The class for representing atoms. More...

#include <Atom.h>

Inheritance diagram for RDKit::Atom:

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

enum	ChiralType { CHI_UNSPECIFIED = 0, CHI_TETRAHEDRAL_CW, CHI_TETRAHEDRAL_CCW, CHI_OTHER }
	store type of chirality More...

typedef boost::shared_ptr< Atom >	ATOM_SPTR

typedef boost::shared_ptr< const Atom >	C_ATOM_SPTR

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

	Atom (const Atom &other)

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...

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

unsigned int	getNumExplicitHs () const
	returns our number of explict 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...

void	invertChirality ()
	inverts our `chiralTag` 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 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...

virtual bool	Match (const ATOM_SPTR &what) const

STR_VECT	getPropList () const
	returns a list with the names of our `properties` More...

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

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

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

template<typename T >
void	getProp (const std::string &key, T &res) const

template<typename T >
T	getProp (const char *key) const

template<typename T >
T	getProp (const std::string &key) const

template<typename T >
bool	getPropIfPresent (const char *key, T &res) const

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

bool	hasProp (const char *key) const
	returns whether or not we have a `property` with name `key` More...

bool	hasProp (const std::string &key) const

void	clearProp (const char *key) const
	clears the value of a `property` More...

void	clearProp (const std::string &key) const

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

int	getPerturbationOrder (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...

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

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

void	initAtom ()

Protected Attributes
bool	df_isAromatic

bool	df_noImplicit

boost::uint8_t	d_numExplicitHs

boost::int8_t	d_formalCharge

boost::uint8_t	d_atomicNum

boost::int8_t	d_implicitValence

boost::int8_t	d_explicitValence

boost::uint8_t	d_numRadicalElectrons

boost::uint8_t	d_chiralTag

boost::uint8_t	d_hybrid

atomindex_t	d_index

boost::uint16_t	d_isotope

ROMol *	dp_mol

Dict *	dp_props

AtomMonomerInfo *	dp_monomerInfo

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 67 of file Atom.h.

Member Typedef Documentation

◆ ATOM_SPTR

typedef boost::shared_ptr<Atom> RDKit::Atom::ATOM_SPTR

Definition at line 73 of file Atom.h.

◆ C_ATOM_SPTR

typedef boost::shared_ptr<const Atom> RDKit::Atom::C_ATOM_SPTR

Definition at line 74 of file Atom.h.

◆ QUERYATOM_QUERY

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

Definition at line 76 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

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
SP3D
SP3D2
OTHER	unrecognized hybridization

Definition at line 79 of file Atom.h.

Constructor & Destructor Documentation

◆ Atom() [1/4]

RDKit::Atom::Atom ( )

◆ Atom() [2/4]

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

explicit

construct an Atom with a particular atomic number

◆ Atom() [3/4]

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

explicit

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

◆ Atom() [4/4]

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

◆ ~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

Referenced by clearComputedProps().

◆ calcImplicitValence()

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

calculates and returns our implicit valence

Notes:

requires an owning molecule

Referenced by clearComputedProps().

◆ clearComputedProps()

void RDKit::Atom::clearComputedProps ( ) const

inline

clears all of our computed properties

Definition at line 432 of file Atom.h.

References calcExplicitValence(), calcImplicitValence(), RDKit::Dict::clearVal(), detail::computedPropName, dp_props, getPerturbationOrder(), getPropIfPresent(), needsUpdatePropertyCache(), RDKit::Dict::setVal(), and updatePropertyCache().

◆ clearProp() [1/2]

void RDKit::Atom::clearProp ( const char * key ) const

inline

clears the value of a property

Notes:

if no property with name key exists, a KeyErrorException will be thrown.
if the property is marked as computed, it will also be removed from our list of computedProperties

Definition at line 414 of file Atom.h.

◆ clearProp() [2/2]

void RDKit::Atom::clearProp ( const std::string & key ) const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 419 of file Atom.h.

References RDKit::Dict::clearVal(), detail::computedPropName, dp_props, getPropIfPresent(), and RDKit::Dict::setVal().

◆ 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.

Referenced by hasQuery().

◆ getAtomicNum()

int RDKit::Atom::getAtomicNum ( ) const

inline

returns our atomic number

Definition at line 115 of file Atom.h.

