::assign_WC_edges_to_base_pair12(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), core::io::silent::RNA_SilentStruct::init_from_lines(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::swa::protein::output_silent_struct(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::output_to_silent_file(), and parse_energies().

void core::io::silent::SilentStruct::add_parent_remark ( std::string const  name,
std::string const  value 
)
void core::io::silent::SilentStruct::add_string_value ( std::string  scorename,
std::string const &  value 
)
void core::io::silent::SilentStruct::clear_comments ( )
virtual void core::io::silent::SilentStruct::clear_energies ( ) [inline, virtual]

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.

Referenced by energies_from_pose().

virtual SilentStructOP core::io::silent::SilentStruct::clone ( ) const [pure virtual]
void core::io::silent::SilentStruct::comment_from_line ( std::string const &  line)
void core::io::silent::SilentStruct::copy_scores ( const SilentStruct src_ss)
std::string core::io::silent::SilentStruct::decoy_tag ( ) const [inline]
void core::io::silent::SilentStruct::decoy_tag ( std::string const &  tag) [inline]

sets the tag associated with this SilentStruct.

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

@ brief helper to detect fullatom input

@ brief helper to detect fullatom input @ detail

References core::chemical::num_canonical_aas, core::sequence::AnnotatedSequence::one_letter(), sequence(), and core::io::silent::tr().

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

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

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

Referenced by energies_into_pose(), and energy_names().

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

References add_comment(), core::pose::add_score_line_string(), core::pose::Pose::data(), core::sequence::end, energies(), core::pose::Pose::energies(), get_all_comments(), core::scoring::ScoreTypeManager::is_score_type(), core::scoring::ScoreTypeManager::score_type_from_name(), core::scoring::Energies::total_energies(), core::io::silent::tr(), and core::scoring::Energies::weights().

Referenced by finish_pose().

EnergyNames core::io::silent::SilentStruct::energy_names ( ) const
void core::io::silent::SilentStruct::erase_comment ( std::string const &  name)
void core::io::silent::SilentStruct::fill_pose ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  residue_set 
) 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::import_pose::PDBSilentStruct, core::io::silent::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, and core::io::silent::ScoreFileSilentStruct.

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

void core::io::silent::SilentStruct::fill_pose ( core::pose::Pose pose) const [virtual]
virtual void core::io::silent::SilentStruct::fill_struct ( core::pose::Pose const &  pose,
std::string  tag = "empty_tag" 
) [pure virtual]
void core::io::silent::SilentStruct::finish_pose ( core::pose::Pose pose) const
std::map< std::string, std::string > core::io::silent::SilentStruct::get_all_comments ( ) const
virtual ObjexxFCL::FArray2D< Real > core::io::silent::SilentStruct::get_CA_xyz ( ) const [pure virtual]
std::string core::io::silent::SilentStruct::get_comment ( std::string const &  name) const
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::import_pose::PDBSilentStruct, core::io::silent::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, and core::io::silent::ScoreFileSilentStruct.

core::Real core::io::silent::SilentStruct::get_energy ( std::string const &  scorename) const
std::string core::io::silent::SilentStruct::get_parent_remark ( std::string const &  name) const
void core::io::silent::SilentStruct::get_parent_remark_from_line ( std::string const  line)
utility::vector1< SilentEnergy > core::io::silent::SilentStruct::get_silent_energies ( ) [inline]
SilentEnergy const & core::io::silent::SilentStruct::get_silent_energy ( std::string const &  scorename) const

Returns the SilentEnergy associated with this scorename.

References core::sequence::end, and has_energy().

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

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

returns true if this SilentStruct has an energy for the given scorename, returns false otherwise.

References core::sequence::end.

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

bool core::io::silent::SilentStruct::has_parent_remark ( std::string const &  name) const
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::import_pose::PDBSilentStruct, core::io::silent::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, and core::io::silent::ScoreFileSilentStruct.

virtual core::Size core::io::silent::SilentStruct::mem_footprint ( ) const [inline, virtual]
virtual Size core::io::silent::SilentStruct::nres ( ) const [inline, virtual]

returns the number of residues contained by this SilentStruct.

