Rosetta 3.4
Public Types | Public Member Functions
core::chemical::ICoorAtomID Class Reference

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

#include <AtomICoor.hh>

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List of all members.

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
 ICoorAtomID (std::string name, ResidueType const &rsd_type)
 construct ICoorAtomID by atom name and its ResidueType
Size atomno () const
 get ICoorAtomID atomno
void atomno (int const atomno_in)
 set ICoorAtomID atomno
Type const & type () const
 get ICoordAtomID type
bool is_internal () const
bool is_polymer_lower () const
bool is_polymer_upper () const
bool is_connect (Size const connid) const
Vector const & xyz (Residue const &rsd, Conformation const &conformation) const
Vector xyz (ResidueType const &rsd_type) const
Vector const & xyz (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 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/.
id::AtomID atom_id (Size const seqpos, Conformation const &conformation) const

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 ( ) [inline]

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(), and core::chemical::ResidueType::n_residue_connections().


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

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

get ICoordAtomID type

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

Vector const & core::chemical::ICoorAtomID::xyz ( 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 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(), and core::conformation::Atom::xyz().

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

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