#include <Atom.hh>

Public Member Functions
	Atom ()
	Construct a new atom type with its name and element. More...

	Atom (std::string const &name_in, std::string const &mm_name, ElementCOP element, Real const charge, Vector const &ideal_xyz)
	Construct a new atom with the name, mm type, element, charge and position. More...

bool	operator== (Atom const &atom) const

std::string const &	name () const

std::string const &	mm_name () const

Size const &	atom_type_index () const

ElementCOP	element_type () const

core::chemical::element::Elements	element () const
	Convenience function to go directly to the element enum. More...

gasteiger::GasteigerAtomTypeDataCOP	gasteiger_atom_type () const

bool const &	is_backbone () const

bool const &	is_actcoord () const
	Is this atom part of the action coordinate centers? More...

int const &	formal_charge () const

Real const &	charge () const

Vector const &	ideal_xyz () const

MutableICoorRecordCOP	icoor () const
	The ICoor record for this residue – may be null. More...

char	absolute_stereochemistry () const
	Return the absolute stereochemistry (R/S designation) of this stereocenter. More...

GreekDistance	greek_distance () const
	How far (in Greek letters) is this atom from the primary functional group of the molecule? More...

utility::vector1< core::Size > const &	bonded_orbitals () const
	Which orbital indicies are attached to this atom? More...

void	element_type (ElementCOP element)

void	mm_name (std::string const &name)

void	gasteiger_atom_type (core::chemical::gasteiger::GasteigerAtomTypeDataCOP gasteiger_atom_type)

void	is_backbone (bool setting)

void	is_actcoord (bool setting)

void	formal_charge (int charge)

void	charge (Real const &charge)

void	ideal_xyz (Vector const &ideal_xyz)

void	icoor (MutableICoorRecordCOP icoor_record)

void	set_absolute_stereochemistry (char const setting)
	Set the absolute stereochemistry (R/S designation) of this stereocenter. More...

void	greek_distance (GreekDistance const setting)
	Set how far (in Greek letters) this atom is from the primary functional group of the molecule. More...

void	set_bonded_orbitals (utility::vector1< core::Size > const &setting)

void	add_bonded_orbital (Size orbital_index)

AtomProperties const &	properties () const
	Access the collection of properties for this Atom. IMPORTANT – This only looks at manually set properties, not any automatically derived ones. More...

bool	has_property (std::string const &property) const
	Generic property access. IMPORTANT – This only looks at manually set properties, not any automatically derived ones. More...

bool	has_property (AtomProperty const property) const
	Generic property access. IMPORTANT – This only looks at manually set properties, not any automatically derived ones. More...

void	set_property (std::string const &property, bool const setting)
	Generic property setting. More...

void	set_property (AtomProperty const property, bool const setting)

void	reset_all_properies (AtomProperties const &setting)
	Discard all the current properties, and set the the passed values. More...

void	is_virtual (bool setting)
	Set whether or not this atom is virtual. More...

bool	is_hydrogen () const

bool	is_virtual () const
	Get whether or not this atom is virtual. More...

bool	is_fake () const
	Return true if this represents a fake/mock atom. More...

void	show (std::ostream &out=std::cout) const
	Generate string representation of chemical::Atom for debugging purposes. More...

Protected Member Functions
void	name (std::string const &name)

void	atom_type_index (Size const &atom_type_index)

Protected Attributes
friend	MutableResidueType

Private Attributes
std::string	name_

std::string	mm_name_

Size	atom_type_index_ = 0

ElementCOP	element_

gasteiger::GasteigerAtomTypeDataCOP	gasteiger_atom_type_
	Gasteiger atom-type. More...

bool	is_backbone_ = false

bool	is_actcoord_ = false

int	formal_charge_ = 0
	The formal (integral) charge on the atom. More...

Real	charge_ = 0.0

char	abs_stereochem_ = '\0'

GreekDistance	greek_d_ = NA_GREEK_DISTANCE

Vector	ideal_xyz_ {0,0,0}

MutableICoorRecordCOP	icoor_
	Internal coordinates on how to build the given atom - used in preference to ideal_xyz if set. More...

utility::pointer::DeepCopyOP < AtomProperties >	properties_

utility::vector1< Size >	bonded_orbitals_

Detailed Description

This class contains the "chemical" information for atoms in a MutableResidueType. This does not contain the actual xyz coordinates of the atom, (which are found in core/conformation/Atom.hh) It is also not used for the plain ResidueType class, which holds the corresponding information intenrally. This class should contain the information that's associated with the atom, calculated from other info. (Do that in the MutableResidueType -> ResidueType transition. )

Note: chemical::Atoms are stored in chemical::MutableResidueType (within its ResidueGraph); conformation::Atoms are stored in conformation::Residue

Constructor & Destructor Documentation

core::chemical::Atom::Atom ( )

Construct a new atom type with its name and element.

