Rosetta Core  2014.35
Public Types | Public Member Functions | Private Attributes | List of all members
core::chemical::ICoorAtomID Class Reference

Atom 's ID in internal coordinates in a ResidueType. More...

#include <AtomICoor.hh>

Public Types

enum  Type { INTERNAL = 1, POLYMER_LOWER, POLYMER_UPPER, CONNECT }
 ICoordAtomID type. More...
 
typedef conformation::Residue Residue
 
typedef conformation::Conformation Conformation
 

Public Member Functions

 ICoorAtomID ()
 default constructor More...
 
 ICoorAtomID (std::string name, ResidueType const &rsd_type)
 construct ICoorAtomID by atom name and its ResidueType More...
 
 ICoorAtomID (VD vd, ResidueType const &rsd_type)
 construct ICoorAtomID by VD and its ResidueType More...
 
Size atomno () const
 get ICoorAtomID atomno More...
 
void atomno (int const atomno_in)
 set ICoorAtomID atomno More...
 
VD vertex () const
 
void vertex (VD vertex)
 
Type const & type () const
 get ICoordAtomID type More...
 
bool is_internal () const
 
bool is_polymer_lower () const
 
bool is_polymer_upper () const
 
bool is_connect (Size const connid) const
 Returns true if this is the specified connection id. More...
 
bool is_connect () const
 Returns true if this is a connection. More...
 
Vector const & xyz (Residue const &rsd, Conformation const &conformation) const
 
Vector xyz (ResidueType const &rsd_type) const
 
Vector xyz (conformation::Residue const &rsd) const
 WARNING: Slightly dangerous function intended for black magic use only. Rebuilds atom location from stub atoms. If stub atom are not internal atoms, their location will be rebuilt from their residue stub atom's locations, as opposed to being retrieved from connected residues via a conformation. More...
 
id::AtomID atom_id (Size const seqpos, Conformation const &conformation) const
 

Private Attributes

Type type_
 atom's "connection" type More...
 
Size atomno_
 atom's index number More...
 
VD vd_
 vertex descriptor associated with the icoor More...
 

Detailed Description

Atom 's ID in internal coordinates in a ResidueType.

Member Typedef Documentation

Member Enumeration Documentation

ICoordAtomID type.

  • INTERNAL: atoms which inherently belong to this ResidueType
  • POLYMER_LOWER: atom at the polymer lower connection, such as backbone C in the previous residue (N-term side)
  • POLYMER_UPPER: atom at the polymer upper connection, such as backbone N in the next residue (C-term side)
  • CONNECT: atoms from a non-adjacent residue which connect to this residue by non-polymer connection, such as disulfide
Enumerator
INTERNAL 
POLYMER_LOWER 
POLYMER_UPPER 
CONNECT 

Constructor & Destructor Documentation

core::chemical::ICoorAtomID::ICoorAtomID ( )

default constructor

core::chemical::ICoorAtomID::ICoorAtomID ( std::string  name,
ResidueType const &  rsd_type 
)

construct ICoorAtomID by atom name and its ResidueType

After atom name is read in from residue param file, ICoorAtomID type_ and atomno_ is defined as:

  • Anything less than four character is considered as INTERNAL atom name and its atom index number is assigned as atomno_;
  • "LOWER" and "UPPER" for polymer lower and upper connections. Since they are unique, no atomno_ is given ( e.g., 0)
  • Non-polymer connections are flagged by "CONN*" in which * represents the index number of this connection in the ResidueType ( from 1 to ResidueType.n_connection() ). This number is assigned as atomno_.

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_vertex(), atomno_, CONNECT, INTERNAL, core::chemical::ResidueType::n_residue_connections(), core::chemical::ResidueType::name(), core::chemical::ResidueType::null_vertex, POLYMER_LOWER, POLYMER_UPPER, core::chemical::tw, type_, utility_exit_with_message, and vd_.

core::chemical::ICoorAtomID::ICoorAtomID ( VD  vd,
ResidueType const &  rsd_type 
)

construct ICoorAtomID by VD and its ResidueType

A Icoord to an atom given via a vertex descriptor is by definition INTERNAL.

References core::chemical::ResidueType::atom_index(), atomno_, core::chemical::ResidueType::has(), INTERNAL, type_, and vd_.

Member Function Documentation

id::AtomID core::chemical::ICoorAtomID::atom_id ( Size const  seqpos,
Conformation const &  conformation 
) const
Size core::chemical::ICoorAtomID::atomno ( ) const
inline
void core::chemical::ICoorAtomID::atomno ( int const  atomno_in)
inline

set ICoorAtomID atomno

References atomno_.

bool core::chemical::ICoorAtomID::is_connect ( Size const  connid) const
inline

Returns true if this is the specified connection id.

References atomno_, CONNECT, and type_.

Referenced by core::chemical::AtomICoor::depends_on_residue_connection(), and core::conformation::Conformation::fill_missing_atoms().

bool core::chemical::ICoorAtomID::is_connect ( ) const
inline

Returns true if this is a connection.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References CONNECT, and type_.

bool core::chemical::ICoorAtomID::is_internal ( ) const
inline
bool core::chemical::ICoorAtomID::is_polymer_lower ( ) const
inline
bool core::chemical::ICoorAtomID::is_polymer_upper ( ) const
inline
Type const& core::chemical::ICoorAtomID::type ( ) const
inline
VD core::chemical::ICoorAtomID::vertex ( ) const
inline
void core::chemical::ICoorAtomID::vertex ( VD  vertex)
inline

References vd_, and vertex().

Vector const & core::chemical::ICoorAtomID::xyz ( Residue const &  rsd,
Conformation const &  conformation 
) const
Vector core::chemical::ICoorAtomID::xyz ( ResidueType const &  rsd_type) const
Vector core::chemical::ICoorAtomID::xyz ( conformation::Residue const &  rsd) const

WARNING: Slightly dangerous function intended for black magic use only. Rebuilds atom location from stub atoms. If stub atom are not internal atoms, their location will be rebuilt from their residue stub atom's locations, as opposed to being retrieved from connected residues via a conformation.

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

References core::conformation::Residue::atom(), atomno_, core::chemical::AtomICoor::build(), CONNECT, core::chemical::ResidueConnection::icoor(), INTERNAL, core::chemical::ResidueType::lower_connect(), POLYMER_LOWER, POLYMER_UPPER, core::chemical::ResidueType::residue_connection(), core::conformation::Residue::type(), type_, core::chemical::ResidueType::upper_connect(), utility_exit_with_message, and core::conformation::Atom::xyz().

Member Data Documentation

Size core::chemical::ICoorAtomID::atomno_
private

atom's index number

Referenced by atom_id(), atomno(), ICoorAtomID(), is_connect(), and xyz().

Type core::chemical::ICoorAtomID::type_
private
VD core::chemical::ICoorAtomID::vd_
private

vertex descriptor associated with the icoor

Referenced by ICoorAtomID(), vertex(), and xyz().


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