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Rosetta
2020.50
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#include <SilentStruct.hh>
Public Member Functions | |
SilentStruct (SilentFileOptions const &opts) | |
~SilentStruct () override | |
SilentStruct (SilentStruct const &) | |
SilentStruct & | operator= (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 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>="">: | |
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< SilentEnergy > | get_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< Real > | get_CA_xyz () const =0 |
returns the positions of the CA atoms in this ProteinSilentStruct. Useful for RMS calculations. More... | |
utility::vector1< SilentEnergy > | energies () 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< SilentEnergy > | silent_energies_ |
utility::vector1< std::string > | cache_remarks_ |
utility::vector1< std::string > | pdbinfo_labels_ |
utility::vector1< int > | residue_numbers_ |
utility::vector1< char > | chains_ |
utility::vector1< SilentStructOP > | other_struct_list_ |
core::pose::full_model_info::FullModelParametersCOP | full_model_parameters_ |
utility::vector1< std::string > | segment_IDs_ |
utility::vector1 < core::pose::full_model_info::SubMotifInfoOP > | submotif_info_list_ |
core::Size | precision_ |
std::string | scoreline_prefix_ |
SilentFileOptions | options_ |
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private |
core::io::silent::SilentStruct::SilentStruct | ( | SilentFileOptions const & | opts | ) |
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overridedefault |
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default |
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().
void core::io::silent::SilentStruct::add_energy | ( | std::string const & | scorename, |
Real | value, | ||
Real | weight = 1.0 |
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) |
add a score of a given name and value to this SilentStruct. Takes an optional weight that defaults to 1.0.
References protocols::mean_field::max(), 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::simple_filters::PredictedBurialEvaluator::apply(), protocols::simple_filters::ContactMapEvaluator::apply(), protocols::simple_filters::StructuralSimilarityEvaluator::apply(), protocols::simple_filters::JScoreEvaluator::apply(), protocols::comparative_modeling::Align_RotamerEvaluator::apply(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), protocols::topology_broker::ConstraintEvaluatorWrapper::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::constraints_additional::CombinedConstraintEvaluator::apply(), protocols::constraints_additional::ConstraintEvaluator::apply(), protocols::evaluation::SingleValuePoseEvaluator< T >::apply(), protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator::apply(), protocols::abinitio::PcaEvaluator::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), protocols::rna::denovo::RNA_DeNovoProtocol::calc_rmsds(), core::import_pose::PDBSilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), protocols::recces::RECCES_Mover::more_dump_stuff(), 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(), and parse_energies().
void core::io::silent::SilentStruct::add_other_struct | ( | SilentStructOP | silent_struct | ) |
References core::sequence::end, and other_struct_list_.
Referenced by fill_other_struct_list().
void core::io::silent::SilentStruct::add_parent_remark | ( | std::string const & | name, |
std::string const & | value | ||
) |
References parent_remarks_map_, and core::io::silent::tr().
Referenced by get_parent_remark_from_line().
void core::io::silent::SilentStruct::add_string_value | ( | std::string const & | scorename, |
std::string const & | value, | ||
int const | index = -1 |
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) |
add a non-floating point score of a given name and value to this SilentStruct.
References protocols::mean_field::max(), protocols::forge::methods::replace(), and silent_energies_.
Referenced by core::pose::rna::add_number_base_pairs(), core::pose::rna::add_number_native_base_pairs(), protocols::simple_filters::BatchEvaluator::apply(), protocols::constraints_additional::ConstraintEvaluator::apply(), protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator::apply(), energies_from_pose(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), and parse_energies().
void core::io::silent::SilentStruct::add_submotif_info_from_line | ( | std::istream & | line_stream | ) |
References full_model_parameters_, and submotif_info_list_.
Referenced by core::io::silent::BinarySilentStruct::init_from_lines(), and core::io::silent::RNA_SilentStruct::init_from_lines().
void core::io::silent::SilentStruct::clear_comments | ( | ) |
References silent_comments_.
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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 energies_from_pose().
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pure virtual |
Implemented in core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, core::io::silent::ScoreJumpFileSilentStruct, core::import_pose::PDBSilentStruct, and core::io::silent::ScoreFileSilentStruct.
Referenced by protocols::wum::SilentStructStore::add(), core::io::silent::SilentFileData::add_structure(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_add_n_replace(), and fill_other_struct_list().
void core::io::silent::SilentStruct::comment_from_line | ( | std::string const & | line | ) |
Referenced by core::io::silent::BinarySilentStruct::init_from_lines().
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.
[in] | line | Input comment line, of the format "REMARK key value [value]*" |
[in] | include_silentfile_comments | If true, 'REMARK XXX SILENTFILE' lines will be added to comments. |
References add_comment(), core::io::silent::tr(), and protocols::hybridization::val.
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_.
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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::ScoreFileSilentStruct::fill_struct(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), core::import_pose::PDBSilentStruct::fill_struct(), fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), protocols::mpi_refinement::MPI_Refinement::format_silent_struct(), core::import_pose::PDBSilentStruct::init_from_lines(), core::io::silent::BinarySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), parse_energies(), core::import_pose::PDBSilentStruct::PDBSilentStruct(), core::io::silent::ScoreJumpFileSilentStruct::print_conformation(), core::io::silent::BinarySilentStruct::print_conformation(), core::io::silent::RNA_SilentStruct::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().
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inline |
sets the tag associated with this SilentStruct.
References decoy_tag_.
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protected |
@ brief helper to detect fullatom input
@ brief helper to detect fullatom input @ detail
References protocols::cluster::calibur::aa, core::chemical::aa_vrt, core::chemical::num_canonical_aas, core::sequence::AnnotatedSequence::one_letter(), sequence(), and core::io::silent::tr().
Referenced by core::io::silent::BinarySilentStruct::init_from_lines().
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inline |
Returns the vector of SilentEnergy objects associated with this SilentStruct object.
References silent_energies_.
Referenced by energies_into_pose(), and energy_names().
void core::io::silent::SilentStruct::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.
References core::io::raw_data::ScoreMap::add_arbitrary_score_data_from_pose(), core::io::raw_data::ScoreMap::add_arbitrary_string_data_from_pose(), add_comment(), add_string_value(), clear_energies(), core::pose::Pose::energies(), core::pose::get_all_comments(), core::pose::get_all_score_line_strings(), protocols::mean_field::max(), core::scoring::name_from_score_type(), silent_energies_, core::scoring::Energies::total_energies(), core::io::silent::tr(), update_score(), and core::scoring::Energies::weights().
Referenced by core::io::silent::ScoreFileSilentStruct::fill_struct(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), core::import_pose::PDBSilentStruct::fill_struct(), fill_struct(), and core::io::silent::RNA_SilentStruct::fill_struct().
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 core::pose::add_comment(), core::pose::add_score_line_string(), core::pose::Pose::data(), energies(), core::pose::Pose::energies(), get_all_comments(), core::io::silent::SilentFileOptions::in_silent_score_prefix(), core::io::silent::SilentFileOptions::in_silent_scores_wanted(), core::io::silent::SilentFileOptions::in_silent_scores_wanted_set(), options_, core::scoring::score_type_from_name(), protocols::kinmatch::str(), core::scoring::Energies::total_energies(), core::io::silent::tr(), and core::scoring::Energies::weights().
Referenced by core::io::silent::ScoreFileSilentStruct::fill_pose(), core::io::silent::ScoreJumpFileSilentStruct::fill_pose(), and finish_pose().
EnergyNames core::io::silent::SilentStruct::energy_names | ( | ) | const |
Returns the EnergyNames that this SilentStruct contains.
References energies(), and core::io::silent::EnergyNames::energy_names().
Referenced by core::io::silent::SilentFileData::write_silent_struct().
void core::io::silent::SilentStruct::erase_comment | ( | std::string const & | name | ) |
References silent_comments_.
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protected |
add string serialization of all WriteableCacheableData in as comments.
pose | a pose containing a datacache with WriteableCacheableData. |
References add_comment(), and core::pose::Pose::data().
Referenced by fill_struct().
void core::io::silent::SilentStruct::figure_out_residue_numbers_from_line | ( | std::istream & | line_stream | ) |
void core::io::silent::SilentStruct::figure_out_segment_ids_from_line | ( | std::istream & | line_stream | ) |
References residue_numbers_, and set_segment_IDs().
Referenced by core::io::silent::BinarySilentStruct::init_from_lines(), and core::io::silent::RNA_SilentStruct::init_from_lines().
void core::io::silent::SilentStruct::fill_other_struct_list | ( | pose::Pose const & | pose | ) |
References add_other_struct(), clone(), core::pose::full_model_info::const_full_model_info(), decoy_tag_, core::pose::full_model_info::full_model_info_defined(), full_model_parameters(), core::pose::full_model_info::FullModelInfo::other_pose_list(), and set_full_model_parameters().
Referenced by core::io::silent::BinarySilentStruct::fill_struct().
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virtual |
Reimplemented in core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, and core::import_pose::PDBSilentStruct.
References core::chemical::FULL_ATOM_t, nres_, and core::pose::Pose::residue_type_set_for_pose().
Referenced by protocols::mpi_refinement::add_poseinfo_to_ss(), protocols::evaluation::PoseEvaluator::apply(), protocols::abinitio::KinematicAbinitio::apply(), fill_pose(), protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(), and protocols::jd3::pose_inputters::SilentFilePoseInputter::pose_from_input_source().
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().
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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::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.
References core::io::silent::tr().
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virtual |
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
Reimplemented in core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.
References core::pose::Pose::annotated_sequence(), decoy_tag(), energies_from_pose(), extract_writeable_cacheable_data(), core::pose::Pose::pdb_info(), pdbinfo_labels_, sequence(), set_tag_from_pose(), and core::io::silent::tr().
Referenced by core::io::silent::BinarySilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), and protocols::abinitio::AbrelaxApplication::process_decoy().
void core::io::silent::SilentStruct::fill_struct_with_residue_numbers | ( | pose::Pose const & | pose | ) |
void core::io::silent::SilentStruct::fill_struct_with_submotif_info_list | ( | pose::Pose const & | pose | ) |
void core::io::silent::SilentStruct::finish_pose | ( | core::pose::Pose & | pose | ) | const |
calls optH if command line requests optH. must be called by derived classes.
References cache_remarks_, core::pose::Pose::data(), energies_into_pose(), full_model_info_into_pose(), core::io::silent::SilentFileOptions::keep_input_scores(), options_, core::pose::Pose::pdb_info(), pdbinfo_labels_, residue_numbers_into_pose(), core::io::silent::tr(), and core::pose::datacache::CacheableDataType::WRITEABLE_DATA.
Referenced by core::import_pose::PDBSilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_pose(), and core::io::silent::RNA_SilentStruct::fill_pose().
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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().
void core::io::silent::SilentStruct::full_model_info_into_pose | ( | pose::Pose & | pose | ) | const |
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References full_model_parameters_.
Referenced by fill_other_struct_list(), and core::io::silent::BinarySilentStruct::print_header().
std::map< std::string, std::string > core::io::silent::SilentStruct::get_all_comments | ( | ) | const |
References silent_comments_.
Referenced by energies_into_pose().
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returns the positions of the CA atoms in this ProteinSilentStruct. Useful for RMS calculations.
Implemented in core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::RigidBodySilentStruct, core::io::silent::BinarySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.
Referenced by protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), and protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate().
std::string core::io::silent::SilentStruct::get_comment | ( | std::string const & | name | ) | const |
References silent_comments_.
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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::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::RigidBodySilentStruct, core::io::silent::BinarySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.
core::Real core::io::silent::SilentStruct::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.
References get_silent_energy(), has_energy(), and core::io::silent::SilentEnergy::value().
Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_single_replace(), protocols::loophash::MPI_LoopHashRefine_Emperor::add_structures_to_library(), protocols::abinitio::KinematicAbinitio::dump_jump_log(), protocols::loophash::MPI_LoopHashRefine::format_silent_struct(), protocols::mpi_refinement::MPI_Refinement::format_silent_struct(), protocols::mpi_refinement::MultiObjective::formatted_objs_values(), protocols::mpi_refinement::MultiObjective::get_fobj(), protocols::loophash::MPI_LoopHashRefine::objective_function(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::loophash::MPI_LoopHashRefine::score(), and protocols::mpi_refinement::MPI_Refinement::score().
std::string core::io::silent::SilentStruct::get_parent_remark | ( | std::string const & | name | ) | const |
References parent_remarks_map_.
void core::io::silent::SilentStruct::get_parent_remark_from_line | ( | std::string const & | line | ) |
References add_parent_remark(), and protocols::hybridization::val.
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References silent_energies_.
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().
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().
bool core::io::silent::SilentStruct::has_comment | ( | std::string const & | name | ) | const |
References silent_comments_.
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 silent_energies_.
Referenced by protocols::rna::denovo::RNA_DeNovoProtocol::add_chem_shift_info(), 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 |
References parent_remarks_map_.
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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::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, core::io::silent::ScoreJumpFileSilentStruct, core::import_pose::PDBSilentStruct, and core::io::silent::ScoreFileSilentStruct.
