Rosetta 3.4
Public Member Functions | Protected Attributes
core::import_pose::PDBSilentStruct Class Reference

#include <PDBSilentStruct.hh>

Inheritance diagram for core::import_pose::PDBSilentStruct:
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Collaboration diagram for core::import_pose::PDBSilentStruct:
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List of all members.

Public Member Functions

 PDBSilentStruct ()
 Constructors.
virtual void print_header (std::ostream &out)
 PDBSilentStruct (core::pose::Pose const &pose, std::string tag="empty_tag")
virtual
core::io::silent::SilentStructOP 
clone () const
 ~PDBSilentStruct ()
PDBSilentStructoperator= (PDBSilentStruct const &src)
 Test if this PDBSilentStruct is equal to the given PDBSilentStruct in terms of conformation. Doesn't check energies.
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.
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.
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.
virtual void fill_struct (core::pose::Pose const &pose, std::string tag="empty_tag")
 opposite of fill_pose
virtual void print_conformation (std::ostream &output) const
 Prints the conformation information within this PDBSilentStruct to the given std::ostream.
core::io::pdb::FileData file_data () const
 data getters/setters
void file_data (core::io::pdb::FileData new_fd)
std::string get_pdb_lines () const
virtual ObjexxFCL::FArray2D< Realget_CA_xyz () const
 returns the positions of the CA atoms in this PDBSilentStruct. Useful for RMS calculations.
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.

Protected Attributes

core::io::pdb::FileData fd_
std::string pdb_lines_

Constructor & Destructor Documentation

core::import_pose::PDBSilentStruct::PDBSilentStruct ( ) [inline]

Constructors.

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" 
)
core::import_pose::PDBSilentStruct::~PDBSilentStruct ( ) [inline]

Member Function Documentation

virtual core::io::silent::SilentStructOP core::import_pose::PDBSilentStruct::clone ( ) const [inline, virtual]
core::io::pdb::FileData core::import_pose::PDBSilentStruct::file_data ( ) const [inline]

data getters/setters

References fd_.

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

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.

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.

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.

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.

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.

References core::import_pose::tr().

std::string core::import_pose::PDBSilentStruct::get_pdb_lines ( ) const [inline]

References pdb_lines_.

bool core::import_pose::PDBSilentStruct::init_from_lines ( utility::vector1< std::string > const &  lines,
core::io::silent::SilentFileData container 
) [virtual]
PDBSilentStruct & core::import_pose::PDBSilentStruct::operator= ( PDBSilentStruct const &  src)

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

void core::import_pose::PDBSilentStruct::print_conformation ( std::ostream &  output) const [virtual]

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

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

References core::io::pdb::PDB_DReader::createPDBData().

void core::import_pose::PDBSilentStruct::print_header ( std::ostream &  out) [virtual]

Member Data Documentation

Referenced by file_data().

Referenced by get_pdb_lines().


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