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...

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 More...

	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. More...

int	getAtomicNum () const
	returns our atomic number More...

void	setAtomicNum (int newNum)
	sets our atomic number More...

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

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

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

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

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

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

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 More...

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

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

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

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

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

void	setNumRadicalElectrons (unsigned int num)

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

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

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

bool	getNoImplicit () const
	returns the `noImplicit` flag More...

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

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

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

bool	getIsAromatic () const
	returns our `isAromatic` flag More...

double	getMass () const
	returns our mass More...

void	setIsotope (unsigned int what)
	sets our isotope number More...

unsigned int	getIsotope () const
	returns our isotope number More...

void	setChiralTag (ChiralType what)
	sets our `chiralTag` More...

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

ChiralType	getChiralTag () const
	returns our `chiralTag` More...

void	setHybridization (HybridizationType what)
	sets our hybridization More...

HybridizationType	getHybridization () const
	returns our hybridization More...

virtual bool	hasQuery () const

virtual std::string	getQueryType () const

virtual void	setQuery (QUERYATOM_QUERY *what)
	NOT CALLABLE. More...

virtual QUERYATOM_QUERY *	getQuery () const
	NOT CALLABLE. More...

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

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

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

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

bool	needsUpdatePropertyCache () const

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

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

AtomMonomerInfo *	getMonomerInfo ()

const AtomMonomerInfo *	getMonomerInfo () const

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

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

int	getAtomMapNum () const

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 More...

Dict &	getDict ()

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

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

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

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. More...

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. More...

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

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

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

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

void	setOwningMol (ROMol &other)
	sets our owning molecule More...

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

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 More...

class	ROMol

class	RWMol

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 68 of file Atom.h.

Member Typedef Documentation

◆ QUERYATOM_QUERY

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

Definition at line 75 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 91 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 78 of file Atom.h.

Constructor & Destructor Documentation

◆ Atom() [1/5]

RDKit::Atom::Atom ( )

◆ 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 )

◆ Atom() [5/5]

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

default

◆ ~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

◆ 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.

◆ 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.

◆ getAtomicNum()

int RDKit::Atom::getAtomicNum ( ) const

inline

returns our atomic number

Definition at line 126 of file Atom.h.

Referenced by RDDepict::getAtomDepictRank(), RDKit::isAnyAtomWithMultipleNeighborsOrNotUserRLabel(), RDKit::queryAtomHasAliphaticHeteroatomNbrs(), RDKit::queryAtomHasHeteroatomNbrs(), RDKit::queryAtomNum(), RDKit::queryAtomNumAliphaticHeteroatomNbrs(), RDKit::queryAtomNumHeteroatomNbrs(), RDKit::queryAtomType(), RDKit::RGroupDecompData::relabelCore(), and RDKit::RGroupDecompData::relabelRGroup().

◆ 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 388 of file Atom.h.

References RDKit::common_properties::molAtomMapNumber.

Referenced by RDKit::RGroupDecompData::getRlabel().

◆ getChiralTag()

ChiralType RDKit::Atom::getChiralTag ( ) const

inline

returns our chiralTag

Definition at line 247 of file Atom.h.

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)

Notes:

requires an owning molecule

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

◆ getExplicitValence()

int RDKit::Atom::getExplicitValence ( ) const

returns the explicit valence (including Hs) of this atom

Referenced by RDKit::queryAtomExplicitValence().

◆ getFormalCharge()

int RDKit::Atom::getFormalCharge ( ) const

inline

returns the formal charge of this atom

Definition at line 214 of file Atom.h.

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

◆ getHybridization()

HybridizationType RDKit::Atom::getHybridization ( ) const

inline

returns our hybridization

Definition at line 254 of file Atom.h.

Referenced by RDKit::queryAtomHybridization().

◆ getIdx()

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

inline

returns our index within the ROMol

Definition at line 143 of file Atom.h.

