The class for representing atoms. More...

#include <Atom.h>

Inheritance diagram for RDKit::Atom:

Public Types
enum	HybridizationType { UNSPECIFIED = 0 , S , SP , SP2 , SP3 , SP2D , SP3D , SP3D2 , OTHER }
	store hybridization More...

enum	ChiralType { CHI_UNSPECIFIED = 0 , CHI_TETRAHEDRAL_CW , CHI_TETRAHEDRAL_CCW , CHI_OTHER , CHI_TETRAHEDRAL , CHI_ALLENE , CHI_SQUAREPLANAR , CHI_TRIGONALBIPYRAMIDAL , CHI_OCTAHEDRAL }
	store type of chirality More...

enum class	ValenceType : std::uint8_t { IMPLICIT = 0 , EXPLICIT }

typedef Queries::Query< int, Atom const *, true >	QUERYATOM_QUERY

Public Member Functions
	Atom ()

	Atom (unsigned int num)
	construct an Atom with a particular atomic number

	Atom (const std::string &what)

	Atom (const Atom &other)

Atom &	operator= (const Atom &other)

	Atom (Atom &&other)=default

Atom &	operator= (Atom &&other)=default

virtual	~Atom ()

virtual Atom *	copy () const
	makes a copy of this Atom and returns a pointer to it.

int	getAtomicNum () const
	returns our atomic number

void	setAtomicNum (int newNum)
	sets our atomic number

std::string	getSymbol () const
	returns our symbol (determined by our atomic number)

bool	hasOwningMol () const
	returns whether or not this instance belongs to a molecule

ROMol &	getOwningMol () const
	returns a reference to the ROMol that owns this instance

unsigned int	getIdx () const
	returns our index within the ROMol

void	setIdx (unsigned int index)
	sets our index within the ROMol

template<class U>
void	setIdx (const U index)
	overload

unsigned int	getDegree () const

unsigned int	getTotalDegree () const

unsigned int	getTotalNumHs (bool includeNeighbors=false) const
	returns the total number of Hs (implicit and explicit) that this Atom is bound to

unsigned int	getTotalValence () const
	returns the total valence (implicit and explicit) for an atom

unsigned int	getNumImplicitHs () const
	returns the number of implicit Hs this Atom is bound to

unsigned int	getValence (ValenceType which) const
	returns the valence (explicit or implicit) of this atom

int	getExplicitValence () const
	returns the explicit valence (including Hs) of this atom

int	getImplicitValence () const
	returns the implicit valence for this Atom

bool	hasValenceViolation () const
	returns whether the atom has a valency violation or not

unsigned int	getNumRadicalElectrons () const
	returns the number of radical electrons for this Atom

void	setNumRadicalElectrons (unsigned int num)

int	getFormalCharge () const
	returns the formal charge of this atom

void	setFormalCharge (int what)
	set's the formal charge of this atom

void	setNoImplicit (bool what)
	sets our `noImplicit` flag, indicating whether or not we are allowed to have implicit Hs

bool	getNoImplicit () const
	returns the `noImplicit` flag

void	setNumExplicitHs (unsigned int what)
	sets our number of explicit Hs

unsigned int	getNumExplicitHs () const
	returns our number of explicit Hs

void	setIsAromatic (bool what)
	sets our `isAromatic` flag, indicating whether or not we are aromatic

bool	getIsAromatic () const
	returns our `isAromatic` flag

double	getMass () const
	returns our mass

void	setIsotope (unsigned int what)
	sets our isotope number

unsigned int	getIsotope () const
	returns our isotope number

void	setChiralTag (ChiralType what)
	sets our `chiralTag`

bool	invertChirality ()
	inverts our `chiralTag`, returns whether or not a change was made

ChiralType	getChiralTag () const
	returns our `chiralTag`

void	setHybridization (HybridizationType what)
	sets our hybridization

HybridizationType	getHybridization () const
	returns our hybridization

virtual bool	hasQuery () const

virtual std::string	getQueryType () const

virtual void	setQuery (QUERYATOM_QUERY *what)
	NOT CALLABLE.

virtual QUERYATOM_QUERY *	getQuery () const
	NOT CALLABLE.

virtual void	expandQuery (QUERYATOM_QUERY *what, Queries::CompositeQueryType how=Queries::COMPOSITE_AND, bool maintainOrder=true)
	NOT CALLABLE.

