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core::chemical::MutableICoorRecord Class Reference

A basic class containing basic info of internal coordinates needed for building an atom within a ResidueType This is a simplified representation, used for MutableResidueType. It contains all the information, but is intended to be somewhat easier to update for added/deleted atoms than the standard AtomICoor. More...

#include <MutableICoorRecord.hh>

Public Member Functions

 MutableICoorRecord ()
 default constructor More...
 
 MutableICoorRecord (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)
 constructor More...
 
bool operator== (MutableICoorRecord const &rhs) const
 
Real phi () const
 accessor to stub_atom1 ICoorAtomID More...
 
Real theta () const
 
Real d () const
 
std::string const & stub_atom1 () const
 
std::string const & stub_atom2 () const
 
std::string const & stub_atom3 () const
 
std::string const & stub_atom (int const atm) const
 accessor to stub_atom ICoorAtomID More...
 
ICoordAtomIDType stub_type1 () const
 
ICoordAtomIDType stub_type2 () const
 
ICoordAtomIDType stub_type3 () const
 
ICoordAtomIDType stub_type (int const atm) const
 accessor to stub_type ICoorAtomID More...
 
void show (std::ostream &out) const
 
bool buildable (MutableResidueType const &rsd_type, bool verbose=false) const
 Can valid coordinates be built for this MutableICoorRecord, given the residue type? More...
 
Vector build (MutableResidueType const &rsd_type) const
 Build the location of the built atom, given the other atoms in the residue type. More...
 
Vector xyz (core::Size stubno, MutableResidueType const &restype) const
 Given a the stub designation (1/2/3) find the coordinate from the MutableResidueType. More...
 

Static Public Member Functions

static Vector build_xyz (std::string const &stub, MutableResidueType const &restype)
 Given a stub designation (atom name, UPPER/LOWER/CONN, etc.) find the coordinate from the MutableResidueType. More...
 

Private Attributes

Real phi_
 
Real theta_
 
Real d_
 
std::string stub_atom1_
 
std::string stub_atom2_
 
std::string stub_atom3_
 
ICoordAtomIDType stub_type1_
 
ICoordAtomIDType stub_type2_
 
ICoordAtomIDType stub_type3_
 

Detailed Description

A basic class containing basic info of internal coordinates needed for building an atom within a ResidueType This is a simplified representation, used for MutableResidueType. It contains all the information, but is intended to be somewhat easier to update for added/deleted atoms than the standard AtomICoor.

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. MutableICoorRecord information is stored in the residue param files and some terms are defined as following:

Constructor & Destructor Documentation

core::chemical::MutableICoorRecord::MutableICoorRecord ( )

default constructor

References core::chemical::INTERNAL.

core::chemical::MutableICoorRecord::MutableICoorRecord ( 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 
)

constructor

Member Function Documentation

Vector core::chemical::MutableICoorRecord::build ( MutableResidueType const &  rsd_type) const

Build the location of the built atom, given the other atoms in the residue type.

References core::kinematics::Stub::create_orthogonal(), d_, phi_, core::kinematics::Stub::spherical(), theta_, and xyz().

Referenced by build_xyz(), and xyz().

Vector core::chemical::MutableICoorRecord::build_xyz ( std::string const &  stub,
MutableResidueType const &  restype 
)
static

Given a stub designation (atom name, UPPER/LOWER/CONN, etc.) find the coordinate from the MutableResidueType.

References core::chemical::MutableResidueType::atom(), build(), core::chemical::CONNECT, core::chemical::get_connection_number(), core::chemical::MutableResidueConnection::icoor(), core::chemical::Atom::ideal_xyz(), core::chemical::INTERNAL, core::chemical::MutableResidueType::lower_connect(), core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, core::chemical::MutableResidueType::residue_connection(), core::chemical::string_to_icoord_type(), and core::chemical::MutableResidueType::upper_connect().

Referenced by core::chemical::fill_ideal_xyz_from_icoor().

bool core::chemical::MutableICoorRecord::buildable ( MutableResidueType const &  rsd_type,
bool  verbose = false 
) const

Can valid coordinates be built for this MutableICoorRecord, given the residue type?

References core::chemical::CONNECT, core::chemical::get_connection_number(), core::chemical::MutableResidueType::has(), core::chemical::INTERNAL, core::chemical::MutableResidueType::lower_connect_id(), core::chemical::MutableResidueType::n_possible_residue_connections(), core::chemical::ResidueTypeBase::name(), core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, stub_atom(), stub_type(), core::chemical::TR(), and core::chemical::MutableResidueType::upper_connect_id().