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

Notes:

requires an owning molecule

Referenced by RDKit::queryAtomImplicitValence().

◆ getIsAromatic()

bool RDKit::Atom::getIsAromatic ( ) const

inline

returns our isAromatic flag

Definition at line 232 of file Atom.h.

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 240 of file Atom.h.

Referenced by RDKit::RGroupDecompData::getRlabel(), 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 370 of file Atom.h.

◆ getMonomerInfo() [2/2]

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

inline

Definition at line 371 of file Atom.h.

◆ getNoImplicit()

bool RDKit::Atom::getNoImplicit ( ) const

inline

returns the noImplicit flag

Definition at line 222 of file Atom.h.

◆ getNumExplicitHs()

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

inline

returns our number of explicit Hs

Definition at line 227 of file Atom.h.

Referenced by RDKit::queryAtomExplicitValence().

◆ getNumImplicitHs()

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

returns the number of implicit Hs this Atom is bound to

Notes:

requires an owning molecule

◆ getNumRadicalElectrons()

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

inline

returns the number of radical electrons for this Atom

Notes:

requires an owning molecule

Definition at line 210 of file Atom.h.

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 137 of file Atom.h.

References PRECONDITION.

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().

◆ getQueryType()

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

inlinevirtual

Reimplemented in RDKit::QueryAtom.

Definition at line 273 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)

Notes:

requires an owning molecule

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

Notes:

requires an owning molecule

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

Notes:

requires an owning molecule

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

◆ hasOwningMol()

bool RDKit::Atom::hasOwningMol ( ) const

inline

returns whether or not this instance belongs to a molecule

Definition at line 134 of file Atom.h.

◆ hasQuery()

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

inlinevirtual

Reimplemented in RDKit::QueryAtom.

Definition at line 271 of file Atom.h.

Referenced by RDKit::describeQuery().

◆ initAtom()

void RDKit::Atom::initAtom ( )

protected

◆ initFromOther()

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

protected

◆ 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.

◆ needsUpdatePropertyCache()

bool RDKit::Atom::needsUpdatePropertyCache ( ) const

◆ operator=() [1/2]

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

default

◆ operator=() [2/2]

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

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

◆ setAtomicNum()

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

inline

sets our atomic number

Definition at line 128 of file Atom.h.

Referenced by RDKit::RGroupDecompData::relabelRGroup().

◆ setAtomMapNum()

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

inline

Set the atom map Number of the atom.

Definition at line 376 of file Atom.h.

References RDKit::common_properties::molAtomMapNumber, and PRECONDITION.

Referenced by RDKit::RGroupDecompData::setRlabel().

◆ setChiralTag()

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

inline

sets our chiralTag

Definition at line 243 of file Atom.h.

◆ setFormalCharge()

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

inline

set's the formal charge of this atom

Definition at line 216 of file Atom.h.

◆ setHybridization()

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

inline

sets our hybridization

Definition at line 252 of file Atom.h.

◆ setIdx() [1/2]

template<class U >

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

inline

overload

Definition at line 153 of file Atom.h.

◆ 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 150 of file Atom.h.

◆ setIsAromatic()

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

inline

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

Definition at line 230 of file Atom.h.

◆ setIsotope()

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

sets our isotope number

Referenced by RDKit::RGroupDecompData::relabelRGroup(), and RDKit::RGroupDecompData::setRlabel().

◆ setMonomerInfo()

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

inline

takes ownership of the pointer

Definition at line 373 of file Atom.h.

◆ 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 220 of file Atom.h.

Referenced by RDKit::RGroupDecompData::relabelRGroup().

◆ setNumExplicitHs()

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

inline

sets our number of explicit Hs

Definition at line 225 of file Atom.h.

◆ setNumRadicalElectrons()

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

inline

Definition at line 211 of file Atom.h.

◆ setOwningMol() [1/2]

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

inlineprotected

sets our owning molecule

Definition at line 398 of file Atom.h.

