Rosetta Core  2014.35
Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Static Protected Attributes | Private Types | Private Member Functions | Private Attributes | List of all members
core::io::silent::ProteinSilentStruct_Template< T > Class Template Reference

#include <silent.fwd.hh>

Public Member Functions

 ProteinSilentStruct_Template (core::pose::Pose const &pose, std::string tag="empty_tag", bool fa=false)
 
 ProteinSilentStruct_Template (Size const nres_in)
 Constructors. More...
 
 ProteinSilentStruct_Template ()
 
virtual SilentStructOP clone () const
 Returns a new ProteinSilentStruct with a copy of the information in this ProteinSilentStruct. More...
 
 ~ProteinSilentStruct_Template ()
 
ProteinSilentStruct_Template< T > & operator= (ProteinSilentStruct_Template< T > const &src)
 Test if this ProteinSilentStruct is equal to the given ProteinSilentStruct_Template<T> in terms of conformation. Doesn't check energies. More...
 
virtual bool init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)
 Tells this ProteinSilentStruct object to initialize itself from. More...
 
virtual void fill_pose (core::pose::Pose &pose) const
 Configure the conformation of the given Pose with the conformational data within this ProteinSilentStruct. 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 ProteinSilentStruct. 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. More...
 
bool fullatom () const
 data getters/setters More...
 
virtual void fullatom (bool fullatom)
 
Real phi (Size const seqpos) const
 
Real psi (Size const seqpos) const
 
Real omega (Size const seqpos) const
 
char secstruct (Size const seqpos) const
 
Real chi (Size const seqpos, Size const chi_num) const
 
Size n_chi (Size const seqpos) const
 returns the number of chis at this position. More...
 
numeric::xyzVector< T > const & coords (Size const seqpos) const
 
utility::vector1
< numeric::xyzVector< T >
> const & 
coords () const
 
void phi (Size const seqpos, Real const phi)
 
void psi (Size const seqpos, Real const psi)
 
void omega (Size const seqpos, Real const omega)
 
void secstruct (Size const seqpos, char const ss)
 
utility::vector1< Size > const & chain_endings () const
 
void chain_endings (utility::vector1< Size > const &endings)
 set the list of chain endings More...
 
void add_chain_ending (Size const seqpos)
 add a chain ending to the list More...
 
void chi (Size const seqpos, utility::vector1< T > const &chis)
 
void chi (Size const seqpos, Size const chi_num, Real const chi)
 
Size max_chi () const
 
void coords (Size const seqpos, numeric::xyzVector< T > const &coords)
 
void fold_tree (kinematics::FoldTree const &f)
 
kinematics::FoldTree const & fold_tree () const
 
bool is_symmetric () const
 
void symmetry_info (core::conformation::symmetry::SymmetryInfo &s)
 
core::conformation::symmetry::SymmetryInfoCOP symmetry_info () const
 
void add_jump (kinematics::Jump const &jump)
 
void add_rt (kinematics::RT const &rt)
 
Size njumps () const
 returns the number of jumps held in this container. More...
 
kinematics::RT const & jump (Size const jump_num) const
 
virtual ObjexxFCL::FArray2D< Realget_CA_xyz () const
 returns the positions of the CA atoms in this ProteinSilentStruct. Useful for RMS calculations. More...
 
virtual Real CA_rmsd (ProteinSilentStruct_Template< T > other_pss)
 
virtual Real get_debug_rmsd ()
 calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this ProteinSilentStruct and the C-alpha atoms from this ProteinSilentStruct. More...
 
virtual core::Size mem_footprint () const
 end accessors More...
 
template<>
bool is_single_precision ()
 
template<>
bool is_single_precision ()
 
- Public Member Functions inherited from core::io::silent::SilentStruct
 SilentStruct ()
 
virtual ~SilentStruct ()
 
 SilentStruct (SilentStruct const &)
 
SilentStructoperator= (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 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...
 
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< 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...
 
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...
 

Static Public Member Functions

static bool is_single_precision ()
 

Protected Member Functions

void parse_chain_endings (std::istream &stream)
 parse the chain endings string from an input stream More...
 
std::string chain_endings_str () const
 return the chain endings string More...
 
- 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...
 

Protected Attributes

bool fullatom_
 
utility::vector1< char > secstruct_
 
utility::vector1< Tphi_
 
utility::vector1< Tpsi_
 
utility::vector1< Tomega_
 
utility::vector1
< numeric::xyzVector< T > > 
coords_
 
utility::vector1< kinematics::RTjumps_
 
bool bJumps_use_IntraResStub_
 
kinematics::FoldTree fold_tree_
 
core::conformation::symmetry::SymmetryInfoOP symminfo_
 
utility::vector1< Sizechain_endings_
 

Static Protected Attributes

static const Size max_chi_ = 4
 

Private Types

typedef SilentStruct Parent
 

Private Member Functions

void resize (Size const nres_in)
 Re-dimension the storage capacity of this ProteinSilentStruct to the given number of residues. More...
 
void resize_chi ()
 

Private Attributes

utility::vector1
< utility::vector1< T > > 
chi_
 

Member Typedef Documentation

Constructor & Destructor Documentation

template<class T>
core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template ( core::pose::Pose const &  pose,
std::string  tag = "empty_tag",
bool  fa = false 
)
inline
template<class T>
core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template ( Size const  nres_in)
inline

Member Function Documentation

template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::add_chain_ending ( Size const  seqpos)

add a chain ending to the list

Remarks
All positions in the list must be strictly less than the number of residues in the data. If this condition is not met the routine will fail-fast, so remember to resize() properly prior to calling this function.

References nres, core::io::silent::pss_tr, and utility_exit.

template<class T>
void core::io::silent::ProteinSilentStruct_Template< T >::add_jump ( kinematics::Jump const &  jump)
inline
template<class T>
void core::io::silent::ProteinSilentStruct_Template< T >::add_rt ( kinematics::RT const &  rt)
inline
template<class T >
Real core::io::silent::ProteinSilentStruct_Template< T >::CA_rmsd ( ProteinSilentStruct_Template< T other_pss)
virtual
template<class T>
utility::vector1< Size > const& core::io::silent::ProteinSilentStruct_Template< T >::chain_endings ( ) const
inline
template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::chain_endings ( utility::vector1< Size > const &  endings)

set the list of chain endings

Remarks
All positions in the list must be strictly less than the number of residues in the data. If this condition is not met the routine will fail-fast, so remember to resize() properly prior to calling this function.

References nres, core::io::silent::pss_tr, and utility_exit.

template<class T >
std::string core::io::silent::ProteinSilentStruct_Template< T >::chain_endings_str ( ) const
protected

return the chain endings string

References begin, core::sequence::end, and ss.

template<class T >
Real core::io::silent::ProteinSilentStruct_Template< T >::chi ( Size const  seqpos,
Size const  chi_num 
) const
template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::chi ( Size const  seqpos,
utility::vector1< T > const &  chis 
)
template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::chi ( Size const  seqpos,
Size const  chi_num,
Real const  chi 
)
template<class T>
virtual SilentStructOP core::io::silent::ProteinSilentStruct_Template< T >::clone ( ) const
inlinevirtual

Returns a new ProteinSilentStruct with a copy of the information in this ProteinSilentStruct.

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

template<class T>
numeric::xyzVector<T> const& core::io::silent::ProteinSilentStruct_Template< T >::coords ( Size const  seqpos) const
inline
template<class T>
utility::vector1< numeric::xyzVector<T> > const& core::io::silent::ProteinSilentStruct_Template< T >::coords ( ) const
inline
template<class T>
void core::io::silent::ProteinSilentStruct_Template< T >::coords ( Size const  seqpos,
numeric::xyzVector< T > const &  coords 
)
inline
template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::fill_pose ( core::pose::Pose pose) const
virtual

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

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

References core::chemical::CENTROID, core::chemical::FA_STANDARD, fullatom, and core::io::silent::pss_tr.

template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::fill_pose ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  residue_set 
) const
virtual
template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::fill_struct ( core::pose::Pose const &  pose,
std::string  tag = "empty_tag" 
)
virtual
template<class T>
void core::io::silent::ProteinSilentStruct_Template< T >::fold_tree ( kinematics::FoldTree const &  f)
inline
template<class T>
kinematics::FoldTree const& core::io::silent::ProteinSilentStruct_Template< T >::fold_tree ( ) const
inline
template<class T>
bool core::io::silent::ProteinSilentStruct_Template< T >::fullatom ( ) const
inline
template<class T>
virtual void core::io::silent::ProteinSilentStruct_Template< T >::fullatom ( bool  fullatom)
inlinevirtual
template<class T >
ObjexxFCL::FArray2D< Real > core::io::silent::ProteinSilentStruct_Template< T >::get_CA_xyz ( ) const
virtual

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

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

References nres.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::CA_rmsd().

template<class T >
Real core::io::silent::ProteinSilentStruct_Template< T >::get_debug_rmsd ( )
virtual

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

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

References core::pose::Pose::residue(), numeric::model_quality::rms_wrapper(), rmsd, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

template<class T >
bool core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines ( utility::vector1< std::string > const &  lines,
SilentFileData container 
)
virtual
template<>
bool core::io::silent::ProteinSilentStruct_Template< float >::is_single_precision ( )
template<>
bool core::io::silent::ProteinSilentStruct_Template< core::Real >::is_single_precision ( )
template<class T>
static bool core::io::silent::ProteinSilentStruct_Template< T >::is_single_precision ( )
static
template<class T>
bool core::io::silent::ProteinSilentStruct_Template< T >::is_symmetric ( ) const
inline
template<class T>
kinematics::RT const& core::io::silent::ProteinSilentStruct_Template< T >::jump ( Size const  jump_num) const
inline
template<class T >
Size core::io::silent::ProteinSilentStruct_Template< T >::max_chi ( ) const
template<class T >
core::Size core::io::silent::ProteinSilentStruct_Template< T >::mem_footprint ( ) const
virtual

end accessors

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

References sum().

template<class T >
Size core::io::silent::ProteinSilentStruct_Template< T >::n_chi ( Size const  seqpos) const

returns the number of chis at this position.

template<class T>
Size core::io::silent::ProteinSilentStruct_Template< T >::njumps ( ) const
inline

returns the number of jumps held in this container.

References core::io::silent::ProteinSilentStruct_Template< T >::jumps_.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::operator=().

template<class T>
Real core::io::silent::ProteinSilentStruct_Template< T >::omega ( Size const  seqpos) const
inline
template<class T>
void core::io::silent::ProteinSilentStruct_Template< T >::omega ( Size const  seqpos,
Real const  omega 
)
inline
template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::parse_chain_endings ( std::istream &  stream)
protected

parse the chain endings string from an input stream

References s.

template<class T>
Real core::io::silent::ProteinSilentStruct_Template< T >::phi ( Size const  seqpos) const
inline
template<class T>
void core::io::silent::ProteinSilentStruct_Template< T >::phi ( Size const  seqpos,
Real const  phi 
)
inline
template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::print_conformation ( std::ostream &  output) const
virtual
template<class T>
Real core::io::silent::ProteinSilentStruct_Template< T >::psi ( Size const  seqpos) const
inline
template<class T>
void core::io::silent::ProteinSilentStruct_Template< T >::psi ( Size const  seqpos,
Real const  psi 
)
inline
template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::resize ( Size const  nres_in)
private

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

References nres.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template().

template<class T >
void core::io::silent::ProteinSilentStruct_Template< T >::resize_chi ( )
private

References nres.

template<class T>
char core::io::silent::ProteinSilentStruct_Template< T >::secstruct ( Size const  seqpos) const
inline
template<class T>
void core::io::silent::ProteinSilentStruct_Template< T >::secstruct ( Size const  seqpos,
char const  ss 
)
inline
template<class T>
void core::io::silent::ProteinSilentStruct_Template< T >::symmetry_info ( core::conformation::symmetry::SymmetryInfo s)
inline

Member Data Documentation

template<class T>
bool core::io::silent::ProteinSilentStruct_Template< T >::bJumps_use_IntraResStub_
protected
template<class T>
utility::vector1< Size > core::io::silent::ProteinSilentStruct_Template< T >::chain_endings_
protected
template<class T>
kinematics::FoldTree core::io::silent::ProteinSilentStruct_Template< T >::fold_tree_
protected
template<class T>
bool core::io::silent::ProteinSilentStruct_Template< T >::fullatom_
protected
template<class T>
const Size core::io::silent::ProteinSilentStruct_Template< T >::max_chi_ = 4
staticprotected
template<class T>
utility::vector1< T > core::io::silent::ProteinSilentStruct_Template< T >::omega_
protected
template<class T>
utility::vector1< T > core::io::silent::ProteinSilentStruct_Template< T >::phi_
protected
template<class T>
utility::vector1< T > core::io::silent::ProteinSilentStruct_Template< T >::psi_
protected
template<class T>
utility::vector1< char > core::io::silent::ProteinSilentStruct_Template< T >::secstruct_
protected

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