All its properties are un-set by default.

core::chemical::Atom::Atom	(	std::string const &	name_in,
		std::string const &	mm_name,
		ElementCOP	element,
		Real const	charge,
		Vector const &	ideal_xyz
	)

Construct a new atom with the name, mm type, element, charge and position.

Rosetta AtomTypes should be set through the ResidueType to ensure data consistency.

Member Function Documentation

char core::chemical::Atom::absolute_stereochemistry ( ) const

inline

Return the absolute stereochemistry (R/S designation) of this stereocenter.

References abs_stereochem_.

void core::chemical::Atom::add_bonded_orbital ( Size orbital_index )

inline

References bonded_orbitals_.

Size const& core::chemical::Atom::atom_type_index ( ) const

inline

References atom_type_index_.

Referenced by core::chemical::ResidueType::copy_atom_info(), core::chemical::HeavyAtomWithPolarHydrogensFilter::operator()(), core::chemical::HeavyAtomWithHydrogensFilter::operator()(), core::chemical::rosetta_retype_fullatom(), and core::chemical::MutableResidueType::set_atom_type().

void core::chemical::Atom::atom_type_index ( Size const & atom_type_index )

inlineprotected

References atom_type_index(), and atom_type_index_.

Referenced by atom_type_index().

utility::vector1< core::Size > const& core::chemical::Atom::bonded_orbitals ( ) const

inline

Which orbital indicies are attached to this atom?

References bonded_orbitals_.

Real const& core::chemical::Atom::charge ( ) const

inline

References charge_.

Referenced by core::chemical::SetAtomicCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::VirtualizeAll::apply(), core::chemical::VirtualizeSidechain::apply(), core::chemical::sdf::MolWriter::compose_atoms(), formal_charge(), core::chemical::real_to_virtual(), and core::chemical::rosetta_recharge_fullatom().

void core::chemical::Atom::charge ( Real const & charge )

inline

References charge(), and charge_.

Referenced by charge().

core::chemical::element::Elements core::chemical::Atom::element ( ) const

Convenience function to go directly to the element enum.

References element_, and core::chemical::element::UnknownElement.

Referenced by element_type(), and is_hydrogen().

ElementCOP core::chemical::Atom::element_type ( ) const

inline

References element_.

Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), core::chemical::sdf::MolFileIOMolecule::create_dummy_atom(), core::chemical::find_chi_bonds(), core::chemical::find_nbr_dist(), core::chemical::RigidDistanceVisitor::is_nub(), core::chemical::rdkit::RestypeToRDMol::Mol(), core::chemical::rename_atoms(), core::chemical::retype_is_aromatic(), core::chemical::rosetta_retype_fullatom(), and core::chemical::MutableResidueType::set_atom_type().

void core::chemical::Atom::element_type ( ElementCOP element )

inline

References element(), and element_.

int const& core::chemical::Atom::formal_charge ( ) const

inline

References formal_charge_.

Referenced by core::chemical::SetFormalCharge::apply(), core::chemical::sdf::MolWriter::compose_properties(), core::chemical::rdkit::RestypeToRDMol::Mol(), and core::chemical::rosetta_recharge_fullatom().

void core::chemical::Atom::formal_charge ( int charge )

inline

References charge(), and formal_charge_.

gasteiger::GasteigerAtomTypeDataCOP core::chemical::Atom::gasteiger_atom_type ( ) const

References gasteiger_atom_type_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), gasteiger_atom_type(), core::chemical::MutableResidueType::set_gasteiger_atom_type(), and show().

void core::chemical::Atom::gasteiger_atom_type ( core::chemical::gasteiger::GasteigerAtomTypeDataCOP gasteiger_atom_type )

References gasteiger_atom_type(), and gasteiger_atom_type_.

GreekDistance core::chemical::Atom::greek_distance ( ) const

inline

How far (in Greek letters) is this atom from the primary functional group of the molecule?

References greek_d_.

void core::chemical::Atom::greek_distance ( GreekDistance const setting )

inline

Set how far (in Greek letters) this atom is from the primary functional group of the molecule.

References greek_d_.

bool core::chemical::Atom::has_property ( std::string const & property ) const

Generic property access. IMPORTANT – This only looks at manually set properties, not any automatically derived ones.

