core::chemical::AtomICoor Class Reference

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 (std::string const &built_atom_name, Real const phi_in, Real const theta_in, Real const d_in, ICoorAtomID const &stub_atom1, ICoorAtomID const &stub_atom2, ICoorAtomID const &stub_atom3, ResidueType const &rsd_type)
	AtomICoorID 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_a_true_index (utility::vector1< bool > const &atomvect) const
	Given a Boolean vector corresponding to atom indices, determine whether any of the stub indices depends on one of the atoms that are "true". More...
bool	depends_on_polymer_lower () const
	Is this icoor immediately dependent on LOWER? More...
bool	depends_on_polymer_upper () const
	Is this icoor immediately dependent on UPPER? More...
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...
std::string const &	built_atom () const
	The name of the atom being built by this icoor. More...
void	show (std::ostream &) const
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 Member Functions
Vector	build (Vector v1, Vector v2, Vector v3) const
	Internal, centralized implementation of the build() functions. More...

Private Attributes
std::string	built_atom_
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	(	std::string const &	built_atom_name,
		Real const	phi_in,
		Real const	theta_in,
		Real const	d_in,
		ICoorAtomID const &	stub_atom1,
		ICoorAtomID const &	stub_atom2,
		ICoorAtomID const &	stub_atom3,
		ResidueType const &	rsd_type
	)

AtomICoorID version.

Member Function Documentation

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

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

Referenced by protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), build(), core::conformation::Residue::build_atom_ideal(), core::conformation::Residue::connection_distance(), core::conformation::Conformation::detect_bonds(), core::conformation::Residue::fill_missing_atoms(), core::conformation::idealize_hydrogens(), core::conformation::improper_build(), core::conformation::orient_residue_for_ideal_bond(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and core::chemical::ICoorAtomID::xyz().

Vector core::chemical::AtomICoor::build

(

ResidueType const &

rsd_type

)

const

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

Vector core::chemical::AtomICoor::build ( Vector  v1, Vector  v2, Vector  v3  ) const

private

Internal, centralized implementation of the build() functions.

References core::kinematics::Stub::create_orthogonal(), d_, phi_, core::kinematics::Stub::spherical(), and theta_.

std::string const& core::chemical::AtomICoor::built_atom ( ) const

inline

The name of the atom being built by this icoor.

References built_atom_.

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

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

inline

References d_.

Referenced by core::chemical::compare_atom_icoor(), core::chemical::MutableResidueType::copy_atom_info(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::fill_missing_atoms(), protocols::loops::loop_closure::ccd::get_deviation(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), core::conformation::missing_stubs_build(), core::conformation::Residue::orient_onto_residue_peptoid(), core::chemical::pretty_print_atomicoor(), and core::chemical::write_topology_file().

bool core::chemical::AtomICoor::depends_on_a_true_index ( utility::vector1< bool > const &  atomvect ) const

inline

Given a Boolean vector corresponding to atom indices, determine whether any of the stub indices depends on one of the atoms that are "true".

Called by ResidueType::update_polymer_dependent_groups() when figuring out which atoms depend on atoms that depend on a connection.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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

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

inline

Is this icoor immediately dependent on LOWER?

Returns true if stub atom 1, 2, or 3 is LOWER.

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

Referenced by core::conformation::Residue::place(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

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

inline

Is this icoor immediately dependent on UPPER?

Returns true if stub atom 1, 2, or 3 is UPPER.

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

Referenced by core::conformation::Residue::place(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

bool core::chemical::AtomICoor::depends_on_residue_connection ( Size const  connid ) const

inline

Returns true if any of the stub atoms is the specified connection ID.

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

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

inline

Returns true if any of the stub atoms is a connection ID.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

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

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

inline

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

Referenced by core::conformation::missing_stubs_build(), and core::conformation::orient_residue_for_ideal_bond().

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

inline

accessor to stub_atom1 ICoorAtomID

References phi_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), core::chemical::compare_atom_icoor(), core::chemical::MutableResidueType::copy_atom_info(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::fill_missing_atoms(), core::conformation::Residue::orient_onto_residue_peptoid(), core::chemical::pretty_print_atomicoor(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), and core::chemical::write_topology_file().

void core::chemical::AtomICoor::show

(

std::ostream &

out

)

const

References core::chemical::ICoorAtomID::atomno(), d_, phi_, stub_atom1(), stub_atom2(), stub_atom3(), and theta_.

ICoorAtomID& core::chemical::AtomICoor::stub_atom ( int const  atm )

inline

accessor to stub_atom ICoorAtomID

References stub_atom1_, stub_atom2_, and stub_atom3_.

Referenced by protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Residue::fill_missing_atoms(), core::conformation::idealize_hydrogens(), core::conformation::missing_stubs_build(), core::chemical::pretty_print_atomicoor(), and protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms().

ICoorAtomID const& core::chemical::AtomICoor::stub_atom ( int const  atm ) const

inline

constant accessor to stub_atom ICoorAtomID

References stub_atom1_, stub_atom2_, and stub_atom3_.

ICoorAtomID const& core::chemical::AtomICoor::stub_atom1 ( ) const

inline

References stub_atom1_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), core::chemical::compare_atom_icoor(), core::chemical::MutableResidueType::copy_atom_info(), core::conformation::Conformation::fill_missing_atoms(), core::conformation::Residue::place(), core::chemical::pretty_print_atomicoor(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length(), show(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), and core::chemical::write_topology_file().

ICoorAtomID const& core::chemical::AtomICoor::stub_atom2 ( ) const

inline

accessor to stub_atom2 ICoorAtomID

References stub_atom2_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), core::chemical::compare_atom_icoor(), core::chemical::MutableResidueType::copy_atom_info(), core::conformation::Conformation::fill_missing_atoms(), core::conformation::orient_residue_for_ideal_bond(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), show(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), and core::chemical::write_topology_file().

ICoorAtomID const& core::chemical::AtomICoor::stub_atom3 ( ) const

inline

accessor to stub_atom3 ICoorAtomID

References stub_atom3_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), core::chemical::compare_atom_icoor(), core::chemical::MutableResidueType::copy_atom_info(), core::conformation::Conformation::fill_missing_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), show(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), and core::chemical::write_topology_file().

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

inline

References theta_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), core::chemical::compare_atom_icoor(), core::chemical::MutableResidueType::copy_atom_info(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::fill_missing_atoms(), protocols::loops::loop_closure::ccd::get_deviation(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), core::conformation::missing_stubs_build(), core::conformation::Residue::orient_onto_residue_peptoid(), core::chemical::pretty_print_atomicoor(), and core::chemical::write_topology_file().

Member Data Documentation

std::string core::chemical::AtomICoor::built_atom_

private

Referenced by built_atom().

Real core::chemical::AtomICoor::d_

private

Referenced by build(), d(), and show().

Real core::chemical::AtomICoor::phi_

private

Referenced by build(), phi(), and show().

ICoorAtomID core::chemical::AtomICoor::stub_atom1_

private

Referenced by build(), depends_on_a_true_index(), depends_on_polymer_lower(), depends_on_polymer_upper(), depends_on_residue_connection(), is_internal(), stub_atom(), and stub_atom1().

ICoorAtomID core::chemical::AtomICoor::stub_atom2_

private

Referenced by build(), depends_on_a_true_index(), depends_on_polymer_lower(), depends_on_polymer_upper(), depends_on_residue_connection(), is_internal(), stub_atom(), and stub_atom2().

ICoorAtomID core::chemical::AtomICoor::stub_atom3_

private

Referenced by build(), depends_on_a_true_index(), depends_on_polymer_lower(), depends_on_polymer_upper(), depends_on_residue_connection(), is_internal(), stub_atom(), and stub_atom3().

Real core::chemical::AtomICoor::theta_

private

Referenced by build(), show(), and theta().

---

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

• src/core/chemical/AtomICoor.hh
• src/core/chemical/AtomICoor.cc