References d_atomicNum.

Referenced by RDKit::Drawing::DrawMol(), RDDepict::getAtomDepictRank(), RDKit::Drawing::detail::getAtomSymbolAndOrientation(), and RDKit::queryAtomNum().

◆ getChiralTag()

ChiralType RDKit::Atom::getChiralTag ( ) const

inline

returns our chiralTag

Definition at line 232 of file Atom.h.

References d_chiralTag.

◆ 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::Drawing::detail::getAtomSymbolAndOrientation(), RDKit::queryAtomExplicitDegree(), RDKit::queryAtomUnsaturated(), and setIdx().

◆ getExplicitValence()

int RDKit::Atom::getExplicitValence ( ) const

returns the explicit valence (including Hs) of this atom

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

◆ getFormalCharge()

int RDKit::Atom::getFormalCharge ( ) const

inline

returns the formal charge of this atom

Definition at line 199 of file Atom.h.

References d_formalCharge.

Referenced by RDKit::Drawing::detail::getAtomSymbolAndOrientation(), and RDKit::queryAtomFormalCharge().

◆ getHybridization()

HybridizationType RDKit::Atom::getHybridization ( ) const

inline

returns our hybridization

Definition at line 239 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 126 of file Atom.h.

References d_index.

Referenced by RDKit::SLNParse::addAtomToMol(), RDKit::FMCS::RingMatchTableSet::computeRingMatchTable(), 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(), RDKit::queryAtomTotalValence(), and setIdx().

◆ getIsAromatic()

bool RDKit::Atom::getIsAromatic ( ) const

inline

returns our isAromatic flag

Definition at line 217 of file Atom.h.

References df_isAromatic, getMass(), and setIsotope().

Referenced by RDKit::queryAtomAliphatic(), and RDKit::queryAtomAromatic().

◆ getIsotope()

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

inline

returns our isotope number

Definition at line 225 of file Atom.h.

References d_isotope.

Referenced by RDKit::Drawing::detail::getAtomSymbolAndOrientation(), and RDKit::queryAtomIsotope().

◆ getMass()

double RDKit::Atom::getMass ( ) const

returns our mass

Referenced by getIsAromatic(), and RDKit::queryAtomMass().

◆ getMonomerInfo() [1/2]

AtomMonomerInfo* RDKit::Atom::getMonomerInfo ( )

inline

Definition at line 491 of file Atom.h.

References dp_monomerInfo.

◆ getMonomerInfo() [2/2]

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

inline

Definition at line 492 of file Atom.h.

References dp_monomerInfo.

◆ getNoImplicit()

bool RDKit::Atom::getNoImplicit ( ) const

inline

returns the noImplicit flag

Definition at line 207 of file Atom.h.

References df_noImplicit.

◆ getNumExplicitHs()

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

inline

returns our number of explict Hs

Definition at line 212 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

Notes:

requires an owning molecule

Referenced by setIdx().

◆ 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 193 of file Atom.h.

References d_numRadicalElectrons.

Referenced by RDKit::Drawing::detail::getAtomSymbolAndOrientation().

◆ getOwningMol()

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

inline

returns a reference to the ROMol that owns this Atom

Definition at line 123 of file Atom.h.

References dp_mol.

Referenced by RDKit::queryAtomHasRingBond(), RDKit::queryAtomIsInRingOfSize(), RDKit::queryAtomMinRingSize(), RDKit::queryAtomRingBondCount(), RDKit::queryAtomRingMembership(), RDKit::queryIsAtomInNRings(), and RDKit::queryIsAtomInRing().

◆ getPerturbationOrder()

int RDKit::Atom::getPerturbationOrder ( 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

Referenced by clearComputedProps().

◆ getProp() [1/4]

template<typename T >

void RDKit::Atom::getProp	(	const char *	key,
		T &	res
	)		const

inline

allows retrieval of a particular property value

Parameters

key	the name under which the `property` should be stored. If a `property` is already stored under this name, it will be replaced.
res	a reference to the storage location for the value.

Notes:

if no property with name key exists, a KeyErrorException will be thrown.
the boost::lexical_cast machinery is used to attempt type conversions. If this fails, a boost::bad_lexical_cast exception will be thrown.

Definition at line 363 of file Atom.h.

References dp_props, and RDKit::Dict::getVal().