References properties_.

Referenced by is_virtual().

bool core::chemical::Atom::has_property ( AtomProperty const property ) const

Generic property access. IMPORTANT – This only looks at manually set properties, not any automatically derived ones.

References properties_.

MutableICoorRecordCOP core::chemical::Atom::icoor ( ) const

inline

The ICoor record for this residue – may be null.

References icoor_.

Referenced by core::chemical::MutableResidueType::atom_base(), core::chemical::MutableResidueType::clear_icoor(), and core::chemical::MutableResidueType::set_icoor().

void core::chemical::Atom::icoor ( MutableICoorRecordCOP icoor_record )

inline

References icoor_.

Vector const& core::chemical::Atom::ideal_xyz ( ) const

inline

References ideal_xyz_.

Referenced by core::chemical::MutableICoorRecord::build_xyz(), core::chemical::clean_up_dangling_connect(), core::chemical::sdf::MolWriter::compose_atoms(), core::chemical::detect_ld_chirality_from_polymer_residue(), core::chemical::RigidDistanceVisitor::examine_edge(), core::chemical::RigidDistanceVisitor::examine_vertex(), ideal_xyz(), core::chemical::RerootRestypeVisitor::initialize_vertex(), core::chemical::rdkit::RestypeToRDMol::Mol(), core::chemical::MutableResidueType::set_ideal_xyz(), and core::chemical::MutableICoorRecord::xyz().

void core::chemical::Atom::ideal_xyz ( Vector const & ideal_xyz )

inline

References ideal_xyz(), and ideal_xyz_.

bool const& core::chemical::Atom::is_actcoord ( ) const

inline

Is this atom part of the action coordinate centers?

The geometric center of all atoms listed as actcoords are the residue's "action coordinate" (for pair energy)

References is_actcoord_.

Referenced by core::chemical::MutableResidueType::add_actcoord_atom(), and core::chemical::MutableResidueType::delete_actcoord_atom().

void core::chemical::Atom::is_actcoord ( bool setting )

inline

References is_actcoord_.

bool const& core::chemical::Atom::is_backbone ( ) const

inline

References is_backbone_.

Referenced by core::chemical::annotate_backbone(), and show().

void core::chemical::Atom::is_backbone ( bool setting )

inline

References is_backbone_.

bool core::chemical::Atom::is_fake ( ) const

Return true if this represents a fake/mock atom.

Note: (Real atoms have elements that exist on the periodic table.)

References element_, is_virtual(), name(), and core::chemical::TR().

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types().

bool core::chemical::Atom::is_hydrogen ( ) const

inline

References element(), and core::chemical::element::H.

Referenced by core::chemical::SetAllAtomsRepulsive::apply(), core::chemical::AddConnectDeleteChildProton::apply(), core::chemical::MutableResidueType::bonded_heavyatoms(), core::chemical::MutableResidueType::bonded_hydrogens(), core::chemical::sdf::MolWriter::compose_atoms(), and core::chemical::RerootEdgeSorter::operator()().

void core::chemical::Atom::is_virtual ( bool setting )

inline

Set whether or not this atom is virtual.

References set_property(), and core::chemical::VIRTUAL_ATOM.

Referenced by core::chemical::SetAtomType::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::VirtualizeAll::apply(), core::chemical::VirtualizeSidechain::apply(), core::chemical::rdkit::RestypeToRDMol::Mol(), core::chemical::RerootEdgeSorter::operator()(), core::chemical::real_to_virtual(), and core::chemical::MutableResidueType::set_atom_type().

bool core::chemical::Atom::is_virtual ( ) const

inline

Get whether or not this atom is virtual.

References has_property(), and core::chemical::VIRTUAL_ATOM.

Referenced by is_fake(), and show().

std::string const& core::chemical::Atom::mm_name ( ) const

inline

References mm_name_.

Referenced by core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::VirtualizeAll::apply(), and core::chemical::VirtualizeSidechain::apply().

void core::chemical::Atom::mm_name ( std::string const & name )

inline

References mm_name_, and name().

std::string const& core::chemical::Atom::name ( ) const

inline

References name_.

Referenced by core::chemical::MutableResidueType::add_atom(), is_fake(), mm_name(), core::chemical::rdkit::RestypeToRDMol::Mol(), core::chemical::RerootEdgeSorter::operator()(), core::chemical::rename_atoms(), core::chemical::MutableResidueType::show_all_atom_names(), and core::chemical::MutableResidueType::validate_residue_type().

void core::chemical::Atom::name ( std::string const & name )

inlineprotected

References name(), and name_.

