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core::import_pose::PDBSilentStruct Class Reference

#include <PDBSilentStruct.hh>

Inheritance diagram for core::import_pose::PDBSilentStruct:
Inheritance graph
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Public Member Functions

 PDBSilentStruct (core::io::silent::SilentFileOptions const &opts)
 Constructors. More...
 
 PDBSilentStruct (core::io::silent::SilentFileOptions const &opts, core::pose::Pose const &pose, std::string tag="empty_tag")
 
core::io::silent::SilentStructOP clone () const override
 
 ~PDBSilentStruct () override=default
 
virtual void print_header (std::ostream &out)
 
PDBSilentStructoperator= (PDBSilentStruct const &src)
 Test if this PDBSilentStruct is equal to the given PDBSilentStruct in terms of conformation. Doesn't check energies. More...
 
bool init_from_lines (utility::vector1< std::string > const &lines, core::io::silent::SilentFileData &container) override
 Tells this PDBSilentStruct 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 PDBSilentStruct. 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 PDBSilentStruct. 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="empty_tag") override
 opposite of fill_pose More...
 
void print_conformation (std::ostream &output) const override
 Prints the conformation information within this PDBSilentStruct to the given std::ostream. More...
 
core::io::StructFileRep const struct_file_rep () const
 data getters/setters More...
 
void struct_file_rep (core::io::StructFileRep new_sfr)
 
std::string get_pdb_lines () const
 
ObjexxFCL::FArray2D< Realget_CA_xyz () const override
 returns the positions of the CA atoms in this PDBSilentStruct. Useful for RMS calculations. More...
 
Real get_debug_rmsd () override
 calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this PDBSilentStruct and the C-alpha atoms from this PDBSilentStruct. More...
 
- Public Member Functions inherited from core::io::silent::SilentStruct
 SilentStruct (SilentFileOptions const &opts)
 
 ~SilentStruct () override
 
 SilentStruct (SilentStruct const &)
 
SilentStructoperator= (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_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>="">:

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< 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...
 
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< 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 Attributes

core::io::StructFileRepOP sfr_
 
std::string pdb_lines_
 

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...
 

Constructor & Destructor Documentation

core::import_pose::PDBSilentStruct::PDBSilentStruct ( core::io::silent::SilentFileOptions const &  opts)
core::import_pose::PDBSilentStruct::PDBSilentStruct ( core::io::silent::SilentFileOptions const &  opts,
core::pose::Pose const &  pose,
std::string  tag = "empty_tag" 
)

References fill_struct().

core::import_pose::PDBSilentStruct::~PDBSilentStruct ( )
overridedefault

Member Function Documentation

core::io::silent::SilentStructOP core::import_pose::PDBSilentStruct::clone ( ) const
inlineoverridevirtual
void core::import_pose::PDBSilentStruct::fill_pose ( core::pose::Pose pose,
bool const  metapatches = true 
) const
overridevirtual

Configure the conformation of the given Pose with the conformational data within this PDBSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.

Reimplemented from core::io::silent::SilentStruct.

References core::io::silent::SilentStruct::finish_pose(), core::chemical::FULL_ATOM_t, and core::pose::Pose::residue_type_set_for_pose().

void core::import_pose::PDBSilentStruct::fill_pose ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  residue_set,
bool const  metapatches = true 
) const
overridevirtual

Configure the conformation of the given Pose with the conformational data within this PDBSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the / user-specified residue types.

Reimplemented from core::io::silent::SilentStruct.

References core::import_pose::build_pose(), pdb_lines_, core::import_pose::read_additional_pdb_data(), and sfr_.

void core::import_pose::PDBSilentStruct::fill_struct ( core::pose::Pose const &  pose,
std::string  tag = "empty_tag" 
)
overridevirtual
ObjexxFCL::FArray2D< Real > core::import_pose::PDBSilentStruct::get_CA_xyz ( ) const
overridevirtual

returns the positions of the CA atoms in this PDBSilentStruct. Useful for RMS calculations.

Implements core::io::silent::SilentStruct.

References core::import_pose::tr().

Real core::import_pose::PDBSilentStruct::get_debug_rmsd ( )
overridevirtual

calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this PDBSilentStruct and the C-alpha atoms from this PDBSilentStruct.

Implements core::io::silent::SilentStruct.

References core::import_pose::tr().

std::string core::import_pose::PDBSilentStruct::get_pdb_lines ( ) const
inline

References pdb_lines_.

bool core::import_pose::PDBSilentStruct::init_from_lines ( utility::vector1< std::string > const &  lines,
core::io::silent::SilentFileData container 
)
overridevirtual
PDBSilentStruct & core::import_pose::PDBSilentStruct::operator= ( PDBSilentStruct const &  src)

Test if this PDBSilentStruct is equal to the given PDBSilentStruct in terms of conformation. Doesn't check energies.

void core::import_pose::PDBSilentStruct::print_conformation ( std::ostream &  output) const
overridevirtual

Prints the conformation information within this PDBSilentStruct to the given std::ostream.

Implements core::io::silent::SilentStruct.

References core::io::pdb::create_pdb_contents_from_sfr(), and sfr_.

void core::import_pose::PDBSilentStruct::print_header ( std::ostream &  out)
virtual
core::io::StructFileRep const core::import_pose::PDBSilentStruct::struct_file_rep ( ) const
inline

data getters/setters

References sfr_.

void core::import_pose::PDBSilentStruct::struct_file_rep ( core::io::StructFileRep  new_sfr)
inline

Member Data Documentation

std::string core::import_pose::PDBSilentStruct::pdb_lines_
protected
core::io::StructFileRepOP core::import_pose::PDBSilentStruct::sfr_
protected

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