virtual bool	Match (Atom const *what) const
	returns whether or not we match the argument

int	getPerturbationOrder (const INT_LIST &probe) const
	returns the perturbation order for a list of integers

void	updatePropertyCache (bool strict=true)
	calculates any of our lazy `properties`

bool	needsUpdatePropertyCache () const

void	clearPropertyCache ()

int	calcExplicitValence (bool strict=true)
	calculates and returns our explicit valence

int	calcImplicitValence (bool strict=true)
	calculates and returns our implicit valence

AtomMonomerInfo *	getMonomerInfo ()

const AtomMonomerInfo *	getMonomerInfo () const

void	setMonomerInfo (AtomMonomerInfo *info)
	takes ownership of the pointer

void	setAtomMapNum (int mapno, bool strict=true)
	Set the atom map Number of the atom.

int	getAtomMapNum () const

void	setFlags (std::uint64_t flags)

std::uint64_t	getFlags () const

std::uint64_t &	getFlags ()

Public Member Functions inherited from RDKit::RDProps
	RDProps ()

	RDProps (const RDProps &rhs)

RDProps &	operator= (const RDProps &rhs)

	RDProps (RDProps &&o) noexcept=default

RDProps &	operator= (RDProps &&rhs) noexcept=default

void	clear ()

const Dict &	getDict () const
	gets the underlying Dictionary

Dict &	getDict ()

STR_VECT	getPropList (bool includePrivate=true, bool includeComputed=true) const
	returns a list with the names of our `properties`

template<typename T>
void	setProp (const std::string &key, T val, bool computed=false) const
	sets a `property` value

template<typename T>
void	getProp (const std::string &key, T &res) const
	allows retrieval of a particular property value

template<typename T>
T	getProp (const std::string &key) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<typename T>
bool	getPropIfPresent (const std::string &key, T &res) const

bool	hasProp (const std::string &key) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

void	clearProp (const std::string &key) const
	clears the value of a `property`

void	clearComputedProps () const
	clears all of our `computed` `properties`

void	updateProps (const RDProps &source, bool preserveExisting=false)
	update the properties from another

Static Public Attributes
static constexpr unsigned int	NOATOM

Protected Member Functions
void	setOwningMol (ROMol *other)
	sets our owning molecule

void	setOwningMol (ROMol &other)
	sets our owning molecule

void	initAtom ()

void	initFromOther (const Atom &other)

Protected Attributes
bool	df_isAromatic

bool	df_noImplicit

std::uint8_t	d_numExplicitHs

std::int8_t	d_formalCharge

std::uint8_t	d_atomicNum

std::int8_t	d_implicitValence

std::int8_t	d_explicitValence

std::uint8_t	d_numRadicalElectrons

std::uint8_t	d_chiralTag

std::uint8_t	d_hybrid

std::uint16_t	d_isotope

atomindex_t	d_index

std::uint64_t	d_flags = 0ul

ROMol *	dp_mol

AtomMonomerInfo *	dp_monomerInfo

Protected Attributes inherited from RDKit::RDProps
Dict	d_props

Friends
class	MolPickler
	the pickler needs access to our privates

class	ROMol

class	RWMol

std::ostream &	operator<<) (std::ostream &target, const ::RDKit::Atom &at)

int	calculateImplicitValence (const Atom &, bool, bool)

Detailed Description

The class for representing atoms.

Notes:

many of the methods of Atom require that the Atom be associated with a molecule (an ROMol).
each Atom maintains a Dict of properties:
- Each property is keyed by name and can store an arbitrary type.
- Properties can be marked as calculated, in which case they will be cleared when the clearComputedProps() method is called.
- Because they have no impact upon chemistry, all property operations are const, this allows extra flexibility for clients who need to store extra data on Atom objects.
Atom objects are lazy about computing their explicit and implicit valence values. These will not be computed until their values are requested.

Chirality:

The chirality of an Atom is determined by two things:

its chiralTag
the input order of its bonds (see note below for handling of implicit Hs)

For tetrahedral coordination, the chiralTag tells you what direction you have to rotate to get from bond 2 to bond 3 while looking down bond 1. This is pretty much identical to the SMILES representation of chirality.

NOTE: if an atom has an implicit H, the bond to that H is considered to be at the end of the list of other bonds.

Definition at line 74 of file Atom.h.

Member Typedef Documentation

◆ QUERYATOM_QUERY

typedef Queries::Query<int, Atom const *, true> RDKit::Atom::QUERYATOM_QUERY

Definition at line 89 of file Atom.h.

Member Enumeration Documentation

◆ ChiralType

enum RDKit::Atom::ChiralType

store type of chirality

Enumerator
CHI_UNSPECIFIED	chirality that hasn't been specified
CHI_TETRAHEDRAL_CW	tetrahedral: clockwise rotation (SMILES @@)
CHI_TETRAHEDRAL_CCW	tetrahedral: counter-clockwise rotation (SMILES
CHI_OTHER	some unrecognized type of chirality
CHI_TETRAHEDRAL	tetrahedral, use permutation flag
CHI_ALLENE	allene, use permutation flag
CHI_SQUAREPLANAR	square planar, use permutation flag
CHI_TRIGONALBIPYRAMIDAL	trigonal bipyramidal, use permutation flag
CHI_OCTAHEDRAL	octahedral, use permutation flag

Definition at line 105 of file Atom.h.

◆ HybridizationType

enum RDKit::Atom::HybridizationType

store hybridization

Enumerator
UNSPECIFIED	hybridization that hasn't been specified
S
SP
SP2
SP3
SP2D
SP3D
SP3D2
OTHER	unrecognized hybridization

Definition at line 92 of file Atom.h.

◆ ValenceType

enum class RDKit::Atom::ValenceType : std::uint8_t

strong

Enumerator
IMPLICIT
EXPLICIT

Definition at line 118 of file Atom.h.

Constructor & Destructor Documentation

◆ Atom() [1/5]

RDKit::Atom::Atom ( )

Referenced by Atom(), Atom(), calculateImplicitValence, copy(), RDKit::QueryAtom::copy(), initFromOther(), Match(), RDKit::QueryAtom::Match(), operator=(), operator=(), RDKit::QueryAtom::QueryAtom(), RDKit::QueryAtom::QueryAtom(), RDKit::QueryAtom::QueryAtom(), RDKit::QueryAtom::QueryAtom(), and RDKit::QueryAtom::QueryAtom().

◆ Atom() [2/5]

RDKit::Atom::Atom ( unsigned int num )

explicit

construct an Atom with a particular atomic number

◆ Atom() [3/5]

RDKit::Atom::Atom ( const std::string & what )

explicit

construct an Atom with a particular symbol (looked up in the PeriodicTable)

◆ Atom() [4/5]

RDKit::Atom::Atom ( const Atom & other )

References Atom().

◆ Atom() [5/5]

RDKit::Atom::Atom ( Atom && other )

default

References Atom().

◆ ~Atom()

virtual RDKit::Atom::~Atom ( )

virtual

Member Function Documentation

◆ calcExplicitValence()

int RDKit::Atom::calcExplicitValence ( bool strict = true )

calculates and returns our explicit valence

Notes:

requires an owning molecule

◆ calcImplicitValence()

int RDKit::Atom::calcImplicitValence ( bool strict = true )

calculates and returns our implicit valence

Notes:

requires an owning molecule

◆ clearPropertyCache()

void RDKit::Atom::clearPropertyCache ( )

◆ copy()

virtual Atom * RDKit::Atom::copy ( ) const

virtual

makes a copy of this Atom and returns a pointer to it.

Note: the caller is responsible for deleteing the result

Reimplemented in RDKit::QueryAtom.

References Atom().

◆ expandQuery()

virtual void RDKit::Atom::expandQuery	(	QUERYATOM_QUERY *	what,
		Queries::CompositeQueryType	how = Queries::COMPOSITE_AND,
		bool	maintainOrder = true )

virtual

NOT CALLABLE.

Reimplemented in RDKit::QueryAtom.

References Queries::COMPOSITE_AND.

◆ getAtomicNum()

int RDKit::Atom::getAtomicNum ( ) const

inline

returns our atomic number

Definition at line 145 of file Atom.h.

References d_atomicNum.

Referenced by RDDepict::getAtomDepictRank(), RDKit::isAnyAtomWithMultipleNeighborsOrNotUserRLabel(), RDKit::isAtomDummy(), RDKit::QueryAtom::QueryAtom(), RDKit::queryAtomHasAliphaticHeteroatomNbrs(), RDKit::queryAtomHasHeteroatomNbrs(), RDKit::queryAtomNum(), RDKit::queryAtomNumAliphaticHeteroatomNbrs(), RDKit::queryAtomNumHeteroatomNbrs(), and RDKit::queryAtomType().

◆ getAtomMapNum()

int RDKit::Atom::getAtomMapNum ( ) const

inline

Gets the atom map Number of the atom, if no atom map exists, 0 is returned.

Definition at line 386 of file Atom.h.

References RDKit::RDProps::getPropIfPresent(), and RDKit::common_properties::molAtomMapNumber.

◆ getChiralTag()

ChiralType RDKit::Atom::getChiralTag ( ) const

inline

returns our chiralTag

Definition at line 244 of file Atom.h.

References d_chiralTag.

Referenced by RDKit::queryAtomHasChiralTag(), and RDKit::queryAtomMissingChiralTag().

◆ getDegree()

unsigned int RDKit::Atom::getDegree ( ) const

returns the explicit degree of the Atom (number of bonded neighbors in the graph)

Referenced by RDDepict::getAtomDepictRank(), and RDKit::queryAtomExplicitDegree().

◆ getExplicitValence()

int RDKit::Atom::getExplicitValence ( ) const

returns the explicit valence (including Hs) of this atom

◆ getFlags() [1/2]

std::uint64_t & RDKit::Atom::getFlags ( )

inline

Definition at line 398 of file Atom.h.

References d_flags.

◆ getFlags() [2/2]

std::uint64_t RDKit::Atom::getFlags ( ) const

inline

Definition at line 397 of file Atom.h.

References d_flags.

◆ getFormalCharge()

int RDKit::Atom::getFormalCharge ( ) const

inline

returns the formal charge of this atom

Definition at line 211 of file Atom.h.

References d_formalCharge.

Referenced by RDKit::QueryAtom::QueryAtom(), RDKit::queryAtomFormalCharge(), and RDKit::queryAtomNegativeFormalCharge().

◆ getHybridization()

HybridizationType RDKit::Atom::getHybridization ( ) const

inline

returns our hybridization

Definition at line 251 of file Atom.h.

References d_hybrid.

Referenced by RDKit::queryAtomHybridization().

◆ getIdx()

unsigned int RDKit::Atom::getIdx ( ) const

inline

returns our index within the ROMol

Definition at line 162 of file Atom.h.

References d_index.

Referenced by RDKit::SLNParse::addAtomToMol(), RDKit::SLNParse::addBranchToMol(), RDKit::SLNParse::closeRingBond(), RDKit::RecursiveStructureQuery::getAtIdx(), RDKit::queryAtomIsInRingOfSize(), RDKit::queryAtomMinRingSize(), RDKit::queryAtomRingMembership(), RDKit::queryIsAtomInNRings(), and RDKit::queryIsAtomInRing().

◆ getImplicitValence()

int RDKit::Atom::getImplicitValence ( ) const

returns the implicit valence for this Atom

◆ getIsAromatic()

bool RDKit::Atom::getIsAromatic ( ) const

inline

returns our isAromatic flag

Definition at line 229 of file Atom.h.

References df_isAromatic.

Referenced by RDKit::queryAtomAliphatic(), RDKit::queryAtomAromatic(), RDKit::queryAtomHasAliphaticHeteroatomNbrs(), RDKit::queryAtomNumAliphaticHeteroatomNbrs(), and RDKit::queryAtomType().

◆ getIsotope()

unsigned int RDKit::Atom::getIsotope ( ) const

inline

returns our isotope number

Definition at line 237 of file Atom.h.

References d_isotope.

Referenced by RDKit::QueryAtom::QueryAtom(), and RDKit::queryAtomIsotope().

◆ getMass()

double RDKit::Atom::getMass ( ) const

returns our mass

Referenced by RDKit::queryAtomMass().

◆ getMonomerInfo() [1/2]

AtomMonomerInfo * RDKit::Atom::getMonomerInfo ( )

inline

Definition at line 368 of file Atom.h.

References dp_monomerInfo.

◆ getMonomerInfo() [2/2]

const AtomMonomerInfo * RDKit::Atom::getMonomerInfo ( ) const

inline

Definition at line 369 of file Atom.h.

References dp_monomerInfo.

◆ getNoImplicit()

bool RDKit::Atom::getNoImplicit ( ) const

inline

returns the noImplicit flag

Definition at line 219 of file Atom.h.

References df_noImplicit.

◆ getNumExplicitHs()

unsigned int RDKit::Atom::getNumExplicitHs ( ) const

inline

returns our number of explicit Hs

Definition at line 224 of file Atom.h.

References d_numExplicitHs.

Referenced by RDKit::queryAtomExplicitValence().

◆ getNumImplicitHs()

unsigned int RDKit::Atom::getNumImplicitHs ( ) const

returns the number of implicit Hs this Atom is bound to

◆ getNumRadicalElectrons()

unsigned int RDKit::Atom::getNumRadicalElectrons ( ) const

inline

returns the number of radical electrons for this Atom

Definition at line 207 of file Atom.h.

References d_numRadicalElectrons.

Referenced by RDKit::QueryAtom::QueryAtom(), and RDKit::queryAtomNumRadicalElectrons().

◆ getOwningMol()

ROMol & RDKit::Atom::getOwningMol ( ) const

inline

returns a reference to the ROMol that owns this instance

Definition at line 156 of file Atom.h.

References dp_mol, PRECONDITION, and ROMol.

Referenced by RDKit::queryAtomHasAliphaticHeteroatomNbrs(), RDKit::queryAtomHasHeteroatomNbrs(), RDKit::queryAtomHasRingBond(), RDKit::queryAtomHeavyAtomDegree(), RDKit::queryAtomIsInRingOfSize(), RDKit::queryAtomMinRingSize(), RDKit::queryAtomNonHydrogenDegree(), RDKit::queryAtomNumAliphaticHeteroatomNbrs(), RDKit::queryAtomNumHeteroatomNbrs(), RDKit::queryAtomRingBondCount(), RDKit::queryAtomRingMembership(), RDKit::queryIsAtomInNRings(), and RDKit::queryIsAtomInRing().

◆ getPerturbationOrder()

int RDKit::Atom::getPerturbationOrder ( const INT_LIST & probe ) const

returns the perturbation order for a list of integers

This value is associated with chirality.

Parameters

probe a list of bond indices. This must be the same length as our number of incoming bonds (our degree).

Returns

the number of swaps required to convert the ordering of the probe list to match the order of our incoming bonds: e.g. if our incoming bond order is: [0,1,2,3]

  getPerturbationOrder([1,0,2,3]) = 1
  getPerturbationOrder([1,2,3,0]) = 3
  getPerturbationOrder([1,2,0,3]) = 2

See the class documentation for a more detailed description of our representation of chirality.

Notes:

requires an owning molecule

◆ getQuery()

virtual QUERYATOM_QUERY * RDKit::Atom::getQuery ( ) const

virtual

NOT CALLABLE.

Reimplemented in RDKit::QueryAtom.

Referenced by RDKit::describeQuery(), and RDKit::isAtomDummy().

◆ getQueryType()

virtual std::string RDKit::Atom::getQueryType ( ) const

inlinevirtual

Reimplemented in RDKit::QueryAtom.

Definition at line 270 of file Atom.h.

◆ getSymbol()

std::string RDKit::Atom::getSymbol ( ) const

returns our symbol (determined by our atomic number)

◆ getTotalDegree()

unsigned int RDKit::Atom::getTotalDegree ( ) const

returns the total degree of the Atom (number of bonded neighbors + number of Hs)

Referenced by RDKit::queryAtomTotalDegree(), and RDKit::queryAtomUnsaturated().

◆ getTotalNumHs()

unsigned int RDKit::Atom::getTotalNumHs ( bool includeNeighbors = false ) const

returns the total number of Hs (implicit and explicit) that this Atom is bound to

Referenced by RDKit::queryAtomHasImplicitH(), RDKit::queryAtomHCount(), and RDKit::queryAtomImplicitHCount().

◆ getTotalValence()

unsigned int RDKit::Atom::getTotalValence ( ) const

returns the total valence (implicit and explicit) for an atom

Referenced by RDKit::queryAtomTotalValence(), and RDKit::queryAtomUnsaturated().

