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

#include <AtomICoor.hh>

Collaboration diagram for core::chemical::ICoorAtomID:

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...

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 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/. 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...

Detailed Description

Atom 's ID in internal coordinates in a ResidueType.

Definition at line 44 of file AtomICoor.hh.

Member Typedef Documentation

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

Definition at line 47 of file AtomICoor.hh.

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

Definition at line 46 of file AtomICoor.hh.

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

Definition at line 60 of file AtomICoor.hh.

Constructor & Destructor Documentation

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

inline

default constructor

Definition at line 70 of file AtomICoor.hh.

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_.

Definition at line 64 of file AtomICoor.cc.

References core::chemical::ResidueType::atom_index(), protocols::swa::monte_carlo::INTERNAL, and core::chemical::ResidueType::n_residue_connections().

Member Function Documentation

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

Definition at line 176 of file AtomICoor.cc.

References core::id::BOGUS_ATOM_ID, core::conformation::Conformation::inter_residue_connection_partner(), protocols::swa::monte_carlo::INTERNAL, 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

Definition at line 84 of file AtomICoor.hh.

References atomno_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), core::chemical::ResidueType::assign_internal_coordinates(), protocols::simple_moves::MinimalRotamer::atom_is_ideal(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::idealize_hydrogens(), protocols::simple_moves::MinimalRotamer::record_internal_geometry(), core::chemical::ResidueType::reorder_primary_data(), and core::chemical::write_topology_file().

void core::chemical::ICoorAtomID::atomno ( int const atomno_in)

inline

set ICoorAtomID atomno

Definition at line 91 of file AtomICoor.hh.

References atomno_.

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

inline

Definition at line 126 of file AtomICoor.hh.

References atomno_, CONNECT, and type_.

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

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

inline

Definition at line 105 of file AtomICoor.hh.

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

Definition at line 112 of file AtomICoor.hh.

References POLYMER_LOWER, and type_.

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

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

inline

Definition at line 119 of file AtomICoor.hh.

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

Definition at line 98 of file AtomICoor.hh.

References type_.

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

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

Definition at line 90 of file AtomICoor.cc.

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

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

Definition at line 140 of file AtomICoor.cc.

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

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/.

Definition at line 167 of file AtomICoor.cc.

References core::conformation::Residue::atom(), protocols::swa::monte_carlo::INTERNAL, and core::conformation::Atom::xyz().

Member Data Documentation

Size core::chemical::ICoorAtomID::atomno_

private

atom's index number

Definition at line 169 of file AtomICoor.hh.

Referenced by atomno(), and is_connect().

Type core::chemical::ICoorAtomID::type_

private

atom's "connection" type

Definition at line 167 of file AtomICoor.hh.

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

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

src/core/chemical/AtomICoor.hh
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