A basic class containing info of internal coordinates needed for building an atom within a ResidueType. More...

#include <AtomICoor.hh>

Public Member Functions
	AtomICoor ()
	default constructor More...

	AtomICoor (std::string const &built_atom_name, Real const phi_in, Real const theta_in, Real const d_in, std::string const &stub_atom1_name, std::string const &stub_atom2_name, std::string const &stub_atom3_name, ResidueType const &rsd_type)
	constructor More...

	AtomICoor (VD const &built_atom_vd, Real const phi_in, Real const theta_in, Real const d_in, VD const &stub_atom1_vd, VD const &stub_atom2_vd, VD const &stub_atom3_vd, ResidueType const &rsd_type)
	Vertex descriptor version. More...

Real	phi () const
	accessor to stub_atom1 ICoorAtomID More...

Real	theta () const

Real	d () const

ICoorAtomID const &	stub_atom1 () const

ICoorAtomID const &	stub_atom2 () const
	accessor to stub_atom2 ICoorAtomID More...

ICoorAtomID const &	stub_atom3 () const
	accessor to stub_atom3 ICoorAtomID More...

bool	is_internal () const

bool	depends_on_polymer_lower () const

bool	depends_on_polymer_upper () const

bool	depends_on_residue_connection (Size const connid) const
	Returns true if any of the stub atoms is the specified connection ID. More...

bool	depends_on_residue_connection () const
	Returns true if any of the stub atoms is a connection ID. More...

ICoorAtomID &	stub_atom (int const atm)
	accessor to stub_atom ICoorAtomID More...

ICoorAtomID const &	stub_atom (int const atm) const
	constant accessor to stub_atom ICoorAtomID More...

void	built_atom_vertex (core::chemical::VD vd)

core::chemical::VD	built_atom_vertex () const
	The vertex descriptor of the atom being built by this icoor Can be null_vertex if this AtomICoor doesn't build a physical atom. (e.g. CONNECT, UPPER, LOWER) More...

Vector	build (conformation::Residue const &rsd, conformation::Conformation const &conformation) const

Vector	build (ResidueType const &rsd_type) const

Vector	build (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...

Private Attributes
VD	built_vd_

Real	phi_

Real	theta_

Real	d_

ICoorAtomID	stub_atom1_

ICoorAtomID	stub_atom2_

ICoorAtomID	stub_atom3_

Detailed Description

A basic class containing info of internal coordinates needed for building an atom within a ResidueType.

In atom tree, each atom is defined by its internal coordinates, which include a bond distance, a bond angle and a torsion angle. Of course, all these internal coordinates are only meaningful in the context of three reference (stub) atoms. AtomICoor information is stored in the residue param files and some terms are defined as following:

bond distance d_ is that between the atom to be built (child) and stub_atom1 (parent)
bond angle theta_ is that defined by child-parent-stub2(angle)
torsion angle phi_ is that defined by child-parent-stub2-stub3(torsion)

Constructor & Destructor Documentation

core::chemical::AtomICoor::AtomICoor ( )

default constructor

core::chemical::AtomICoor::AtomICoor	(	std::string const &	built_atom_name,
		Real const	phi_in,
		Real const	theta_in,
		Real const	d_in,
		std::string const &	stub_atom1_name,
		std::string const &	stub_atom2_name,
		std::string const &	stub_atom3_name,
		ResidueType const &	rsd_type
	)

constructor

core::chemical::AtomICoor::AtomICoor	(	VD const &	built_atom_vd,
		Real const	phi_in,
		Real const	theta_in,
		Real const	d_in,
		VD const &	stub_atom1_vd,
		VD const &	stub_atom2_vd,
		VD const &	stub_atom3_vd,
		ResidueType const &	rsd_type
	)

Vertex descriptor version.

Member Function Documentation

Vector core::chemical::AtomICoor::build	(	conformation::Residue const &	rsd,
		conformation::Conformation const &	conformation
	)		const

References d_, phi_, stub_atom1_, stub_atom2_, stub_atom3_, theta_, and core::chemical::ICoorAtomID::xyz().

Vector core::chemical::AtomICoor::build ( ResidueType const & rsd_type ) const

References d_, phi_, stub_atom1_, stub_atom2_, stub_atom3_, theta_, and core::chemical::ICoorAtomID::xyz().

Vector core::chemical::AtomICoor::build ( 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 AtomICoor /and all it's stub atoms/ can't be anything but real atoms on the given residue, and where a conformation is absolutely not availible. If you /can/ use AtomICoor::build( Residue const &, Conformation const &), you /should/.

References d_, phi_, core::kinematics::Stub::spherical(), stub_atom1_, stub_atom2_, stub_atom3_, theta_, and core::chemical::ICoorAtomID::xyz().

void core::chemical::AtomICoor::built_atom_vertex ( core::chemical::VD vd )

inline

References built_vd_.

Referenced by core::chemical::pretty_print_atomicoor(), and core::chemical::ResidueType::ResidueType().

core::chemical::VD core::chemical::AtomICoor::built_atom_vertex ( ) const

inline

The vertex descriptor of the atom being built by this icoor Can be null_vertex if this AtomICoor doesn't build a physical atom. (e.g. CONNECT, UPPER, LOWER)

References built_vd_.

Real core::chemical::AtomICoor::d ( ) const

inline

References d_.

Referenced by core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::fill_missing_atoms(), core::conformation::Residue::orient_onto_residue_peptoid(), core::chemical::pretty_print_atomicoor(), and core::chemical::write_topology_file().

bool core::chemical::AtomICoor::depends_on_polymer_lower ( ) const

inline

References core::chemical::ICoorAtomID::is_polymer_lower(), stub_atom1_, stub_atom2_, and stub_atom3_.

Referenced by core::conformation::Residue::fill_missing_atoms(), and core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms().

bool core::chemical::AtomICoor::depends_on_polymer_upper ( ) const

inline

References core::chemical::ICoorAtomID::is_polymer_upper(), stub_atom1_, stub_atom2_, and stub_atom3_.