◆ getValence()

unsigned int RDKit::Atom::getValence ( ValenceType which ) const

returns the valence (explicit or implicit) of this atom

Referenced by RDKit::queryAtomExplicitValence(), and RDKit::queryAtomImplicitValence().

◆ hasOwningMol()

bool RDKit::Atom::hasOwningMol ( ) const

inline

returns whether or not this instance belongs to a molecule

Definition at line 153 of file Atom.h.

References dp_mol.

◆ hasQuery()

virtual bool RDKit::Atom::hasQuery ( ) const

inlinevirtual

Reimplemented in RDKit::QueryAtom.

Definition at line 268 of file Atom.h.

Referenced by RDKit::describeQuery(), and RDKit::isAtomDummy().

◆ hasValenceViolation()

bool RDKit::Atom::hasValenceViolation ( ) const

returns whether the atom has a valency violation or not

◆ initAtom()

void RDKit::Atom::initAtom ( )

protected

◆ initFromOther()

void RDKit::Atom::initFromOther ( const Atom & other )

protected

References Atom().

◆ invertChirality()

bool RDKit::Atom::invertChirality ( )

inverts our chiralTag, returns whether or not a change was made

◆ Match()

virtual bool RDKit::Atom::Match ( Atom const * what ) const

virtual

returns whether or not we match the argument

Notes: The general rule is that if a property on this atom has a non-default value, the property on the other atom must have the same value. The exception to this is H counts, which are ignored. These turns out to be impossible to handle generally, so rather than having odd and hard-to-explain exceptions, we ignore them entirely.

Here are the rules for atom-atom matching: | This | Other | Match | Reason | CCO | CCO | Yes | | CCO | CC[O-] | Yes | | CC[O-] | CCO | No | Charge | CC[O-] | CC[O-] | Yes | | CC[OH] | CC[O-] | Yes | | CC[OH] | CCOC | Yes | | CCO | CCOC | Yes | | CCC | CCC | Yes | | CCC | CC[14C] | Yes | | CC[14C] | CCC | No | Isotope | CC[14C] | CC[14C] | Yes | | C | OCO | Yes | | [CH] | OCO | Yes | | [CH2] | OCO | Yes | | [CH3] | OCO | No | Radical | C | O[CH2]O | Yes | | [CH2] | O[CH2]O | Yes |

Reimplemented in RDKit::QueryAtom.

References Atom().

◆ needsUpdatePropertyCache()

bool RDKit::Atom::needsUpdatePropertyCache ( ) const

◆ operator=() [1/2]

Atom & RDKit::Atom::operator= ( Atom && other )

default

References Atom().

◆ operator=() [2/2]

Atom & RDKit::Atom::operator= ( const Atom & other )

References Atom().

Referenced by RDKit::QueryAtom::operator=().

◆ setAtomicNum()

void RDKit::Atom::setAtomicNum ( int newNum )

inline

sets our atomic number

Definition at line 147 of file Atom.h.

References d_atomicNum.

◆ setAtomMapNum()

void RDKit::Atom::setAtomMapNum	(	int	mapno,
		bool	strict = true )

inline

Set the atom map Number of the atom.

Definition at line 374 of file Atom.h.

References RDKit::RDProps::clearProp(), RDKit::RDProps::hasProp(), RDKit::common_properties::molAtomMapNumber, PRECONDITION, and RDKit::RDProps::setProp().

◆ setChiralTag()

void RDKit::Atom::setChiralTag ( ChiralType what )

inline

sets our chiralTag

Definition at line 240 of file Atom.h.

References d_chiralTag.

◆ setFlags()

void RDKit::Atom::setFlags ( std::uint64_t flags )

inline

Flags that can be used by to store information on atoms. These are not serialized and should be treated as temporary values. No guarantees are made about preserving these flags across library calls.

Definition at line 396 of file Atom.h.

References d_flags.

◆ setFormalCharge()

void RDKit::Atom::setFormalCharge ( int what )

inline

set's the formal charge of this atom

Definition at line 213 of file Atom.h.

References d_formalCharge.

◆ setHybridization()

void RDKit::Atom::setHybridization ( HybridizationType what )

inline

sets our hybridization

Definition at line 249 of file Atom.h.

References d_hybrid.

