Rosetta Core  2014.35
Public Member Functions | Protected Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
core::io::silent::SilentStruct Class Referenceabstract

#include <SilentStruct.hh>

Public Member Functions

 SilentStruct ()
 
virtual ~SilentStruct ()
 
 SilentStruct (SilentStruct const &)
 
SilentStructoperator= (SilentStruct const &)
 
virtual SilentStructOP clone () const =0
 
virtual void fill_pose (core::pose::Pose &pose) const
 
virtual void fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set) 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>="">:

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_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 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...
 
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 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...
 
virtual ObjexxFCL::FArray2D< Realget_CA_xyz () const =0
 returns the positions of the CA atoms in this ProteinSilentStruct. Useful for RMS calculations. 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< Size > const &residue_numbers)
 
void set_chains (utility::vector1< char > const &chains)
 
void fill_struct_with_residue_numbers (pose::Pose const &pose)
 
void residue_numbers_into_pose (pose::Pose &pose) const
 
void figure_out_residue_numbers_from_line (std::istream &line_stream)
 
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...
 

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...
 
bool strict_column_mode_
 
Size nres_
 
std::string decoy_tag_
 
core::sequence::AnnotatedSequence sequence_
 
std::string full_sequence_
 
std::map< std::string,
std::string > 
parent_remarks_map_
 
std::map< std::string,
std::string > 
silent_comments_
 
utility::vector1< SilentEnergysilent_energies_
 
utility::vector1< std::string > cache_remarks_
 
utility::vector1< Sizeresidue_numbers_
 
utility::vector1< char > chains_
 
core::Size precision_
 
std::string scoreline_prefix_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::io::silent::SilentStruct::SilentStruct ( )
core::io::silent::SilentStruct::~SilentStruct ( )
virtual
core::io::silent::SilentStruct::SilentStruct ( SilentStruct const &  src)

Member Function Documentation

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_, silent_comments_, and core::io::silent::tr.

Referenced by comment_from_line(), energies_from_pose(), extract_writeable_cacheable_data(), and core::io::silent::BinarySilentStruct::init_from_lines().

void core::io::silent::SilentStruct::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.

References core::sequence::end, silent_energies_, and width.

Referenced by core::io::silent::RNA_SilentStruct::init_from_lines(), and parse_energies().

void core::io::silent::SilentStruct::add_parent_remark ( std::string const  name,
std::string const  value 
)
void core::io::silent::SilentStruct::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.

References core::sequence::end, silent_energies_, and width.

Referenced by energies_from_pose(), and parse_energies().

void core::io::silent::SilentStruct::clear_comments ( )

References silent_comments_.

virtual void core::io::silent::SilentStruct::clear_energies ( )
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().

virtual SilentStructOP core::io::silent::SilentStruct::clone ( ) const
pure virtual
void core::io::silent::SilentStruct::comment_from_line ( std::string const &  line)
void core::io::silent::SilentStruct::copy_scores ( const SilentStruct src_ss)

Copy the score information in the given SilentStruct into this SilentStruct.

References core::sequence::end, and silent_energies_.

std::string core::io::silent::SilentStruct::decoy_tag ( ) const
inline
void core::io::silent::SilentStruct::decoy_tag ( std::string const &  tag)
inline

sets the tag associated with this SilentStruct.

References decoy_tag_.

void core::io::silent::SilentStruct::detect_fullatom ( core::Size  pos,
core::Size  natoms,
bool fullatom,
bool well_defined 
)
protected
utility::vector1< SilentEnergy > core::io::silent::SilentStruct::energies ( ) const
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)
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(), core::sequence::end, energies(), core::pose::Pose::energies(), get_all_comments(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), option, runtime_assert, core::scoring::score_type_from_name(), basic::datacache::BasicDataCache::set(), in::file::silent_score_prefix, in::file::silent_scores_wanted, core::scoring::Energies::total_energies(), core::io::silent::tr, user, weights, and core::scoring::Energies::weights().

Referenced by finish_pose().

EnergyNames core::io::silent::SilentStruct::energy_names ( ) const
void core::io::silent::SilentStruct::erase_comment ( std::string const &  name)

References silent_comments_.

void core::io::silent::SilentStruct::extract_writeable_cacheable_data ( core::pose::Pose const &  pose)
protected

add string serialization of all WriteableCacheableData in as comments.

Parameters
posea pose containing a datacache with WriteableCacheableData.

References add_comment(), core::pose::Pose::data(), basic::datacache::DataMap::get(), and ss.

Referenced by fill_struct().

void core::io::silent::SilentStruct::figure_out_residue_numbers_from_line ( std::istream &  line_stream)
void core::io::silent::SilentStruct::fill_pose ( core::pose::Pose pose) const
virtual
void core::io::silent::SilentStruct::fill_pose ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  residue_set 
) const
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::RNA_SilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, 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.

void core::io::silent::SilentStruct::fill_struct ( core::pose::Pose const &  pose,
std::string  tag = "empty_tag" 
)
virtual
void core::io::silent::SilentStruct::fill_struct_with_residue_numbers ( pose::Pose const &  pose)
void core::io::silent::SilentStruct::finish_pose ( core::pose::Pose pose) const
virtual bool core::io::silent::SilentStruct::force_bitflip ( ) const
inlinevirtual

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().

std::map< std::string, std::string > core::io::silent::SilentStruct::get_all_comments ( ) const

References silent_comments_.

Referenced by energies_into_pose().

virtual ObjexxFCL::FArray2D< Real > core::io::silent::SilentStruct::get_CA_xyz ( ) const
pure virtual
std::string core::io::silent::SilentStruct::get_comment ( std::string const &  name) const

References silent_comments_.

virtual Real core::io::silent::SilentStruct::get_debug_rmsd ( )
pure virtual

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().

std::string core::io::silent::SilentStruct::get_parent_remark ( std::string const &  name) const
void core::io::silent::SilentStruct::get_parent_remark_from_line ( std::string const  line)
utility::vector1< SilentEnergy > core::io::silent::SilentStruct::get_silent_energies ( )
inline

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 core::sequence::end, 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 get_silent_energy(), has_energy(), and core::io::silent::SilentEnergy::string_value().

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 core::sequence::end, and silent_energies_.

Referenced by 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_.

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

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::RNA_SilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, core::io::silent::ScoreJumpFileSilentStruct, core::import_pose::PDBSilentStruct, and core::io::silent::ScoreFileSilentStruct.

virtual core::Size core::io::silent::SilentStruct::mem_footprint ( ) const
inlinevirtual
virtual Size core::io::silent::SilentStruct::nres ( ) const
inlinevirtual
void core::io::silent::SilentStruct::nres ( Size  nres)
inline

returns the number of residues in this SilentStruct.

References nres(), and nres_.

std::string core::io::silent::SilentStruct::one_letter_sequence ( ) const
SilentStruct & core::io::silent::SilentStruct::operator= ( SilentStruct const &  src)
void core::io::silent::SilentStruct::parse_energies ( std::istream &  input,
utility::vector1< std::string > const &  energy_names 
)
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().

void core::io::silent::SilentStruct::print_comments ( std::ostream &  out) const
virtual

print the comments in this SilentStruct.

References cache_remarks_, core::sequence::end, and silent_comments_.

Referenced by print_scores().

virtual void core::io::silent::SilentStruct::print_conformation ( std::ostream &  out) const
pure virtual
void core::io::silent::SilentStruct::print_header ( std::ostream &  out) const
virtual
void core::io::silent::SilentStruct::print_parent_remarks ( std::ostream &  out) const
void core::io::silent::SilentStruct::print_residue_numbers ( std::ostream &  out) const
virtual
void core::io::silent::SilentStruct::print_score_header ( std::ostream &  out) const
virtual
void core::io::silent::SilentStruct::print_scores ( std::ostream &  out) const
virtual
void core::io::silent::SilentStruct::read_score_headers ( std::string const &  line,
utility::vector1< std::string > &  enames,
SilentFileData container 
)
bool core::io::silent::SilentStruct::read_sequence ( std::string const &  line)

References sequence(), tag, and core::io::silent::tr.

void core::io::silent::SilentStruct::rename_energies ( )
void core::io::silent::SilentStruct::residue_numbers_into_pose ( pose::Pose pose) const
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 print_score_header(), and print_scores().

core::sequence::AnnotatedSequence const& core::io::silent::SilentStruct::sequence ( ) const
inline
void core::io::silent::SilentStruct::sequence ( core::sequence::AnnotatedSequence const &  sequence)
inline

sets the sequence for this SilentStruct.

References sequence(), and sequence_.

void core::io::silent::SilentStruct::set_chains ( utility::vector1< char > const &  chains)
inline
void core::io::silent::SilentStruct::set_decoy_tag ( std::string const &  tag)
inline

set the tag associate with this SilentStruct

References decoy_tag_.

virtual void core::io::silent::SilentStruct::set_force_bitflip ( bool const  setting)
inlinevirtual

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_.

void core::io::silent::SilentStruct::set_residue_numbers ( utility::vector1< Size > const &  residue_numbers)
inline
void core::io::silent::SilentStruct::set_tag_from_pose ( const core::pose::Pose pose)
void core::io::silent::SilentStruct::set_valid_energies ( utility::vector1< std::string >  valid)
void core::io::silent::SilentStruct::silent_energies ( utility::vector1< SilentEnergy > const &  new_se)
inline

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().

void core::io::silent::SilentStruct::update_score ( )
private

Updates the "score" entry in the silent_energies.

References core::sequence::end, runtime_assert, score, and silent_energies_.

Referenced by energies_from_pose().

Member Data Documentation

utility::vector1< std::string > core::io::silent::SilentStruct::cache_remarks_
private
utility::vector1< char > core::io::silent::SilentStruct::chains_
private
std::string core::io::silent::SilentStruct::decoy_tag_
private

Referenced by decoy_tag(), operator=(), and set_decoy_tag().

bool core::io::silent::SilentStruct::force_bitflip_
private

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(), operator=(), and set_force_bitflip().

std::string core::io::silent::SilentStruct::full_sequence_
private
Size core::io::silent::SilentStruct::nres_
private
std::map< std::string, std::string > core::io::silent::SilentStruct::parent_remarks_map_
private
core::Size core::io::silent::SilentStruct::precision_
private

Referenced by operator=(), and precision().

utility::vector1< Size > core::io::silent::SilentStruct::residue_numbers_
private
std::string core::io::silent::SilentStruct::scoreline_prefix_
private

Referenced by operator=(), and scoreline_prefix().

core::sequence::AnnotatedSequence core::io::silent::SilentStruct::sequence_
private

Referenced by operator=(), and sequence().

std::map< std::string, std::string > core::io::silent::SilentStruct::silent_comments_
private
utility::vector1< SilentEnergy > core::io::silent::SilentStruct::silent_energies_
private
bool core::io::silent::SilentStruct::strict_column_mode_
private

Referenced by operator=().


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