Referenced by name().

bool core::chemical::Atom::operator== ( Atom const & atom ) const

References abs_stereochem_, atom_type_index_, bonded_orbitals_, charge_, element_, formal_charge_, gasteiger_atom_type_, greek_d_, icoor_, ideal_xyz_, is_actcoord_, is_backbone_, mm_name_, name_, and properties_.

AtomProperties const& core::chemical::Atom::properties ( ) const

inline

Access the collection of properties for this Atom. IMPORTANT – This only looks at manually set properties, not any automatically derived ones.

References properties_.

void core::chemical::Atom::reset_all_properies ( AtomProperties const & setting )

Discard all the current properties, and set the the passed values.

References properties_.

void core::chemical::Atom::set_absolute_stereochemistry ( char const setting )

Set the absolute stereochemistry (R/S designation) of this stereocenter.

References abs_stereochem_.

void core::chemical::Atom::set_bonded_orbitals ( utility::vector1< core::Size > const & setting )

inline

References bonded_orbitals_.

void core::chemical::Atom::set_property	(	std::string const &	property,
		bool const	setting
	)

Generic property setting.

References properties_.

Referenced by core::chemical::ReplaceProtonWithTrifluoromethyl::apply(), core::chemical::ReplaceProtonWithMethyl::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithChlorine::apply(), core::chemical::ReplaceProtonWithFluorine::apply(), core::chemical::ReplaceProtonWithBromine::apply(), core::chemical::ReplaceProtonWithIodine::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), and is_virtual().

void core::chemical::Atom::set_property	(	AtomProperty const	property,
		bool const	setting
	)

References properties_.

void core::chemical::Atom::show ( std::ostream & out = std::cout ) const

Generate string representation of chemical::Atom for debugging purposes.

References abs_stereochem_, atom_type_index_, charge_, element_, formal_charge_, gasteiger_atom_type(), gasteiger_atom_type_, greek_d_, is_backbone(), is_virtual(), mm_name_, core::chemical::NA_GREEK_DISTANCE, name_, and properties_.

Referenced by core::chemical::operator<<(), and core::chemical::MutableResidueType::show().

Member Data Documentation

char core::chemical::Atom::abs_stereochem_ = '\0'

private

Referenced by absolute_stereochemistry(), operator==(), set_absolute_stereochemistry(), and show().

Size core::chemical::Atom::atom_type_index_ = 0

private

Referenced by atom_type_index(), operator==(), and show().

utility::vector1< Size > core::chemical::Atom::bonded_orbitals_

private

Referenced by add_bonded_orbital(), bonded_orbitals(), operator==(), and set_bonded_orbitals().

Real core::chemical::Atom::charge_ = 0.0

private

Referenced by charge(), operator==(), and show().

ElementCOP core::chemical::Atom::element_

private

Referenced by element(), element_type(), is_fake(), operator==(), and show().

int core::chemical::Atom::formal_charge_ = 0

private

The formal (integral) charge on the atom.

Referenced by formal_charge(), operator==(), and show().

gasteiger::GasteigerAtomTypeDataCOP core::chemical::Atom::gasteiger_atom_type_

private

Gasteiger atom-type.

Referenced by gasteiger_atom_type(), operator==(), and show().

GreekDistance core::chemical::Atom::greek_d_ = NA_GREEK_DISTANCE

private

Referenced by greek_distance(), operator==(), and show().

MutableICoorRecordCOP core::chemical::Atom::icoor_

private

Internal coordinates on how to build the given atom - used in preference to ideal_xyz if set.

Referenced by icoor(), and operator==().

Vector core::chemical::Atom::ideal_xyz_ {0,0,0}

private

Referenced by ideal_xyz(), and operator==().

bool core::chemical::Atom::is_actcoord_ = false

private

Referenced by is_actcoord(), and operator==().

bool core::chemical::Atom::is_backbone_ = false

private

Referenced by is_backbone(), and operator==().

std::string core::chemical::Atom::mm_name_

private

Referenced by mm_name(), operator==(), and show().

friend core::chemical::Atom::MutableResidueType

protected

std::string core::chemical::Atom::name_

private

Referenced by name(), operator==(), and show().

utility::pointer::DeepCopyOP< AtomProperties > core::chemical::Atom::properties_

private

Referenced by has_property(), operator==(), properties(), reset_all_properies(), set_property(), and show().

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

src/core/chemical/Atom.hh
src/core/chemical/Atom.cc

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation