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Rosetta
2021.16
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#include <RNA_SilentStruct.hh>

Public Member Functions | |
| RNA_SilentStruct (SilentFileOptions const &opts, Size const nres_in) | |
| Constructors. More... | |
| RNA_SilentStruct (SilentFileOptions const &opts) | |
| RNA_SilentStruct (SilentFileOptions const &opts, core::pose::Pose const &pose, std::string tag="empty_tag", bool fa=true) | |
| void | resize (Size const nres_in) |
| Re-dimension the storage capacity of this RNA_SilentStruct to the given number of residues. More... | |
| SilentStructOP | clone () const override |
| ~RNA_SilentStruct () override | |
| RNA_SilentStruct & | operator= (RNA_SilentStruct const &src) |
| Test if this RNA_SilentStruct is equal to the given RNA_SilentStruct in terms of conformation. Doesn't check energies. More... | |
| bool | init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container) override |
| Tells this RNA_SilentStruct object to initialize itself from the given set of lines. Lines should be of the format. More... | |
| void | fill_pose (core::pose::Pose &pose, bool const metapatches=true) const override |
| Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types. More... | |
| void | fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set, bool const metapatches=true) const override |
| Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types. More... | |
| void | fill_struct (core::pose::Pose const &pose, std::string tag) override |
| opposite of fill_pose More... | |
| void | print_header (std::ostream &out) const override |
| print header information More... | |
| void | print_conformation (std::ostream &output) const override |
| Prints the conformation information within this RNA_SilentStruct to the given std::ostream. More... | |
| bool | fullatom () const |
| data getters/setters More... | |
| void | fullatom (bool fullatom) |
| char | secstruct (Size seqpos) const |
| utility::vector1< Real > | mainchain_torsions (Size seqpos) const |
| utility::vector1< Real > | chi_torsions (Size seqpos) const |
| Real | mainchain_torsion (Size const &seqpos, Size const &torsion_num) const |
| Real | chi (Size const &seqpos, Size const &torsion_num) const |
| Vector | coords (Size seqpos) const |
| utility::vector1< Vector > | coords () const |
| void | set_secstruct (Size const &seqpos, char const &ss) |
| void | set_mainchain_torsions (Size const &seqpos, utility::vector1< Real > &torsions) |
| void | set_chi_torsions (Size const &seqpos, utility::vector1< Real > &torsions) |
| void | set_coords (Size const &seqpos, Vector const &coords) |
| void | set_non_main_chain_sugar_coords (Size const &seqpos, utility::vector1< Vector > const &vecs) |
| void | set_fold_tree (kinematics::FoldTree const &f) |
| kinematics::FoldTree const & | fold_tree () const |
| void | add_jump (kinematics::Jump const &jump) |
| kinematics::Jump const & | jump (Size const &jump_num) const |
| ObjexxFCL::FArray2D< Real > | get_CA_xyz () const override |
| returns the positions of the CA atoms in this RNA_SilentStruct. Useful for RMS calculations. More... | |
| virtual Real | CA_rmsd (RNA_SilentStruct other_pss) |
| Real | get_debug_rmsd () override |
| calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this RNA_SilentStruct and the C-alpha atoms from this RNA_SilentStruct. More... | |
Public Member Functions inherited from core::io::silent::SilentStruct | |
| SilentStruct (SilentFileOptions const &opts) | |
| ~SilentStruct () override | |
| SilentStruct (SilentStruct const &) | |
| SilentStruct & | operator= (SilentStruct const &) |
| SilentStructCOP | get_self_ptr () const |
| self pointers More... | |
| SilentStructOP | get_self_ptr () |
| 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... | |
| 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 |
| void | finish_pose (core::pose::Pose &pose) const |
| calls optH if command line requests optH. must be called by derived classes. 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_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... | |
| 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... | |
| 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 Attributes | |
| bool | fullatom_ |
| bool | non_main_chain_sugar_coords_defined_ |
| utility::vector1< char > | secstruct_ |
| utility::vector1 < utility::vector1< Real > > | mainchain_torsions_ |
| utility::vector1 < utility::vector1< Real > > | chi_torsions_ |
| utility::vector1< Vector > | coords_ |
| utility::vector1 < utility::vector1< Vector > > | non_main_chain_sugar_coords_ |
| utility::vector1 < kinematics::Jump > | jumps_ |
| kinematics::FoldTree | fold_tree_ |
Additional Inherited Members | |
Protected Member Functions inherited from core::io::silent::SilentStruct | |
| 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... | |
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Constructors.
