#include <PDBSilentStruct.hh>

Inheritance diagram for core::import_pose::PDBSilentStruct:

Collaboration diagram for core::import_pose::PDBSilentStruct:

Public Member Functions
	PDBSilentStruct ()
	Constructors. More...

	PDBSilentStruct (core::pose::Pose const &pose, std::string tag="empty_tag")

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

	~PDBSilentStruct ()

virtual void	print_header (std::ostream &out)

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

virtual bool	init_from_lines (utility::vector1< std::string > const &lines, core::io::silent::SilentFileData &container)
	Tells this PDBSilentStruct object to initialize itself from the given set of lines. Lines should be of the format. More...

virtual void	fill_pose (core::pose::Pose &pose) const
	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...

virtual void	fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set) const
	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...

virtual void	fill_struct (core::pose::Pose const &pose, std::string tag="empty_tag")
	opposite of fill_pose More...

virtual void	print_conformation (std::ostream &output) const
	Prints the conformation information within this PDBSilentStruct to the given std::ostream. More...

core::io::pdb::FileData	file_data () const
	data getters/setters More...

void	file_data (core::io::pdb::FileData new_fd)

std::string	get_pdb_lines () const

virtual ObjexxFCL::FArray2D< Real >	get_CA_xyz () const
	returns the positions of the CA atoms in this PDBSilentStruct. Useful for RMS calculations. More...

virtual Real	get_debug_rmsd ()
	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 ()

virtual	~SilentStruct ()

	SilentStruct (SilentStruct const &)

SilentStruct &	operator= (SilentStruct const &)

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 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 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 scorename, std::string const &value)
	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	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)

Protected Attributes
core::io::pdb::FileData	fd_

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...

Detailed Description

Definition at line 41 of file PDBSilentStruct.hh.

Constructor & Destructor Documentation

core::import_pose::PDBSilentStruct::PDBSilentStruct ( )

inline

Constructors.

Definition at line 46 of file PDBSilentStruct.hh.

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

Referenced by clone().

core::import_pose::PDBSilentStruct::PDBSilentStruct	(	core::pose::Pose const &	pose,
		std::string	tag = `"empty_tag"`
	)

Definition at line 71 of file PDBSilentStruct.cc.

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

inline

Definition at line 60 of file PDBSilentStruct.hh.

Member Function Documentation

virtual core::io::silent::SilentStructOP core::import_pose::PDBSilentStruct::clone ( ) const

inlinevirtual

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

Definition at line 55 of file PDBSilentStruct.hh.

References PDBSilentStruct().

core::io::pdb::FileData core::import_pose::PDBSilentStruct::file_data ( ) const

inline

data getters/setters

Definition at line 105 of file PDBSilentStruct.hh.

References fd_.

void core::import_pose::PDBSilentStruct::file_data ( core::io::pdb::FileData new_fd)

inline

Definition at line 109 of file PDBSilentStruct.hh.

References fd_.

void core::import_pose::PDBSilentStruct::fill_pose ( core::pose::Pose & pose) const

virtual

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.

Definition at line 179 of file PDBSilentStruct.cc.

References core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), and core::chemical::ChemicalManager::residue_type_set().

void core::import_pose::PDBSilentStruct::fill_pose	(	core::pose::Pose &	pose,
		core::chemical::ResidueTypeSet const &	residue_set
	)		const

virtual

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.

Definition at line 171 of file PDBSilentStruct.cc.

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

void core::import_pose::PDBSilentStruct::fill_struct	(	core::pose::Pose const &	pose,
		std::string	tag = `"empty_tag"`
	)

virtual

opposite of fill_pose

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

Definition at line 82 of file PDBSilentStruct.cc.

References core::pose::Pose::sequence().

ObjexxFCL::FArray2D< Real > core::import_pose::PDBSilentStruct::get_CA_xyz ( ) const

virtual

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

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

Definition at line 204 of file PDBSilentStruct.cc.

References core::import_pose::tr().

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

virtual

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.

Definition at line 198 of file PDBSilentStruct.cc.

References core::import_pose::tr().

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

inline

Definition at line 113 of file PDBSilentStruct.hh.

References pdb_lines_.

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