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Public Member Functions | Private Attributes | List of all members
core::chemical::orbitals::ICoorOrbitalData Class Reference

#include <ICoorOrbitalData.hh>

Collaboration diagram for core::chemical::orbitals::ICoorOrbitalData:
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Public Member Functions

 ICoorOrbitalData ()
 default constructor More...
 
 ICoorOrbitalData (Real phi, Real theta, Real distance, std::string stub1, std::string stub2, std::string stub3)
 construct ICoorAtomID by atom name and its ResidueType More...
 
 ICoorOrbitalData (Real phi, Real theata, Real distance, Size stub1, Size stub2, Size stub3)
 
Real phi () const
 return the phi for a given orbital More...
 
Real theta () const
 return the theta for a given orbital More...
 
Real distance () const
 return the distance for a given orbital More...
 
std::string stub1 () const
 return the stub1 for a given orbital More...
 
std::string stub2 () const
 return the stub2 for a given orbital More...
 
std::string stub3 () const
 return the stub3 for a given orbital More...
 
Vector build (Vector stub1_xyz, Vector stub2_xyz, Vector stub3_xyz) const
 build the xyz coordinates for an orbital based upon the stub1, stub2, stub3 xyz coordinates. More...
 
void replace_stub1 (const core::Size atom1)
 
void replace_stub2 (const core::Size atom2)
 
void replace_stub3 (const core::Size atom3)
 
core::Size get_stub1 ()
 
core::Size get_stub2 ()
 
core::Size get_stub3 ()
 

Private Attributes

Real phi_
 
Real theta_
 
Real distance_
 
std::string stub1_
 
std::string stub2_
 
std::string stub3_
 
Size s_stub1_
 
Size s_stub2_
 
Size s_stub3_
 

Constructor & Destructor Documentation

core::chemical::orbitals::ICoorOrbitalData::ICoorOrbitalData ( )

default constructor

construct ICoorOrbitalData.

core::chemical::orbitals::ICoorOrbitalData::ICoorOrbitalData ( Real  phi,
Real  theta,
Real  distance,
std::string  stub1,
std::string  stub2,
std::string  stub3 
)

construct ICoorAtomID by atom name and its ResidueType

construct ICoorOrbitalData.

core::chemical::orbitals::ICoorOrbitalData::ICoorOrbitalData ( Real  phi,
Real  theata,
Real  distance,
Size  stub1,
Size  stub2,
Size  stub3 
)

Member Function Documentation

Vector core::chemical::orbitals::ICoorOrbitalData::build ( Vector  stub1_xyz,
Vector  stub2_xyz,
Vector  stub3_xyz 
) const

build the xyz coordinates for an orbital based upon the stub1, stub2, stub3 xyz coordinates.

Note
NOTE!!!!!!!!!!! The internal coordinates cannot contain an orbital as the stub1, stub2, or stub3 atom. This is because the xyz coordinates are not updated when the conformation changes. The stub1, stub2, stub2 atoms must be actual atoms and not orbitals!!!!11111!!!!!!!11111!(design feature or flaw? you decide)

References distance_, phi_, core::kinematics::Stub::spherical(), and theta_.

Real core::chemical::orbitals::ICoorOrbitalData::distance ( ) const

return the distance for a given orbital

References distance_.

core::Size core::chemical::orbitals::ICoorOrbitalData::get_stub1 ( )
inline

References s_stub1_.

core::Size core::chemical::orbitals::ICoorOrbitalData::get_stub2 ( )
inline

References s_stub2_.

core::Size core::chemical::orbitals::ICoorOrbitalData::get_stub3 ( )
inline

References s_stub3_.

Real core::chemical::orbitals::ICoorOrbitalData::phi ( ) const

return the phi for a given orbital

References phi_.

void core::chemical::orbitals::ICoorOrbitalData::replace_stub1 ( const core::Size  atom1)
inline

References s_stub1_.

void core::chemical::orbitals::ICoorOrbitalData::replace_stub2 ( const core::Size  atom2)
inline

References s_stub2_.

void core::chemical::orbitals::ICoorOrbitalData::replace_stub3 ( const core::Size  atom3)
inline

References s_stub3_.

std::string core::chemical::orbitals::ICoorOrbitalData::stub1 ( ) const

return the stub1 for a given orbital

References stub1_.

std::string core::chemical::orbitals::ICoorOrbitalData::stub2 ( ) const

return the stub2 for a given orbital

References stub2_.

std::string core::chemical::orbitals::ICoorOrbitalData::stub3 ( ) const

return the stub3 for a given orbital

References stub3_.

Real core::chemical::orbitals::ICoorOrbitalData::theta ( ) const

return the theta for a given orbital

References theta_.

Member Data Documentation

Real core::chemical::orbitals::ICoorOrbitalData::distance_
private

Referenced by build(), and distance().

Real core::chemical::orbitals::ICoorOrbitalData::phi_
private

Referenced by build(), and phi().

Size core::chemical::orbitals::ICoorOrbitalData::s_stub1_
private

Referenced by get_stub1(), and replace_stub1().

Size core::chemical::orbitals::ICoorOrbitalData::s_stub2_
private

Referenced by get_stub2(), and replace_stub2().

Size core::chemical::orbitals::ICoorOrbitalData::s_stub3_
private

Referenced by get_stub3(), and replace_stub3().

std::string core::chemical::orbitals::ICoorOrbitalData::stub1_
private

Referenced by stub1().

std::string core::chemical::orbitals::ICoorOrbitalData::stub2_
private

Referenced by stub2().

std::string core::chemical::orbitals::ICoorOrbitalData::stub3_
private

Referenced by stub3().

Real core::chemical::orbitals::ICoorOrbitalData::theta_
private

Referenced by build(), and theta().


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