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

#include <AtomICoor.hh>

Collaboration diagram for core::chemical::AtomICoor:

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

	AtomICoor (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 (Size const index, 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)

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

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	index (core::Size index)

Size	index ()

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. Only to be used for situations where you know the Atom /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/. More...

Private Attributes
Size	index_

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)

Definition at line 182 of file AtomICoor.hh.

Constructor & Destructor Documentation

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

inline

default constructor

Definition at line 185 of file AtomICoor.hh.

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

inline

constructor

Definition at line 196 of file AtomICoor.hh.

core::chemical::AtomICoor::AtomICoor	(	Size const	index,
		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
	)

inline

Definition at line 214 of file AtomICoor.hh.

Member Function Documentation

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

Definition at line 197 of file AtomICoor.cc.

References protocols::fldsgn::potentials::sspot::spherical().

Referenced by core::conformation::Residue::build_atom_ideal(), core::conformation::Residue::connection_distance(), core::conformation::Conformation::detect_bonds(), core::conformation::idealize_hydrogens(), core::conformation::orient_residue_for_ideal_bond(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::chemical::ResidueType::set_icoor(), and core::chemical::ICoorAtomID::xyz().

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

Definition at line 212 of file AtomICoor.cc.

References protocols::fldsgn::potentials::sspot::spherical().

Vector core::chemical::AtomICoor::build ( 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 Atom /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/.

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/.

Definition at line 231 of file AtomICoor.cc.

References protocols::fldsgn::potentials::sspot::spherical().

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

inline

Definition at line 250 of file AtomICoor.hh.

References d_.

Referenced by protocols::loops::loop_closure::ccd::ccd_moves(), core::conformation::Conformation::detect_bonds(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), core::conformation::Conformation::fill_missing_atoms(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close(), and core::chemical::write_topology_file().