Rosetta 3.4
Public Member Functions | Protected Member Functions | Protected Attributes
core::io::silent::BinaryRNASilentStruct Class Reference

#include <BinaryRNASilentStruct.hh>

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

Public Member Functions

 BinaryRNASilentStruct (Size const nres_in)
 Constructors.
 BinaryRNASilentStruct ()
 BinaryRNASilentStruct (core::pose::Pose const &pose, std::string tag="empty_tag")
void resize (Size const nres_in)
 Re-dimension the storage capacity of this BinaryRNASilentStruct to the given number of residues.
virtual SilentStructOP clone () const
 ~BinaryRNASilentStruct ()
virtual bool init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)
 Test if this BinaryRNASilentStruct is equal to the given BinaryRNASilentStruct in terms of conformation. Doesn't check energies.
virtual void fill_pose (core::pose::Pose &pose) const
 Configure the conformation of the given Pose with the conformational data within this BinaryRNASilentStruct. 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 BinaryRNASilentStruct. 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 BinaryRNASilentStruct to the given std::ostream.
virtual ObjexxFCL::FArray2D< Realget_CA_xyz () const
 returns the positions of the CA atoms in this RNA_SilentStruct. Useful for RMS calculations.
virtual Real CA_rmsd (RNA_SilentStruct other_pss)
virtual Real get_debug_rmsd ()
 calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this RNA_SilentStruct and the C-alpha atoms from this RNA_SilentStruct.

Protected Member Functions

void add_jump (kinematics::Jump jump)
kinematics::RT const & jump (Size jump_num) const
void set_fold_tree (kinematics::FoldTree const &f)
kinematics::FoldTree const & fold_tree () const
char secstruct (unsigned int seqpos) const
void secstruct (unsigned int seqpos, char ss)

Protected Attributes

bool fullatom_
utility::vector1< char > secstruct_
utility::vector1
< utility::vector1
< numeric::xyzVector< float > > > 
atm_coords_
utility::vector1< kinematics::RTjumps_
bool bJumps_use_IntraResStub_
kinematics::FoldTree fold_tree_

Constructor & Destructor Documentation

core::io::silent::BinaryRNASilentStruct::BinaryRNASilentStruct ( Size const  nres_in)
core::io::silent::BinaryRNASilentStruct::BinaryRNASilentStruct ( )
core::io::silent::BinaryRNASilentStruct::BinaryRNASilentStruct ( core::pose::Pose const &  pose,
std::string  tag = "empty_tag" 
)
core::io::silent::BinaryRNASilentStruct::~BinaryRNASilentStruct ( ) [inline]

Member Function Documentation

void core::io::silent::BinaryRNASilentStruct::add_jump ( kinematics::Jump  jump) [inline, protected]
Real core::io::silent::BinaryRNASilentStruct::CA_rmsd ( RNA_SilentStruct  other_pss) [virtual]
virtual SilentStructOP core::io::silent::BinaryRNASilentStruct::clone ( ) const [inline, virtual]
void core::io::silent::BinaryRNASilentStruct::fill_pose ( core::pose::Pose pose) const [virtual]

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

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

References atm_coords_, core::chemical::COARSE_RNA, core::chemical::ChemicalManager::get_instance(), core::chemical::ChemicalManager::residue_type_set(), and core::chemical::RNA.

Referenced by get_debug_rmsd().

void core::io::silent::BinaryRNASilentStruct::fill_pose ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  residue_set 
) const [virtual]
void core::io::silent::BinaryRNASilentStruct::fill_struct ( core::pose::Pose const &  pose,
std::string  tag 
) [virtual]
kinematics::FoldTree const& core::io::silent::BinaryRNASilentStruct::fold_tree ( ) const [inline, protected]
ObjexxFCL::FArray2D< Real > core::io::silent::BinaryRNASilentStruct::get_CA_xyz ( ) const [virtual]

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

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

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

Referenced by CA_rmsd().

Real core::io::silent::BinaryRNASilentStruct::get_debug_rmsd ( ) [virtual]

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

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

References atm_coords_, core::conformation::Residue::atom_index(), fill_pose(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

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

References jumps_.

Referenced by init_from_lines(), and print_conformation().

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

print header information

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

References fullatom_.

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

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

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

References atm_coords_, fold_tree_, core::kinematics::FoldTree::is_simple_tree(), core::io::silent::SilentStruct::nres(), secstruct_, and core::kinematics::FoldTree::simple_tree().

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

void core::io::silent::BinaryRNASilentStruct::secstruct ( unsigned int  seqpos,
char  ss 
) [inline, protected]

References secstruct_.

char core::io::silent::BinaryRNASilentStruct::secstruct ( unsigned int  seqpos) const [inline, protected]

References secstruct_.

void core::io::silent::BinaryRNASilentStruct::set_fold_tree ( kinematics::FoldTree const &  f) [inline, protected]

References make_table_of_pilot_apps::f, and fold_tree_.

Referenced by init_from_lines().


Member Data Documentation


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