◆ setIdx() [1/2]

template<class U>

void RDKit::Atom::setIdx ( const U index )

inline

overload

Definition at line 172 of file Atom.h.

References rdcast, and setIdx().

◆ setIdx() [2/2]

void RDKit::Atom::setIdx ( unsigned int index )

inline

sets our index within the ROMol

Notes:

this makes no sense if we do not have an owning molecule
the index should be < this->getOwningMol()->getNumAtoms()

Definition at line 169 of file Atom.h.

References d_index.

Referenced by setIdx().

◆ setIsAromatic()

void RDKit::Atom::setIsAromatic ( bool what )

inline

sets our isAromatic flag, indicating whether or not we are aromatic

Definition at line 227 of file Atom.h.

References df_isAromatic.

◆ setIsotope()

void RDKit::Atom::setIsotope ( unsigned int what )

sets our isotope number

◆ setMonomerInfo()

void RDKit::Atom::setMonomerInfo ( AtomMonomerInfo * info )

takes ownership of the pointer

◆ setNoImplicit()

void RDKit::Atom::setNoImplicit ( bool what )

inline

sets our noImplicit flag, indicating whether or not we are allowed to have implicit Hs

Definition at line 217 of file Atom.h.

References df_noImplicit.

◆ setNumExplicitHs()

void RDKit::Atom::setNumExplicitHs ( unsigned int what )

inline

sets our number of explicit Hs

Definition at line 222 of file Atom.h.

References d_numExplicitHs.

◆ setNumRadicalElectrons()

void RDKit::Atom::setNumRadicalElectrons ( unsigned int num )

inline

Definition at line 208 of file Atom.h.

References d_numRadicalElectrons.

◆ setOwningMol() [1/2]

void RDKit::Atom::setOwningMol ( ROMol & other )

inlineprotected

sets our owning molecule

Definition at line 404 of file Atom.h.

References ROMol, and setOwningMol().

Referenced by setOwningMol().

◆ setOwningMol() [2/2]

void RDKit::Atom::setOwningMol ( ROMol * other )

protected

sets our owning molecule

References ROMol.

Referenced by RDKit::SLNParse::closeRingBond().

◆ setQuery()

virtual void RDKit::Atom::setQuery ( QUERYATOM_QUERY * what )

virtual

NOT CALLABLE.

Reimplemented in RDKit::QueryAtom.

◆ updatePropertyCache()

void RDKit::Atom::updatePropertyCache ( bool strict = true )

calculates any of our lazy properties

Notes:

requires an owning molecule
the current lazy properties are implicit and explicit valence

Friends And Related Symbol Documentation

◆ calculateImplicitValence

int calculateImplicitValence	(	const Atom &	,
		bool	,
		bool	)

friend

References Atom().

◆ MolPickler

friend class MolPickler

friend

the pickler needs access to our privates

Definition at line 75 of file Atom.h.

References MolPickler.

Referenced by MolPickler.

◆ operator<<)

std::ostream & operator<<)	(	std::ostream &	target,
		const ::RDKit::Atom &	at )

friend

◆ ROMol

friend class ROMol

friend

Definition at line 76 of file Atom.h.

References ROMol.

Referenced by getOwningMol(), ROMol, setOwningMol(), and setOwningMol().

◆ RWMol

friend class RWMol

friend

Definition at line 77 of file Atom.h.

References RWMol.

Referenced by RWMol.

Member Data Documentation

◆ d_atomicNum

std::uint8_t RDKit::Atom::d_atomicNum

protected

Definition at line 410 of file Atom.h.

Referenced by getAtomicNum(), and setAtomicNum().

◆ d_chiralTag

std::uint8_t RDKit::Atom::d_chiralTag

protected

Definition at line 416 of file Atom.h.

Referenced by getChiralTag(), and setChiralTag().

◆ d_explicitValence

std::int8_t RDKit::Atom::d_explicitValence

protected

Definition at line 414 of file Atom.h.

◆ d_flags

std::uint64_t RDKit::Atom::d_flags = 0ul

protected

Definition at line 421 of file Atom.h.

Referenced by getFlags(), getFlags(), and setFlags().

◆ d_formalCharge

std::int8_t RDKit::Atom::d_formalCharge

protected

Definition at line 409 of file Atom.h.