References fullatom_, non_main_chain_sugar_coords_defined_, core::io::silent::SilentStruct::nres(), and resize().
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| core::io::silent::RNA_SilentStruct::RNA_SilentStruct | ( | SilentFileOptions const & | opts, |
| core::pose::Pose const & | pose, | ||
| std::string | tag = "empty_tag", |
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| bool | fa = true |
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| ) |
References fill_struct().
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References jumps_.
Referenced by fill_struct(), and init_from_lines().
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References get_CA_xyz(), and core::io::silent::SilentStruct::nres().
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References chi_torsions_.
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References chi_torsions_.
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Implements core::io::silent::SilentStruct.
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References coords_.
Referenced by set_coords().
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Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.
Reimplemented from core::io::silent::SilentStruct.
References core::chemical::FULL_ATOM_t, fullatom(), and core::pose::Pose::residue_type_set_for_pose().
Referenced by get_debug_rmsd().
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Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types.
Reimplemented from core::io::silent::SilentStruct.
References core::pose::rna::apply_non_main_chain_sugar_coords(), core::id::BB, core::id::CHI, chi_torsions_, core::io::silent::SilentStruct::finish_pose(), fold_tree(), core::pose::Pose::fold_tree(), core::chemical::FULL_ATOM_t, fullatom_, jump(), mainchain_torsions_, core::pose::make_pose_from_sequence(), non_main_chain_sugar_coords_, non_main_chain_sugar_coords_defined_, core::io::silent::SilentStruct::nres(), core::kinematics::FoldTree::num_jump(), core::chemical::rna::NUM_RNA_CHI_TORSIONS(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), secstruct_, core::io::silent::SilentStruct::sequence(), core::pose::Pose::set_jump(), core::pose::Pose::set_secstruct(), core::pose::Pose::set_torsion(), core::io::silent::tr(), and core::conformation::Residue::xyz().
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opposite of fill_pose
Reimplemented from core::io::silent::SilentStruct.
References add_jump(), core::conformation::Residue::chi(), chi_torsions_, coords_, core::io::silent::SilentStruct::decoy_tag(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::fill_struct_with_residue_numbers(), fold_tree(), core::pose::Pose::fold_tree(), fold_tree_, fullatom(), core::kinematics::Stub::global2local(), core::pose::Pose::jump(), jumps_, core::conformation::Residue::mainchain_torsions(), mainchain_torsions_, core::chemical::rna::non_main_chain_sugar_atoms, non_main_chain_sugar_coords_, non_main_chain_sugar_coords_defined_, core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), resize(), core::pose::Pose::secstruct(), secstruct_, core::io::silent::SilentStruct::sequence(), core::pose::Pose::sequence(), core::pose::Pose::size(), and core::conformation::Residue::xyz().
Referenced by RNA_SilentStruct().
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References fold_tree_.
Referenced by fill_pose(), fill_struct(), init_from_lines(), and print_conformation().
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data getters/setters
References fullatom_.
Referenced by fill_pose(), fill_struct(), and fullatom().
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References fullatom(), and fullatom_.
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returns the positions of the CA atoms in this RNA_SilentStruct. Useful for RMS calculations.
Implements core::io::silent::SilentStruct.
References coords_, and core::io::silent::SilentStruct::nres().
Referenced by CA_rmsd().
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calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this RNA_SilentStruct and the C-alpha atoms from this RNA_SilentStruct.
Implements core::io::silent::SilentStruct.
References coords_, fill_pose(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().
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Tells this RNA_SilentStruct object to initialize itself from the given set of lines. Lines should be of the format.
Implements core::io::silent::SilentStruct.
