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

#include <RNA_SilentStruct.hh>

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

Public Member Functions

 RNA_SilentStruct (Size const nres_in)
 Constructors.
 RNA_SilentStruct ()
 RNA_SilentStruct (core::pose::Pose const &pose, std::string tag="empty_tag", bool fa=true)
void resize (Size const nres_in)
 Re-dimension the storage capacity of this RNA_SilentStruct to the given number of residues.
virtual SilentStructOP clone () const
 ~RNA_SilentStruct ()
RNA_SilentStructoperator= (RNA_SilentStruct const &src)
 Test if this RNA_SilentStruct is equal to the given RNA_SilentStruct in terms of conformation. Doesn't check energies.
virtual bool init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)
 Tells this RNA_SilentStruct 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 RNA_SilentStruct. 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 RNA_SilentStruct. 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 RNA_SilentStruct to the given std::ostream.
bool fullatom () const
 data getters/setters
void fullatom (bool fullatom)
char secstruct (Size seqpos) const
utility::vector1< Realmainchain_torsions (Size seqpos) const
utility::vector1< Realchi_torsions (Size seqpos) const
Real mainchain_torsion (Size const &seqpos, Size const &torsion_num) const
Real chi (Size const &seqpos, Size const &torsion_num) const
Vector coords (Size seqpos) const
utility::vector1< Vectorcoords () const
void set_secstruct (Size const &seqpos, char const &ss)
void set_mainchain_torsions (Size const &seqpos, utility::vector1< Real > &torsions)
void set_chi_torsions (Size const &seqpos, utility::vector1< Real > &torsions)
void set_coords (Size const &seqpos, Vector const &coords)
void set_non_main_chain_sugar_coords (Size const &seqpos, utility::vector1< Vector > const &vecs)
void set_fold_tree (kinematics::FoldTree const &f)
kinematics::FoldTree const & fold_tree () const
void add_jump (kinematics::Jump const &jump)
kinematics::Jump const & jump (Size const &jump_num) const
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 Attributes

bool fullatom_
bool non_main_chain_sugar_coords_defined_
utility::vector1< char > secstruct_
utility::vector1
< utility::vector1< Real > > 
mainchain_torsions_
utility::vector1
< utility::vector1< Real > > 
chi_torsions_
utility::vector1< Vectorcoords_
utility::vector1
< utility::vector1< Vector > > 
non_main_chain_sugar_coords_
utility::vector1
< kinematics::Jump
jumps_
kinematics::FoldTree fold_tree_

Constructor & Destructor Documentation

core::io::silent::RNA_SilentStruct::RNA_SilentStruct ( Size const  nres_in) [inline]
core::io::silent::RNA_SilentStruct::RNA_SilentStruct ( ) [inline]
core::io::silent::RNA_SilentStruct::RNA_SilentStruct ( core::pose::Pose const &  pose,
std::string  tag = "empty_tag",
bool  fa = true 
)

References fill_struct().

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

Member Function Documentation

void core::io::silent::RNA_SilentStruct::add_jump ( kinematics::Jump const &  jump) [inline]

References jumps_.

Referenced by fill_struct(), and init_from_lines().

Real core::io::silent::RNA_SilentStruct::CA_rmsd ( RNA_SilentStruct  other_pss) [virtual]
Real core::io::silent::RNA_SilentStruct::chi ( Size const &  seqpos,
Size const &  torsion_num 
) const [inline]

References chi_torsions_.

utility::vector1< Real > core::io::silent::RNA_SilentStruct::chi_torsions ( Size  seqpos) const [inline]

References chi_torsions_.

virtual SilentStructOP core::io::silent::RNA_SilentStruct::clone ( ) const [inline, virtual]
Vector core::io::silent::RNA_SilentStruct::coords ( Size  seqpos) const [inline]

References coords_.

utility::vector1< Vector > core::io::silent::RNA_SilentStruct::coords ( ) const [inline]

References coords_.

Referenced by set_coords().

void core::io::silent::RNA_SilentStruct::fill_pose ( core::pose::Pose pose) const [virtual]

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

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

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

Referenced by get_debug_rmsd().

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

data getters/setters

References fullatom_.

Referenced by fill_pose(), fill_struct(), and fullatom().

void core::io::silent::RNA_SilentStruct::fullatom ( bool  fullatom) [inline]

References fullatom(), and fullatom_.

ObjexxFCL::FArray2D< Real > core::io::silent::RNA_SilentStruct::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 coords_, and core::io::silent::SilentStruct::nres().

Referenced by CA_rmsd(), and core::io::silent::BinaryRNASilentStruct::CA_rmsd().

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

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

References jumps_.

Referenced by fill_pose(), init_from_lines(), and print_conformation().

Real core::io::silent::RNA_SilentStruct::mainchain_torsion ( Size const &  seqpos,
Size const &  torsion_num 
) const [inline]

References mainchain_torsions_.

utility::vector1< Real > core::io::silent::RNA_SilentStruct::mainchain_torsions ( Size  seqpos) const [inline]

References mainchain_torsions_.

RNA_SilentStruct & core::io::silent::RNA_SilentStruct::operator= ( RNA_SilentStruct const &  src)

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

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

print header information

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

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

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

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

References chi_torsions_, coords_, fold_tree_, mainchain_torsions_, non_main_chain_sugar_coords_, core::io::silent::SilentStruct::nres(), secstruct_, and core::kinematics::FoldTree::simple_tree().

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

char core::io::silent::RNA_SilentStruct::secstruct ( Size  seqpos) const [inline]

References secstruct_.

void core::io::silent::RNA_SilentStruct::set_chi_torsions ( Size const &  seqpos,
utility::vector1< Real > &  torsions 
) [inline]

References chi_torsions_.

Referenced by init_from_lines().

void core::io::silent::RNA_SilentStruct::set_coords ( Size const &  seqpos,
Vector const &  coords 
) [inline]

References coords(), and coords_.

Referenced by init_from_lines().

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

References make_table_of_pilot_apps::f, and fold_tree_.

Referenced by init_from_lines().

void core::io::silent::RNA_SilentStruct::set_mainchain_torsions ( Size const &  seqpos,
utility::vector1< Real > &  torsions 
) [inline]

References mainchain_torsions_.

Referenced by init_from_lines().

void core::io::silent::RNA_SilentStruct::set_non_main_chain_sugar_coords ( Size const &  seqpos,
utility::vector1< Vector > const &  vecs 
) [inline]
void core::io::silent::RNA_SilentStruct::set_secstruct ( Size const &  seqpos,
char const &  ss 
) [inline]

References secstruct_.

Referenced by init_from_lines().


Member Data Documentation

Referenced by add_jump(), fill_struct(), and jump().


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