Real core::chemical::MutableICoorRecord::d ( ) const
inline

References d_.

Referenced by core::chemical::clean_up_dangling_connect().

bool core::chemical::MutableICoorRecord::operator== ( MutableICoorRecord const &  rhs) const

References d_, phi_, stub_atom1_, stub_atom2_, stub_atom3_, and theta_.

Real core::chemical::MutableICoorRecord::phi ( ) const
inline

accessor to stub_atom1 ICoorAtomID

References phi_.

void core::chemical::MutableICoorRecord::show ( std::ostream &  out) const

References d_, phi_, stub_atom1_, stub_atom2_, stub_atom3_, and theta_.

Referenced by core::chemical::operator<<().

std::string const& core::chemical::MutableICoorRecord::stub_atom ( int const  atm) const
inline

accessor to stub_atom ICoorAtomID

References stub_atom1_, stub_atom2_, and stub_atom3_.

Referenced by buildable(), and xyz().

std::string const& core::chemical::MutableICoorRecord::stub_atom1 ( ) const
inline

References stub_atom1_.

Referenced by core::chemical::clean_up_dangling_connect().

std::string const& core::chemical::MutableICoorRecord::stub_atom2 ( ) const
inline

References stub_atom2_.

Referenced by core::chemical::clean_up_dangling_connect().

std::string const& core::chemical::MutableICoorRecord::stub_atom3 ( ) const
inline

References stub_atom3_.

ICoordAtomIDType core::chemical::MutableICoorRecord::stub_type ( int const  atm) const
inline

accessor to stub_type ICoorAtomID

References stub_type1_, stub_type2_, and stub_type3_.

Referenced by buildable(), and xyz().

ICoordAtomIDType core::chemical::MutableICoorRecord::stub_type1 ( ) const
inline

References stub_type1_.

Referenced by core::chemical::clean_up_dangling_connect().

ICoordAtomIDType core::chemical::MutableICoorRecord::stub_type2 ( ) const
inline

References stub_type2_.

Referenced by core::chemical::clean_up_dangling_connect().

ICoordAtomIDType core::chemical::MutableICoorRecord::stub_type3 ( ) const
inline

References stub_type3_.

Referenced by core::chemical::clean_up_dangling_connect().

Real core::chemical::MutableICoorRecord::theta ( ) const
inline

References theta_.

Referenced by core::chemical::clean_up_dangling_connect().

Vector core::chemical::MutableICoorRecord::xyz ( core::Size  stubno,
MutableResidueType const &  restype 
) const

Given a the stub designation (1/2/3) find the coordinate from the MutableResidueType.

References core::chemical::MutableResidueType::atom(), build(), core::chemical::CONNECT, core::chemical::get_connection_number(), core::chemical::MutableResidueConnection::icoor(), core::chemical::Atom::ideal_xyz(), core::chemical::INTERNAL, core::chemical::MutableResidueType::lower_connect(), core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, core::chemical::MutableResidueType::residue_connection(), stub_atom(), stub_type(), and core::chemical::MutableResidueType::upper_connect().

Referenced by build(), and core::chemical::clean_up_dangling_connect().

Member Data Documentation

Real core::chemical::MutableICoorRecord::d_
private

Referenced by build(), d(), operator==(), and show().

Real core::chemical::MutableICoorRecord::phi_
private

Referenced by build(), operator==(), phi(), and show().

std::string core::chemical::MutableICoorRecord::stub_atom1_
private

Referenced by operator==(), show(), stub_atom(), and stub_atom1().

std::string core::chemical::MutableICoorRecord::stub_atom2_
private

Referenced by operator==(), show(), stub_atom(), and stub_atom2().

std::string core::chemical::MutableICoorRecord::stub_atom3_
private

Referenced by operator==(), show(), stub_atom(), and stub_atom3().

ICoordAtomIDType core::chemical::MutableICoorRecord::stub_type1_
private

Referenced by stub_type(), and stub_type1().

ICoordAtomIDType core::chemical::MutableICoorRecord::stub_type2_
private

Referenced by stub_type(), and stub_type2().

ICoordAtomIDType core::chemical::MutableICoorRecord::stub_type3_
private

Referenced by stub_type(), and stub_type3().

Real core::chemical::MutableICoorRecord::theta_
private

Referenced by build(), operator==(), show(), and theta().

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