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

#include <AtomICoor.hh>

Public Types
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...

ICoordAtomIDType 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...

std::string	name (ResidueType const &rt) const
	Returns the string representation which will build this ICoorAtomID (e.g. atom name, UPPER, LOWER, CONN*. More...

Vector const &	xyz (Residue const &rsd, Conformation const &conformation) const
	What is the coordinates corresponding to this ICoorAtomID, for the given residue and conformation. More...

Vector	xyz (ResidueType const &rsd_type) const
	What is the coordinates corresponding to this ICoorAtomID, for the given idealized ResidueType. More...

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 (Residue const &rsd, Conformation const &conformation) const
	This ICoorAtomID (for the given residue) corresponds to which id::AtomID in the conformation? More...

bool	buildable (Residue const &rsd, Conformation const &conformation) const
	Can valid coordinates be built for this ICoorAtomID, given the residue and conformation? More...

bool	operator== (ICoorAtomID const &other) const

bool	operator!= (ICoorAtomID const &other) const

Private Attributes
ICoordAtomIDType	type_
	atom's "connection" type More...

Size	atomno_
	atom's index number 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

Constructor & Destructor Documentation

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

default constructor

References core::chemical::INTERNAL.

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(), atomno_, core::chemical::CONNECT, core::chemical::get_connection_number(), core::chemical::ResidueType::has(), core::chemical::INTERNAL, core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueTypeBase::name(), core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, core::chemical::string_to_icoord_type(), core::chemical::TR(), and type_.

Member Function Documentation

id::AtomID core::chemical::ICoorAtomID::atom_id	(	Residue const &	rsd,
		Conformation const &	conformation
	)		const

This ICoorAtomID (for the given residue) corresponds to which id::AtomID in the conformation?

Referenced by buildable(), core::conformation::Conformation::fill_missing_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and xyz().

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

inline

get ICoorAtomID atomno

References atomno_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), atom_id(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), core::chemical::AtomICoor::depends_on_a_true_index(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::idealize_hydrogens(), core::conformation::missing_stubs_build(), core::conformation::Residue::place(), core::chemical::pretty_print_atomicoor(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length(), core::chemical::AtomICoor::show(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().

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

inline

set ICoorAtomID atomno

References atomno_.

bool core::chemical::ICoorAtomID::buildable	(	Residue const &	rsd,
		Conformation const &	conformation
	)		const

Can valid coordinates be built for this ICoorAtomID, given the residue and conformation?

References atom_id(), atomno_, core::chemical::CONNECT, core::id::GLOBAL_BOGUS_ATOM_ID, core::chemical::INTERNAL, core::conformation::Residue::natoms(), core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, and type_.

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

inline

Returns true if this is the specified connection id.

References atomno_, core::chemical::CONNECT, and type_.

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

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 core::chemical::CONNECT, and type_.

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

inline

References core::chemical::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 core::chemical::POLYMER_LOWER, and type_.

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

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

inline

References core::chemical::POLYMER_UPPER, and type_.

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

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

Returns the string representation which will build this ICoorAtomID (e.g. atom name, UPPER, LOWER, CONN*.

References core::chemical::ResidueType::atom_name(), atomno_, core::chemical::CONNECT, core::chemical::INTERNAL, core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, core::id::to_string(), and type_.

Referenced by core::chemical::MutableResidueType::copy_atom_info(), and core::chemical::write_topology_file().

bool core::chemical::ICoorAtomID::operator!= ( ICoorAtomID const & other ) const

References atomno_, and type_.

bool core::chemical::ICoorAtomID::operator== ( ICoorAtomID const & other ) const

References atomno_, and type_.

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

inline

get ICoordAtomID type

References type_.

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

What is the coordinates corresponding to this ICoorAtomID, for the given residue and conformation.

References core::conformation::Residue::atom(), atom_id(), atomno_, core::id::AtomID::BOGUS_ATOM_ID(), core::chemical::CONNECT, core::chemical::INTERNAL, core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, type_, core::conformation::Atom::xyz(), and core::conformation::Conformation::xyz().

Referenced by core::chemical::AtomICoor::build(), and core::conformation::orient_residue_for_ideal_bond().

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

What is the coordinates corresponding to this ICoorAtomID, for the given idealized ResidueType.

References atomno_, core::chemical::AtomICoor::build(), core::chemical::CONNECT, core::chemical::ResidueConnection::icoor(), core::chemical::ResidueType::ideal_xyz(), core::chemical::INTERNAL, core::chemical::ResidueType::lower_connect(), core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, core::chemical::ResidueType::residue_connection(), type_, and core::chemical::ResidueType::upper_connect().

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