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core::chemical::AtomICoor Class Reference

A basic class containing info of internal coordinates needed for building an atom within a ResidueType. More...

#include <AtomICoor.hh>

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Public Member Functions

 AtomICoor ()
 default constructor More...
 
 AtomICoor (Real const phi_in, Real const theta_in, Real const d_in, std::string const &stub_atom1_name, std::string const &stub_atom2_name, std::string const &stub_atom3_name, ResidueType const &rsd_type)
 constructor More...
 
 AtomICoor (Size const index, Real const phi_in, Real const theta_in, Real const d_in, std::string const &stub_atom1_name, std::string const &stub_atom2_name, std::string const &stub_atom3_name, ResidueType const &rsd_type)
 
Real phi () const
 accessor to stub_atom1 ICoorAtomID More...
 
Real theta () const
 
Real d () const
 
ICoorAtomID const & stub_atom1 () const
 
ICoorAtomID const & stub_atom2 () const
 accessor to stub_atom2 ICoorAtomID More...
 
ICoorAtomID const & stub_atom3 () const
 accessor to stub_atom3 ICoorAtomID More...
 
bool is_internal () const
 
bool depends_on_polymer_lower () const
 
bool depends_on_polymer_upper () const
 
bool depends_on_residue_connection (Size const connid) const
 
ICoorAtomIDstub_atom (int const atm)
 accessor to stub_atom ICoorAtomID More...
 
ICoorAtomID const & stub_atom (int const atm) const
 constant accessor to stub_atom ICoorAtomID More...
 
void index (core::Size index)
 
Size index ()
 
Vector build (conformation::Residue const &rsd, conformation::Conformation const &conformation) const
 
Vector build (ResidueType const &rsd_type) const
 
Vector build (conformation::Residue const &rsd) const
 WARNING: Slightly dangerous function intended for black magic use only. Only to be used for situations where you know the Atom /and all it's stub atoms/ can't be anything but real atoms on the given residue, and where a conformation is absolutely not availible. If you /can/ use AtomICoor::build( Residue const &, Conformation const &), you /should/. More...
 

Private Attributes

Size index_
 
Real phi_
 
Real theta_
 
Real d_
 
ICoorAtomID stub_atom1_
 
ICoorAtomID stub_atom2_
 
ICoorAtomID stub_atom3_
 

Detailed Description

A basic class containing info of internal coordinates needed for building an atom within a ResidueType.

In atom tree, each atom is defined by its internal coordinates, which include a bond distance, a bond angle and a torsion angle. Of course, all these internal coordinates are only meaningful in the context of three reference (stub) atoms. AtomICoor information is stored in the residue param files and some terms are defined as following:

Constructor & Destructor Documentation

core::chemical::AtomICoor::AtomICoor ( )
inline

default constructor

core::chemical::AtomICoor::AtomICoor ( Real const  phi_in,
Real const  theta_in,
Real const  d_in,
std::string const &  stub_atom1_name,
std::string const &  stub_atom2_name,
std::string const &  stub_atom3_name,
ResidueType const &  rsd_type 
)
inline

constructor

core::chemical::AtomICoor::AtomICoor ( Size const  index,
Real const  phi_in,
Real const  theta_in,
Real const  d_in,
std::string const &  stub_atom1_name,
std::string const &  stub_atom2_name,
std::string const &  stub_atom3_name,
ResidueType const &  rsd_type 
)
inline

Member Function Documentation

Vector core::chemical::AtomICoor::build ( conformation::Residue const &  rsd,
conformation::Conformation const &  conformation 
) const
Vector core::chemical::AtomICoor::build ( ResidueType const &  rsd_type) const
Vector core::chemical::AtomICoor::build ( conformation::Residue const &  rsd) const

WARNING: Slightly dangerous function intended for black magic use only. Only to be used for situations where you know the Atom /and all it's stub atoms/ can't be anything but real atoms on the given residue, and where a conformation is absolutely not availible. If you /can/ use AtomICoor::build( Residue const &, Conformation const &), you /should/.

WARNING: Slightly dangerous function intended for black magic use only. Only to be used for situations where you know the AtomICoor /and all it's stub atoms/ can't be anything but real atoms on the given residue, and where a conformation is absolutely not availible. If you /can/ use AtomICoor::build( Residue const &, Conformation const &), you /should/.

References protocols::fldsgn::potentials::sspot::spherical().

Real core::chemical::AtomICoor::d ( ) const
inline
bool core::chemical::AtomICoor::depends_on_polymer_lower ( ) const
inline
bool core::chemical::AtomICoor::depends_on_polymer_upper ( ) const
inline
bool core::chemical::AtomICoor::depends_on_residue_connection ( Size const  connid) const
inline
void core::chemical::AtomICoor::index ( core::Size  index)
inline

References index(), and index_.

Size core::chemical::AtomICoor::index ( )
inline

References index_.

Referenced by index().

bool core::chemical::AtomICoor::is_internal ( ) const
inline
Real core::chemical::AtomICoor::phi ( ) const
inline
ICoorAtomID& core::chemical::AtomICoor::stub_atom ( int const  atm)
inline
ICoorAtomID const& core::chemical::AtomICoor::stub_atom ( int const  atm) const
inline

constant accessor to stub_atom ICoorAtomID

References stub_atom1_, stub_atom2_, and stub_atom3_.

ICoorAtomID const& core::chemical::AtomICoor::stub_atom1 ( ) const
inline
ICoorAtomID const& core::chemical::AtomICoor::stub_atom2 ( ) const
inline
ICoorAtomID const& core::chemical::AtomICoor::stub_atom3 ( ) const
inline
Real core::chemical::AtomICoor::theta ( ) const
inline

Member Data Documentation

Real core::chemical::AtomICoor::d_
private

Referenced by d().

Size core::chemical::AtomICoor::index_
private

Referenced by index().

Real core::chemical::AtomICoor::phi_
private

Referenced by phi().

ICoorAtomID core::chemical::AtomICoor::stub_atom1_
private
ICoorAtomID core::chemical::AtomICoor::stub_atom2_
private
ICoorAtomID core::chemical::AtomICoor::stub_atom3_
private
Real core::chemical::AtomICoor::theta_
private

Referenced by theta().


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