Rosetta 3.4
Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Static Protected Attributes
core::io::silent::ProteinSilentStruct_Template< T > Class Template Reference

#include <ProteinSilentStruct.hh>

Inheritance diagram for core::io::silent::ProteinSilentStruct_Template< T >:
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Collaboration diagram for core::io::silent::ProteinSilentStruct_Template< T >:
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List of all members.

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.
 ProteinSilentStruct_Template ()
virtual SilentStructOP clone () const
 Returns a new ProteinSilentStruct with a copy of the information in this ProteinSilentStruct.
 ~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.
virtual bool init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)
 Tells this ProteinSilentStruct object to initialize itself from.
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.
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.
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.
bool fullatom () const
 data getters/setters
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.
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
void add_chain_ending (Size const seqpos)
 add a chain ending to the list
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.
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.
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.
virtual core::Size mem_footprint () const
 end accessors
template<>
bool is_single_precision ()
template<>
bool is_single_precision ()

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
std::string chain_endings_str () const
 return the chain endings string

Protected Attributes

bool fullatom_
utility::vector1< char > secstruct_
utility::vector1< T > phi_
utility::vector1< T > psi_
utility::vector1< T > omega_
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

template<class T>
class core::io::silent::ProteinSilentStruct_Template< T >


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 core::io::silent::pss_tr().

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 >
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 core::io::silent::pss_tr().

template<class T>
utility::vector1< Size > const& core::io::silent::ProteinSilentStruct_Template< T >::chain_endings ( ) const [inline]
template<class T >
std::string core::io::silent::ProteinSilentStruct_Template< T >::chain_endings_str ( ) const [protected]

return the chain endings string

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

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 [inline, virtual]

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

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

template<class T>
utility::vector1< numeric::xyzVector<T> > const& core::io::silent::ProteinSilentStruct_Template< T >::coords ( ) const [inline]
template<class T>
numeric::xyzVector<T> const& core::io::silent::ProteinSilentStruct_Template< T >::coords ( Size const  seqpos) 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, core::chemical::ChemicalManager::get_instance(), core::io::silent::pss_tr(), and core::chemical::ChemicalManager::residue_type_set().

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) [inline, virtual]
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.

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(), 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<class T>
static bool core::io::silent::ProteinSilentStruct_Template< T >::is_single_precision ( ) [static]
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>
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 core::pack::interaction_graph::T().

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>
void core::io::silent::ProteinSilentStruct_Template< T >::omega ( Size const  seqpos,
Real const  omega 
) [inline]
template<class T>
Real core::io::silent::ProteinSilentStruct_Template< T >::omega ( Size const  seqpos) const [inline]
template<class T >
ProteinSilentStruct_Template< T > & core::io::silent::ProteinSilentStruct_Template< T >::operator= ( ProteinSilentStruct_Template< T > const &  src)
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

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

Member Data Documentation

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 [static, 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:
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