Referenced by getFormalCharge(), and setFormalCharge().

◆ d_hybrid

std::uint8_t RDKit::Atom::d_hybrid

protected

Definition at line 417 of file Atom.h.

Referenced by getHybridization(), and setHybridization().

◆ d_implicitValence

std::int8_t RDKit::Atom::d_implicitValence

protected

Definition at line 414 of file Atom.h.

◆ d_index

atomindex_t RDKit::Atom::d_index

protected

Definition at line 420 of file Atom.h.

Referenced by getIdx(), and setIdx().

◆ d_isotope

std::uint16_t RDKit::Atom::d_isotope

protected

Definition at line 419 of file Atom.h.

Referenced by getIsotope().

◆ d_numExplicitHs

std::uint8_t RDKit::Atom::d_numExplicitHs

protected

Definition at line 408 of file Atom.h.

Referenced by getNumExplicitHs(), and setNumExplicitHs().

◆ d_numRadicalElectrons

std::uint8_t RDKit::Atom::d_numRadicalElectrons

protected

Definition at line 415 of file Atom.h.

Referenced by getNumRadicalElectrons(), and setNumRadicalElectrons().

◆ df_isAromatic

bool RDKit::Atom::df_isAromatic

protected

Definition at line 406 of file Atom.h.

Referenced by getIsAromatic(), and setIsAromatic().

◆ df_noImplicit

bool RDKit::Atom::df_noImplicit

protected

Definition at line 407 of file Atom.h.

Referenced by getNoImplicit(), and setNoImplicit().

◆ dp_mol

ROMol* RDKit::Atom::dp_mol

protected

Definition at line 423 of file Atom.h.

Referenced by getOwningMol(), and hasOwningMol().

◆ dp_monomerInfo

AtomMonomerInfo* RDKit::Atom::dp_monomerInfo

protected

Definition at line 424 of file Atom.h.

Referenced by getMonomerInfo(), and getMonomerInfo().

◆ NOATOM

unsigned int RDKit::Atom::NOATOM

inlinestaticconstexpr

Initial value:

=

std::numeric_limits<unsigned int>::max()

Definition at line 85 of file Atom.h.

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

Atom.h

Public Types

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ QUERYATOM_QUERY

Member Enumeration Documentation

◆ ChiralType

◆ HybridizationType

◆ ValenceType

Constructor & Destructor Documentation

◆ Atom() [1/5]

◆ Atom() [2/5]

◆ Atom() [3/5]

◆ Atom() [4/5]

◆ Atom() [5/5]

◆ ~Atom()

Member Function Documentation

◆ calcExplicitValence()

◆ calcImplicitValence()

◆ clearPropertyCache()

◆ copy()

◆ expandQuery()

◆ getAtomicNum()

◆ getAtomMapNum()

◆ getChiralTag()

◆ getDegree()

◆ getExplicitValence()

◆ getFlags() [1/2]

◆ getFlags() [2/2]

◆ getFormalCharge()

◆ getHybridization()

◆ getIdx()

◆ getImplicitValence()

◆ getIsAromatic()

◆ getIsotope()

◆ getMass()

◆ getMonomerInfo() [1/2]

◆ getMonomerInfo() [2/2]

◆ getNoImplicit()

◆ getNumExplicitHs()

◆ getNumImplicitHs()

◆ getNumRadicalElectrons()

◆ getOwningMol()

◆ getPerturbationOrder()

◆ getQuery()

◆ getQueryType()

◆ getSymbol()

◆ getTotalDegree()

◆ getTotalNumHs()

◆ getTotalValence()

◆ getValence()

◆ hasOwningMol()

◆ hasQuery()

◆ hasValenceViolation()

◆ initAtom()

◆ initFromOther()

◆ invertChirality()

◆ Match()

◆ needsUpdatePropertyCache()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ setAtomicNum()

◆ setAtomMapNum()

◆ setChiralTag()

◆ setFlags()

◆ setFormalCharge()

◆ setHybridization()

◆ setIdx() [1/2]

◆ setIdx() [2/2]

◆ setIsAromatic()

◆ setIsotope()

◆ setMonomerInfo()

◆ setNoImplicit()

◆ setNumExplicitHs()

◆ setNumRadicalElectrons()

◆ setOwningMol() [1/2]