Referenced by RDKit::Drawing::detail::getAtomSymbolAndOrientation().

◆ getProp() [2/4]

template<typename T >

void RDKit::Atom::getProp	(	const std::string &	key,
		T &	res
	)		const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 368 of file Atom.h.

References dp_props, and RDKit::Dict::getVal().

◆ getProp() [3/4]

template<typename T >

T RDKit::Atom::getProp ( const char * key ) const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 374 of file Atom.h.

References dp_props, and RDKit::Dict::getVal().

◆ getProp() [4/4]

template<typename T >

T RDKit::Atom::getProp ( const std::string & key ) const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 379 of file Atom.h.

References dp_props, and RDKit::Dict::getVal().

◆ getPropIfPresent() [1/2]

template<typename T >

bool RDKit::Atom::getPropIfPresent	(	const char *	key,
		T &	res
	)		const

inline

returns whether or not we have a property with name key and assigns the value if we do

Definition at line 386 of file Atom.h.

References dp_props, and RDKit::Dict::getValIfPresent().

Referenced by clearComputedProps(), clearProp(), and setProp().

◆ getPropIfPresent() [2/2]

template<typename T >

bool RDKit::Atom::getPropIfPresent	(	const std::string &	key,
		T &	res
	)		const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 391 of file Atom.h.

References dp_props, and RDKit::Dict::getValIfPresent().

◆ getPropList()

STR_VECT RDKit::Atom::getPropList ( ) const

inline

returns a list with the names of our properties

Definition at line 313 of file Atom.h.

References dp_props, and RDKit::Dict::keys().

◆ getQuery()

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

virtual

NOT CALLABLE.

Reimplemented in RDKit::QueryAtom.

Referenced by hasQuery().

◆ getSymbol()

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

returns our symbol (determined by our atomic number)

Referenced by RDKit::Drawing::detail::getAtomSymbolAndOrientation(), and setAtomicNum().

◆ 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::queryAtomHeavyAtomDegree(), RDKit::queryAtomTotalDegree(), and setIdx().

◆ 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::Drawing::detail::getAtomSymbolAndOrientation(), RDKit::queryAtomHasImplicitH(), RDKit::queryAtomHCount(), RDKit::queryAtomHeavyAtomDegree(), RDKit::queryAtomImplicitHCount(), and setIdx().

◆ getTotalValence()

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

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

Notes:

requires an owning molecule

Referenced by setIdx().

◆ hasProp() [1/2]

bool RDKit::Atom::hasProp ( const char * key ) const

inline

returns whether or not we have a property with name key

Definition at line 396 of file Atom.h.

References dp_props, and RDKit::Dict::hasVal().

Referenced by RDKit::Drawing::detail::getAtomSymbolAndOrientation().

◆ hasProp() [2/2]

bool RDKit::Atom::hasProp ( const std::string & key ) const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 401 of file Atom.h.

References dp_props, and RDKit::Dict::hasVal().

◆ hasQuery()

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

inlinevirtual

Reimplemented in RDKit::QueryAtom.

Definition at line 256 of file Atom.h.

References Queries::COMPOSITE_AND, expandQuery(), getQuery(), Match(), and setQuery().

◆ initAtom()

void RDKit::Atom::initAtom ( )

protected

◆ invertChirality()

void RDKit::Atom::invertChirality ( )

inverts our chiralTag

Referenced by setChiralTag().

◆ Match() [1/2]

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.

Referenced by hasQuery(), and Match().

◆ Match() [2/2]

virtual bool RDKit::Atom::Match ( const ATOM_SPTR & what ) const

inlinevirtual

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Reimplemented in RDKit::QueryAtom.

Definition at line 303 of file Atom.h.

References Match().

◆ needsUpdatePropertyCache()

bool RDKit::Atom::needsUpdatePropertyCache ( ) const

Referenced by clearComputedProps().

◆ setAtomicNum()

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

inline

sets our atomic number

Definition at line 117 of file Atom.h.

References d_atomicNum, and getSymbol().

◆ setChiralTag()

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

inline

sets our chiralTag

Definition at line 228 of file Atom.h.

References d_chiralTag, and invertChirality().

◆ setFormalCharge()

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

inline

set's the formal charge of this atom

Definition at line 201 of file Atom.h.