Referenced by protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), core::io::silent::BinaryProteinSilentStruct::add_chain_ending(), core::io::silent::BinaryProteinSilentStruct::BinaryProteinSilentStruct(), core::io::silent::BinaryRNASilentStruct::BinaryRNASilentStruct(), core::io::silent::RNA_SilentStruct::CA_rmsd(), core::io::silent::BinaryRNASilentStruct::CA_rmsd(), core::io::silent::BinaryProteinSilentStruct::CA_rmsd(), core::io::silent::BinaryProteinSilentStruct::chain_endings(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::BinaryRNASilentStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::get_CA_xyz(), core::io::silent::BinaryRNASilentStruct::get_CA_xyz(), core::io::silent::BinaryProteinSilentStruct::get_CA_xyz(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::io::silent::BinaryRNASilentStruct::init_from_lines(), core::io::silent::BinaryProteinSilentStruct::init_from_lines(), nres(), core::io::silent::ProteinSilentStruct_Template< T >::operator=(), core::io::silent::RNA_SilentStruct::print_conformation(), core::io::silent::BinaryRNASilentStruct::print_conformation(), core::io::silent::BinaryProteinSilentStruct::print_conformation(), core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template(), core::io::silent::RNA_SilentStruct::resize(), core::io::silent::BinaryRNASilentStruct::resize(), core::io::silent::BinaryProteinSilentStruct::resize(), and core::io::silent::RNA_SilentStruct::RNA_SilentStruct().

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

returns the number of residues in this SilentStruct.

References nres().

std::string core::io::silent::SilentStruct::one_letter_sequence ( ) const
SilentStruct & core::io::silent::SilentStruct::operator= ( SilentStruct const &  src)
void core::io::silent::SilentStruct::parse_energies ( std::istream &  input,
utility::vector1< std::string > const &  energy_names 
)
core::Size core::io::silent::SilentStruct::precision ( ) const

Referenced by precision(), and print_scores().

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

References precision().

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

print the comments in this SilentStruct.

References core::sequence::end.

Referenced by print_scores().

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

print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines: SEQUENCE: <protein sequence>="">: <list of score-types>.

Reimplemented in core::io::silent::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, core::io::silent::RNA_SilentStruct, and core::io::silent::ScoreFileSilentStruct.

References one_letter_sequence(), and print_score_header().

Referenced by core::io::silent::SilentFileData::_write_silent_struct(), and core::io::silent::SilentFileData::write_silent_struct().

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

References core::sequence::end.

void core::io::silent::SilentStruct::print_score_header ( std::ostream &  out) const [virtual]
void core::io::silent::SilentStruct::print_scores ( std::ostream &  out) const [virtual]
void core::io::silent::SilentStruct::read_score_headers ( std::string const &  line,
utility::vector1< std::string > &  enames,
SilentFileData container 
)
bool core::io::silent::SilentStruct::read_sequence ( std::string const &  line)
void core::io::silent::SilentStruct::rename_energies ( )
void core::io::silent::SilentStruct::scoreline_prefix ( std::string const &  prefix)
std::string core::io::silent::SilentStruct::scoreline_prefix ( ) const

Referenced by print_score_header(), and print_scores().

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

sets the sequence for this SilentStruct.

References sequence().

core::sequence::AnnotatedSequence const& core::io::silent::SilentStruct::sequence ( ) const [inline]
void core::io::silent::SilentStruct::set_decoy_tag ( std::string const &  tag) [inline]
void core::io::silent::SilentStruct::set_tag_from_pose ( const core::pose::Pose pose)
void core::io::silent::SilentStruct::set_valid_energies ( utility::vector1< std::string >  valid)
void core::io::silent::SilentStruct::silent_energies ( utility::vector1< SilentEnergy > const &  new_se) [inline]

sets the silent_energies for this SilentStruct.

Referenced by set_valid_energies().

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

sort all the silent energies by their name.

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


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