References core::io::silent::SilentStruct::add_energy(), add_jump(), core::io::silent::SilentStruct::add_submotif_info_from_line(), core::io::silent::SilentStruct::decoy_tag(), core::sequence::end, core::io::silent::energynames, core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(), core::io::silent::SilentStruct::figure_out_segment_ids_from_line(), fold_tree(), fold_tree_, fullatom_, core::io::silent::SilentFileData::get_shared_silent_data(), jump(), core::io::silent::SilentStruct::nres(), core::chemical::rna::NUM_RNA_CHI_TORSIONS(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), resize(), core::io::silent::SilentStruct::sequence(), set_chi_torsions(), set_coords(), set_fold_tree(), set_mainchain_torsions(), set_non_main_chain_sugar_coords(), set_secstruct(), core::io::silent::SilentFileData::set_shared_silent_data(), core::kinematics::FoldTree::simple_tree(), core::io::silent::simplesequencedata, and core::io::silent::tr().
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References jumps_.
Referenced by fill_pose(), init_from_lines(), and print_conformation().
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References mainchain_torsions_.
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References mainchain_torsions_.
| RNA_SilentStruct & core::io::silent::RNA_SilentStruct::operator= | ( | RNA_SilentStruct const & | src | ) |
Test if this RNA_SilentStruct is equal to the given RNA_SilentStruct in terms of conformation. Doesn't check energies.
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Prints the conformation information within this RNA_SilentStruct to the given std::ostream.
Implements core::io::silent::SilentStruct.
References chi_torsions_, coords_, core::io::silent::SilentStruct::decoy_tag(), core::chemical::element::F, fold_tree(), fullatom_, core::chemical::element::I, jump(), mainchain_torsions_, non_main_chain_sugar_coords_, non_main_chain_sugar_coords_defined_, core::io::silent::SilentStruct::nres(), core::kinematics::FoldTree::num_jump(), core::chemical::rna::NUM_RNA_CHI_TORSIONS(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), secstruct_, core::kinematics::FoldTree::size(), and core::io::silent::tr().
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print header information
Reimplemented from core::io::silent::SilentStruct.
References core::io::silent::SilentStruct::print_header().
| void core::io::silent::RNA_SilentStruct::resize | ( | Size const | nres_in | ) |
Re-dimension the storage capacity of this RNA_SilentStruct to the given number of residues.
Resize this silent-struct to the appropriate number of residues.
References chi_torsions_, coords_, fold_tree_, mainchain_torsions_, non_main_chain_sugar_coords_, core::io::silent::SilentStruct::nres(), secstruct_, and core::kinematics::FoldTree::simple_tree().
Referenced by fill_struct(), init_from_lines(), and RNA_SilentStruct().
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References secstruct_.
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References chi_torsions_.
Referenced by init_from_lines().
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References coords(), and coords_.
Referenced by init_from_lines().
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References fold_tree_.
Referenced by init_from_lines().
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References mainchain_torsions_.
Referenced by init_from_lines().
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References non_main_chain_sugar_coords_, and non_main_chain_sugar_coords_defined_.
Referenced by init_from_lines().
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References secstruct_.
Referenced by init_from_lines().
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Referenced by chi(), chi_torsions(), fill_pose(), fill_struct(), print_conformation(), resize(), and set_chi_torsions().
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Referenced by coords(), fill_struct(), get_CA_xyz(), get_debug_rmsd(), print_conformation(), resize(), and set_coords().
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Referenced by fill_struct(), fold_tree(), init_from_lines(), resize(), and set_fold_tree().
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Referenced by fill_pose(), fullatom(), init_from_lines(), print_conformation(), and RNA_SilentStruct().
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Referenced by add_jump(), fill_struct(), and jump().
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Referenced by fill_pose(), fill_struct(), mainchain_torsion(), mainchain_torsions(), print_conformation(), resize(), and set_mainchain_torsions().
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Referenced by fill_pose(), fill_struct(), print_conformation(), resize(), and set_non_main_chain_sugar_coords().
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Referenced by fill_pose(), fill_struct(), print_conformation(), RNA_SilentStruct(), and set_non_main_chain_sugar_coords().
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Referenced by fill_pose(), fill_struct(), print_conformation(), resize(), secstruct(), and set_secstruct().
1.8.7