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Reimplemented in core::io::silent::ProteinSilentStruct_Template< T >.
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References other_struct_list_.
Referenced by core::io::silent::SilentFileData::write_silent_struct().
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returns the number of residues contained by this SilentStruct.
References nres_.
Referenced by protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), core::io::silent::BinarySilentStruct::add_chain_ending(), core::io::silent::BinarySilentStruct::BinarySilentStruct(), core::io::silent::BinarySilentStruct::CA_rmsd(), core::io::silent::RNA_SilentStruct::CA_rmsd(), core::io::silent::BinarySilentStruct::chain_endings(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::get_CA_xyz(), core::io::silent::RNA_SilentStruct::get_CA_xyz(), core::io::silent::BinarySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), nres(), core::io::silent::ProteinSilentStruct_Template< T >::operator=(), core::io::silent::BinarySilentStruct::print_conformation(), core::io::silent::RNA_SilentStruct::print_conformation(), core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template(), core::io::silent::BinarySilentStruct::resize(), core::io::silent::RNA_SilentStruct::resize(), core::io::silent::RigidBodySilentStruct::RigidBodySilentStruct(), and core::io::silent::RNA_SilentStruct::RNA_SilentStruct().
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returns the number of residues in this SilentStruct.
std::string core::io::silent::SilentStruct::one_letter_sequence | ( | ) | const |
strip [...] comment from seqeunce_ and return pure one-letter sequence
References core::sequence::AnnotatedSequence::one_letter_sequence(), and sequence().
Referenced by core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::init_from_lines(), and print_header().
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SilentFileOptions const & core::io::silent::SilentStruct::options | ( | ) | const |
References options_.
Referenced by core::io::silent::BinarySilentStruct::init_from_lines(), and core::io::silent::BinarySilentStruct::print_conformation().
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References other_struct_list_.
Referenced by core::io::silent::BinarySilentStruct::setup_other_poses(), and core::io::silent::SilentFileData::write_silent_struct().
void core::io::silent::SilentStruct::parse_energies | ( | std::istream & | input, |
utility::vector1< std::string > const & | energy_names | ||
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void core::io::silent::SilentStruct::precision | ( | core::Size | precision | ) |
References precision(), and precision_.
core::Size core::io::silent::SilentStruct::precision | ( | ) | const |
References precision_.
Referenced by precision(), and print_scores().
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print the comments in this SilentStruct.
References cache_remarks_, pdbinfo_labels_, and silent_comments_.
Referenced by core::io::silent::SilentFileData::write_silent_struct().
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print the conformation information in SilentStruct to out.
Implemented in core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.
Referenced by core::io::silent::SilentFileData::write_silent_struct().
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print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines: SEQUENCE: <protein sequence>="">:
Reimplemented in core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.
References full_model_parameters_, one_letter_sequence(), and print_score_header().
Referenced by core::io::silent::SilentFileData::_write_silent_struct(), core::io::silent::ScoreJumpFileSilentStruct::print_header(), core::io::silent::BinarySilentStruct::print_header(), core::io::silent::RNA_SilentStruct::print_header(), and core::io::silent::SilentFileData::write_silent_struct().
void core::io::silent::SilentStruct::print_parent_remarks | ( | std::ostream & | out | ) | const |
References parent_remarks_map_.
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print the resnum in this SilentStruct, if filled.
References chains_, decoy_tag(), nres_, residue_numbers_, and segment_IDs_.
Referenced by core::io::silent::SilentFileData::write_silent_struct().
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only print SCORE: header line
References protocols::comparative_modeling::features::A, decoy_tag(), protocols::mean_field::max(), options_, core::io::silent::SilentFileOptions::out_user_tag(), core::io::silent::SilentFileOptions::out_user_tag_set(), scoreline_prefix(), and silent_energies_.
Referenced by core::import_pose::PDBSilentStruct::print_header(), core::io::silent::ScoreFileSilentStruct::print_header(), print_header(), and core::io::silent::SilentFileData::write_silent_struct().
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print out a SCORE line to the given ozstream.
References protocols::comparative_modeling::features::A, decoy_tag(), core::chemical::element::F, protocols::mean_field::min(), options_, core::io::silent::SilentFileOptions::out_user_tag(), core::io::silent::SilentFileOptions::out_user_tag_set(), core::io::silent::SilentFileOptions::out_weight_silent_scores(), precision(), scoreline_prefix(), and silent_energies_.
