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...

Size	atomno () const
	get ICoorAtomID atomno More...

void	atomno (int const atomno_in)
	set ICoorAtomID atomno More...

VD	vertex ()

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

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

typedef conformation::Conformation core::chemical::ICoorAtomID::Conformation

typedef conformation::Residue core::chemical::ICoorAtomID::Residue

Member Enumeration Documentation

enum core::chemical::ICoorAtomID::Type

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(), core::chemical::ResidueType::get_vertex(), core::chemical::ResidueType::n_residue_connections(), core::chemical::ResidueType::name(), core::chemical::tw, and utility_exit_with_message.

Member Function Documentation

id::AtomID core::chemical::ICoorAtomID::atom_id	(	Size const	seqpos,
		Conformation const &	conformation
	)		const

References core::id::BOGUS_ATOM_ID, core::conformation::Conformation::inter_residue_connection_partner(), core::chemical::ResidueType::lower_connect_atom(), core::conformation::Conformation::residue_type(), and core::chemical::ResidueType::upper_connect_atom().

Referenced by core::conformation::Conformation::fill_missing_atoms().

Size core::chemical::ICoorAtomID::atomno ( ) const

inline

get ICoorAtomID atomno

References atomno_.

Referenced by core::chemical::ResidueType::assign_internal_coordinates(), core::chemical::ResidueType::generate_atom_indices(), core::conformation::idealize_hydrogens(), core::chemical::ResidueType::ResidueType(), and core::chemical::write_topology_file().

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

References atomno_, CONNECT, and type_.

Referenced by core::chemical::AtomICoor::depends_on_residue_connection().

bool core::chemical::ICoorAtomID::is_internal ( ) const

inline

References INTERNAL, and type_.

Referenced by core::conformation::idealize_hydrogens(), and core::chemical::AtomICoor::is_internal().

bool core::chemical::ICoorAtomID::is_polymer_lower ( ) const

inline

References POLYMER_LOWER, and type_.

Referenced by core::chemical::AtomICoor::depends_on_polymer_lower().

bool core::chemical::ICoorAtomID::is_polymer_upper ( ) const

inline

References POLYMER_UPPER, and type_.

Referenced by core::chemical::AtomICoor::depends_on_polymer_upper().

Type const& core::chemical::ICoorAtomID::type ( ) const

inline

get ICoordAtomID type

References type_.

Referenced by core::chemical::ResidueType::generate_atom_indices(), and core::chemical::write_topology_file().

VD core::chemical::ICoorAtomID::vertex ( )

inline

References vd_.

Referenced by core::chemical::ResidueType::generate_atom_indices(), core::chemical::ResidueType::ResidueType(), and vertex().

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

References core::conformation::Residue::atom(), core::chemical::ResidueType::lower_connect_atom(), core::conformation::Residue::name(), core::chemical::ResidueType::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), core::conformation::Conformation::residue_type(), core::conformation::Residue::seqpos(), core::conformation::Conformation::size(), core::chemical::tw, core::chemical::ResidueType::upper_connect_atom(), utility_exit_with_message, core::conformation::Atom::xyz(), and core::conformation::Conformation::xyz().

Referenced by core::conformation::orient_residue_for_ideal_bond().

Vector core::chemical::ICoorAtomID::xyz ( ResidueType const & rsd_type ) const

References core::chemical::ResidueType::atom(), core::chemical::AtomICoor::build(), core::chemical::ResidueConnection::icoor(), core::chemical::Atom::ideal_xyz(), core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::residue_connection(), core::chemical::ResidueType::upper_connect(), and utility_exit_with_message.

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(), core::chemical::AtomICoor::build(), core::chemical::ResidueConnection::icoor(), core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::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 atomno(), and is_connect().

Type core::chemical::ICoorAtomID::type_

private

atom's "connection" type

Referenced by is_connect(), is_internal(), is_polymer_lower(), is_polymer_upper(), and type().

VD core::chemical::ICoorAtomID::vd_

private

vertex descriptor associated with the icoor

Referenced by vertex().

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

symlinks/rosetta/src/core/chemical/AtomICoor.hh
symlinks/rosetta/src/core/chemical/AtomICoor.cc

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation