#include <ScoreFileSilentStruct.hh>

Inheritance diagram for core::io::silent::ScoreFileSilentStruct:

Public Member Functions
	ScoreFileSilentStruct (SilentFileOptions const &opts)
	Constructors. More...

	ScoreFileSilentStruct (SilentFileOptions const &opts, core::pose::Pose const &pose, std::string tag="empty_tag")

SilentStructOP	clone () const override

	~ScoreFileSilentStruct () override
	Re-dimension the storage capacity of this ScoreFileSilentStruct to the given number of residues. More...

ScoreFileSilentStruct &	operator= (ScoreFileSilentStruct const &src)
	Test if this ScoreFileSilentStruct is equal to the given ScoreFileSilentStruct in terms of conformation. Doesn't check energies. More...

bool	init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container) override
	Tells this ScoreFileSilentStruct object to initialize itself from the given set of lines. Only initializes energies. 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 ScoreFileSilentStruct. 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_conformation (std::ostream &output) const override
	Prints the conformation information within this ScoreFileSilentStruct to the given std::ostream. More...

void	print_header (std::ostream &out) const override
	Prints the header information within this ScoreFileSilentStruct to the given std::ostream. More...

ObjexxFCL::FArray2D< Real >	get_CA_xyz () const override
	returns the positions of the CA atoms in this ScoreFileSilentStruct. 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 ScoreFileSilentStruct and the C-alpha atoms from this ScoreFileSilentStruct. 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 ()

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...

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

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::io::silent::ScoreFileSilentStruct::ScoreFileSilentStruct ( SilentFileOptions const & opts )

Constructors.

References core::io::silent::SilentStruct::decoy_tag().

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

References core::io::silent::SilentStruct::decoy_tag(), and fill_struct().

core::io::silent::ScoreFileSilentStruct::~ScoreFileSilentStruct ( )

inlineoverride

Re-dimension the storage capacity of this ScoreFileSilentStruct to the given number of residues.

Member Function Documentation

SilentStructOP core::io::silent::ScoreFileSilentStruct::clone ( ) const

inlineoverridevirtual

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

void core::io::silent::ScoreFileSilentStruct::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 ScoreFileSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the / user-specified residue types.

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

References core::io::silent::SilentStruct::energies_into_pose().

void core::io::silent::ScoreFileSilentStruct::fill_struct	(	core::pose::Pose const &	pose,
		std::string	tag
	)

overridevirtual

opposite of fill_pose

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

References core::io::silent::SilentStruct::decoy_tag(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::sequence(), core::pose::Pose::sequence(), and core::io::silent::SilentStruct::set_tag_from_pose().

Referenced by ScoreFileSilentStruct().

ObjexxFCL::FArray2D< Real > core::io::silent::ScoreFileSilentStruct::get_CA_xyz ( ) const

overridevirtual

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

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

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

Real core::io::silent::ScoreFileSilentStruct::get_debug_rmsd ( )

overridevirtual

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

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

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

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

overridevirtual

Tells this ScoreFileSilentStruct object to initialize itself from the given set of lines. Only initializes energies.

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

References core::io::silent::energynames, core::io::silent::SilentFileData::get_shared_silent_data(), and core::io::silent::SilentFileData::set_shared_silent_data().

ScoreFileSilentStruct & core::io::silent::ScoreFileSilentStruct::operator= ( ScoreFileSilentStruct const & src )

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

void core::io::silent::ScoreFileSilentStruct::print_conformation ( std::ostream & output ) const

overridevirtual

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

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

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

overridevirtual

Prints the header information within this ScoreFileSilentStruct to the given std::ostream.

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

References core::io::silent::SilentStruct::print_score_header().

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

src/core/io/silent/ScoreFileSilentStruct.hh
src/core/io/silent/ScoreFileSilentStruct.cc

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation