Rosetta 3.4
Public Member Functions
core::io::silent::BinaryProteinSilentStruct Class Reference

why this inheritance pathway? this makes no sense! More...

#include <BinaryProteinSilentStruct.hh>

Inheritance diagram for core::io::silent::BinaryProteinSilentStruct:
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Collaboration diagram for core::io::silent::BinaryProteinSilentStruct:
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List of all members.

Public Member Functions

 BinaryProteinSilentStruct (Size const nres_in)
 Constructors.
 BinaryProteinSilentStruct ()
 BinaryProteinSilentStruct (core::pose::Pose const &pose, std::string tag="empty_tag")
virtual SilentStructOP clone () const
void resize (Size const nres_in)
 Re-dimension the storage capacity of this BinaryProteinSilentStruct to the given number of residues.
 ~BinaryProteinSilentStruct ()
BinaryProteinSilentStructoperator= (BinaryProteinSilentStruct const &src)
 Test if this BinaryProteinSilentStruct is equal to the given BinaryProteinSilentStruct in terms of conformation. Doesn't check energies.
virtual bool init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)
 Initialize object from a set of lines.
virtual void fill_pose (core::pose::Pose &pose) const
 Configure the conformation of the given Pose with the conformational data within this BinaryProteinSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.
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 BinaryProteinSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types.
virtual void fill_struct (core::pose::Pose const &pose, std::string tag)
 opposite of fill_pose
virtual void print_header (std::ostream &out) const
 print header information
virtual void print_conformation (std::ostream &output) const
 Prints the conformation information within this BinaryProteinSilentStruct to the given std::ostream.
virtual ObjexxFCL::FArray2D< Realget_CA_xyz () const
 returns the positions of the CA atoms
virtual Real CA_rmsd (BinaryProteinSilentStruct 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.
void add_jump (kinematics::Jump jump)
kinematics::RT const & jump (Size jump_num) const
void fold_tree (kinematics::FoldTree f)
kinematics::FoldTree const & fold_tree () const
bool fullatom () const
virtual void fullatom (bool fullatom)
char secstruct (unsigned int seqpos) const
void secstruct (unsigned int seqpos, char ss)
void symmetry_info (core::conformation::symmetry::SymmetryInfo &s)
core::conformation::symmetry::SymmetryInfoCOP symmetry_info () const
bool is_symmetric () const
void parse_chain_endings (std::istream &stream)
void chain_endings (utility::vector1< Size > const &endings)
std::string chain_endings_str () const
utility::vector1< Size > const & chain_endings () const
void add_chain_ending (Size const seqpos)

Detailed Description

why this inheritance pathway? this makes no sense!


Constructor & Destructor Documentation

core::io::silent::BinaryProteinSilentStruct::BinaryProteinSilentStruct ( Size const  nres_in)

Constructors.

References core::io::silent::SilentStruct::nres(), and resize().

core::io::silent::BinaryProteinSilentStruct::BinaryProteinSilentStruct ( )
core::io::silent::BinaryProteinSilentStruct::BinaryProteinSilentStruct ( core::pose::Pose const &  pose,
std::string  tag = "empty_tag" 
)

References fill_struct().

core::io::silent::BinaryProteinSilentStruct::~BinaryProteinSilentStruct ( ) [inline]

Member Function Documentation

void core::io::silent::BinaryProteinSilentStruct::add_chain_ending ( Size const  seqpos)
void core::io::silent::BinaryProteinSilentStruct::add_jump ( kinematics::Jump  jump) [inline]
Real core::io::silent::BinaryProteinSilentStruct::CA_rmsd ( BinaryProteinSilentStruct  other_pss) [virtual]
void core::io::silent::BinaryProteinSilentStruct::chain_endings ( utility::vector1< Size > const &  endings)
utility::vector1< Size > const& core::io::silent::BinaryProteinSilentStruct::chain_endings ( ) const [inline]
std::string core::io::silent::BinaryProteinSilentStruct::chain_endings_str ( ) const
virtual SilentStructOP core::io::silent::BinaryProteinSilentStruct::clone ( ) const [inline, virtual]
void core::io::silent::BinaryProteinSilentStruct::fill_pose ( core::pose::Pose pose) const [virtual]

Configure the conformation of the given Pose with the conformational data within this BinaryProteinSilentStruct. 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(), core::chemical::ChemicalManager::get_instance(), core::chemical::ChemicalManager::residue_type_set(), and core::io::silent::tr().

Referenced by get_debug_rmsd().

void core::io::silent::BinaryProteinSilentStruct::fill_pose ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  residue_set 
) const [virtual]
void core::io::silent::BinaryProteinSilentStruct::fill_struct ( core::pose::Pose const &  pose,
std::string  tag 
) [virtual]
kinematics::FoldTree const& core::io::silent::BinaryProteinSilentStruct::fold_tree ( ) const [inline]
void core::io::silent::BinaryProteinSilentStruct::fold_tree ( kinematics::FoldTree  f) [inline]
bool core::io::silent::BinaryProteinSilentStruct::fullatom ( ) const [inline]
virtual void core::io::silent::BinaryProteinSilentStruct::fullatom ( bool  fullatom) [inline, virtual]

References fullatom().

ObjexxFCL::FArray2D< Real > core::io::silent::BinaryProteinSilentStruct::get_CA_xyz ( ) const [virtual]

returns the positions of the CA atoms

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

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

Referenced by CA_rmsd().

Real core::io::silent::BinaryProteinSilentStruct::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 fill_pose(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

bool core::io::silent::BinaryProteinSilentStruct::init_from_lines ( utility::vector1< std::string > const &  lines,
SilentFileData container 
) [virtual]
bool core::io::silent::BinaryProteinSilentStruct::is_symmetric ( ) const [inline]
kinematics::RT const& core::io::silent::BinaryProteinSilentStruct::jump ( Size  jump_num) const [inline]
BinaryProteinSilentStruct & core::io::silent::BinaryProteinSilentStruct::operator= ( BinaryProteinSilentStruct const &  src)

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

void core::io::silent::BinaryProteinSilentStruct::parse_chain_endings ( std::istream &  stream)

References add_chain_ending().

Referenced by init_from_lines().

void core::io::silent::BinaryProteinSilentStruct::print_conformation ( std::ostream &  output) const [virtual]
void core::io::silent::BinaryProteinSilentStruct::print_header ( std::ostream &  out) const [virtual]

print header information

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

void core::io::silent::BinaryProteinSilentStruct::resize ( Size const  nres_in)

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

Resize this silent-struct to the appropriate number of residues.

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

Referenced by BinaryProteinSilentStruct(), fill_struct(), and init_from_lines().

char core::io::silent::BinaryProteinSilentStruct::secstruct ( unsigned int  seqpos) const [inline]
void core::io::silent::BinaryProteinSilentStruct::secstruct ( unsigned int  seqpos,
char  ss 
) [inline]
core::conformation::symmetry::SymmetryInfoCOP core::io::silent::BinaryProteinSilentStruct::symmetry_info ( ) const [inline]
void core::io::silent::BinaryProteinSilentStruct::symmetry_info ( core::conformation::symmetry::SymmetryInfo s) [inline]

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