References setOwningMol().

Referenced by setOwningMol().

◆ setOwningMol() [2/2]

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

protected

sets our owning molecule

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 Function Documentation

◆ MolPickler

friend class MolPickler

friend

the pickler needs access to our privates

Definition at line 69 of file Atom.h.

◆ ROMol

friend class ROMol

friend

Definition at line 70 of file Atom.h.

◆ RWMol

friend class RWMol

friend

Definition at line 71 of file Atom.h.

Member Data Documentation

◆ d_atomicNum

std::uint8_t RDKit::Atom::d_atomicNum

protected

Definition at line 404 of file Atom.h.

◆ d_chiralTag

std::uint8_t RDKit::Atom::d_chiralTag

protected

Definition at line 410 of file Atom.h.

◆ d_explicitValence

std::int8_t RDKit::Atom::d_explicitValence

protected

Definition at line 408 of file Atom.h.

◆ d_formalCharge

std::int8_t RDKit::Atom::d_formalCharge

protected

Definition at line 403 of file Atom.h.

◆ d_hybrid

std::uint8_t RDKit::Atom::d_hybrid

protected

Definition at line 411 of file Atom.h.

◆ d_implicitValence

std::int8_t RDKit::Atom::d_implicitValence

protected

Definition at line 408 of file Atom.h.

◆ d_index

atomindex_t RDKit::Atom::d_index

protected

Definition at line 414 of file Atom.h.

◆ d_isotope

std::uint16_t RDKit::Atom::d_isotope

protected

Definition at line 413 of file Atom.h.

◆ d_numExplicitHs

std::uint8_t RDKit::Atom::d_numExplicitHs

protected

Definition at line 402 of file Atom.h.

◆ d_numRadicalElectrons

std::uint8_t RDKit::Atom::d_numRadicalElectrons

protected

Definition at line 409 of file Atom.h.

◆ df_isAromatic

bool RDKit::Atom::df_isAromatic

protected

Definition at line 400 of file Atom.h.

◆ df_noImplicit

bool RDKit::Atom::df_noImplicit

protected

Definition at line 401 of file Atom.h.

◆ dp_mol

ROMol* RDKit::Atom::dp_mol

protected

Definition at line 416 of file Atom.h.

◆ dp_monomerInfo

AtomMonomerInfo* RDKit::Atom::dp_monomerInfo

protected

Definition at line 417 of file Atom.h.

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

Atom.h

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ QUERYATOM_QUERY

Member Enumeration Documentation

◆ ChiralType

◆ HybridizationType

Constructor & Destructor Documentation

◆ Atom() [1/5]

◆ Atom() [2/5]

◆ Atom() [3/5]

◆ Atom() [4/5]

◆ Atom() [5/5]

◆ ~Atom()

Member Function Documentation

◆ calcExplicitValence()

◆ calcImplicitValence()

◆ copy()

◆ expandQuery()

◆ getAtomicNum()

◆ getAtomMapNum()

◆ getChiralTag()

◆ getDegree()

◆ getExplicitValence()

◆ 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()

◆ hasOwningMol()

◆ hasQuery()

◆ initAtom()

◆ initFromOther()

◆ invertChirality()

◆ Match()

◆ needsUpdatePropertyCache()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ setAtomicNum()

◆ setAtomMapNum()

◆ setChiralTag()

◆ setFormalCharge()

◆ setHybridization()

◆ setIdx() [1/2]

◆ setIdx() [2/2]

◆ setIsAromatic()

◆ setIsotope()

◆ setMonomerInfo()

◆ setNoImplicit()

◆ setNumExplicitHs()

◆ setNumRadicalElectrons()

◆ setOwningMol() [1/2]

◆ setOwningMol() [2/2]

◆ setQuery()

◆ updatePropertyCache()

Friends And Related Function Documentation

◆ MolPickler

◆ ROMol

◆ RWMol

Member Data Documentation