Referenced by core::io::silent::SilentFileData::write_silent_struct().
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print the submotif_info in this SilentStruct, if filled.
References decoy_tag(), and submotif_info_list_.
Referenced by core::io::silent::SilentFileData::write_silent_struct().
void core::io::silent::SilentStruct::read_score_headers | ( | std::string const & | line, |
utility::vector1< std::string > & | enames, | ||
SilentFileData & | container | ||
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bool core::io::silent::SilentStruct::read_sequence | ( | std::string const & | line | ) |
References sequence(), and core::io::silent::tr().
void core::io::silent::SilentStruct::rename_energies | ( | ) |
References core::sequence::end, core::init::init(), and silent_energies_.
void core::io::silent::SilentStruct::residue_numbers_into_pose | ( | pose::Pose & | pose | ) | const |
References chains_, core::pose::Pose::pdb_info(), residue_numbers_, segment_IDs_, and core::pose::Pose::size().
Referenced by finish_pose().
void core::io::silent::SilentStruct::scoreline_prefix | ( | std::string const & | prefix | ) |
References scoreline_prefix_.
std::string core::io::silent::SilentStruct::scoreline_prefix | ( | ) | const |
References scoreline_prefix_.
Referenced by core::io::silent::BinarySilentStruct::init_from_lines(), print_score_header(), and print_scores().
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returns the sequence associated with this SilentStruct.
References sequence_.
Referenced by detect_fullatom(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::ScoreFileSilentStruct::fill_struct(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), core::import_pose::PDBSilentStruct::fill_struct(), fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::BinarySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), one_letter_sequence(), core::io::silent::BinarySilentStruct::print_conformation(), read_score_headers(), read_sequence(), and sequence().
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sets the sequence for this SilentStruct.
References sequence(), and sequence_.
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References chains_.
Referenced by figure_out_residue_numbers_from_line(), and fill_struct_with_residue_numbers().
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set the tag associate with this SilentStruct
References decoy_tag_, and other_struct_list_.
Referenced by protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate().
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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_.
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References full_model_parameters_.
Referenced by fill_other_struct_list().
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References residue_numbers_.
Referenced by figure_out_residue_numbers_from_line(), and fill_struct_with_residue_numbers().
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References segment_IDs_.
Referenced by figure_out_residue_numbers_from_line(), figure_out_segment_ids_from_line(), and fill_struct_with_residue_numbers().
void core::io::silent::SilentStruct::set_tag_from_pose | ( | const core::pose::Pose & | pose | ) |
Sets the tag from the Pose DataCache.
References core::pose::Pose::data(), decoy_tag(), and protocols::kinmatch::str().
Referenced by core::io::silent::ScoreFileSilentStruct::fill_struct(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), core::import_pose::PDBSilentStruct::fill_struct(), and fill_struct().
void core::io::silent::SilentStruct::set_valid_energies | ( | utility::vector1< std::string > | valid | ) |
References get_silent_energy(), has_energy(), core::io::silent::SilentEnergy::name(), and silent_energies().
Referenced by core::io::silent::SilentFileData::write_silent_struct().
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sets the silent_energies for this SilentStruct.
References silent_energies_.
Referenced by set_valid_energies().
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().
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Updates the "score" entry in the silent_energies.
References protocols::hybridization::score, and silent_energies_.
Referenced by energies_from_pose().
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Referenced by add_comment(), finish_pose(), and print_comments().
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Referenced by full_model_info_into_pose(), print_residue_numbers(), residue_numbers_into_pose(), and set_chains().
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Referenced by decoy_tag(), fill_other_struct_list(), and set_decoy_tag().
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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().
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Referenced by fill_pose(), nres(), and print_residue_numbers().
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Referenced by energies_into_pose(), finish_pose(), options(), print_score_header(), and print_scores().
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Referenced by add_other_struct(), nonconst_other_struct_list(), other_struct_list(), and set_decoy_tag().
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Referenced by add_parent_remark(), get_parent_remark(), has_parent_remark(), and print_parent_remarks().
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Referenced by add_comment(), fill_struct(), finish_pose(), and print_comments().
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Referenced by precision().
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Referenced by scoreline_prefix().
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Referenced by full_model_info_into_pose(), print_residue_numbers(), residue_numbers_into_pose(), and set_segment_IDs().
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Referenced by sequence().
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Referenced by add_comment(), clear_comments(), erase_comment(), get_all_comments(), get_comment(), has_comment(), and print_comments().
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