References d_formalCharge.

◆ setHybridization()

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

inline

sets our hybridization

Definition at line 237 of file Atom.h.

References d_hybrid.

◆ setIdx() [1/2]

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 133 of file Atom.h.

References d_index.

Referenced by setIdx().

◆ setIdx() [2/2]

template<class U >

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

inline

overload

Definition at line 136 of file Atom.h.

References getDegree(), getExplicitValence(), getImplicitValence(), getNumImplicitHs(), getTotalDegree(), getTotalNumHs(), getTotalValence(), and setIdx().

◆ setIsAromatic()

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

inline

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

Definition at line 215 of file Atom.h.

References df_isAromatic.

◆ setIsotope()

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

sets our isotope number

Referenced by getIsAromatic().

◆ setMonomerInfo()

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

inline

takes ownership of the pointer

Definition at line 494 of file Atom.h.

References dp_monomerInfo, and setOwningMol().

◆ 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 205 of file Atom.h.

References df_noImplicit.

◆ setNumExplicitHs()

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

inline

sets our number of explict Hs

Definition at line 210 of file Atom.h.

References d_numExplicitHs.

◆ setNumRadicalElectrons()

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

inline

Definition at line 194 of file Atom.h.

References d_numRadicalElectrons.

◆ setOwningMol() [1/2]

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

protected

sets our owning molecule

Referenced by RDKit::SLNParse::closeRingBond(), and setMonomerInfo().

◆ setOwningMol() [2/2]

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

inlineprotected

sets our owning molecule

Definition at line 500 of file Atom.h.

References df_isAromatic, and setOwningMol().

Referenced by setOwningMol().

◆ setProp() [1/2]

template<typename T >

void RDKit::Atom::setProp	(	const char *	key,
		T	val,
		bool	computed = `false`
	)		const

inline

sets a property value

Parameters

key	the name under which the `property` should be stored. If a `property` is already stored under this name, it will be replaced.
val	the value to be stored
computed	(optional) allows the `property` to be flagged `computed`.

Definition at line 325 of file Atom.h.

◆ setProp() [2/2]

template<typename T >

void RDKit::Atom::setProp	(	const std::string &	key,
		T	val,
		bool	computed = `false`
	)		const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 333 of file Atom.h.

References detail::computedPropName, dp_props, getPropIfPresent(), and RDKit::Dict::setVal().

◆ setQuery()

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

virtual

NOT CALLABLE.

Reimplemented in RDKit::QueryAtom.

Referenced by hasQuery().

◆ 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

Referenced by clearComputedProps().

Friends And Related Function Documentation

◆ MolPickler

friend class MolPickler

friend

the pickler needs access to our privates

Definition at line 68 of file Atom.h.

◆ ROMol

friend class ROMol

friend

Definition at line 69 of file Atom.h.

◆ RWMol

friend class RWMol

friend

Definition at line 70 of file Atom.h.

Member Data Documentation

◆ d_atomicNum

boost::uint8_t RDKit::Atom::d_atomicNum

protected

Definition at line 506 of file Atom.h.

Referenced by getAtomicNum(), and setAtomicNum().

◆ d_chiralTag

boost::uint8_t RDKit::Atom::d_chiralTag

protected

Definition at line 512 of file Atom.h.

Referenced by getChiralTag(), and setChiralTag().

◆ d_explicitValence

boost::int8_t RDKit::Atom::d_explicitValence

protected

Definition at line 510 of file Atom.h.

◆ d_formalCharge

boost::int8_t RDKit::Atom::d_formalCharge

protected

Definition at line 505 of file Atom.h.

Referenced by getFormalCharge(), and setFormalCharge().

◆ d_hybrid

boost::uint8_t RDKit::Atom::d_hybrid

protected

Definition at line 513 of file Atom.h.

Referenced by getHybridization(), and setHybridization().

◆ d_implicitValence

boost::int8_t RDKit::Atom::d_implicitValence

protected

Definition at line 510 of file Atom.h.

◆ d_index

atomindex_t RDKit::Atom::d_index

protected

Definition at line 515 of file Atom.h.

Referenced by getIdx(), and setIdx().

◆ d_isotope

boost::uint16_t RDKit::Atom::d_isotope

protected

Definition at line 516 of file Atom.h.

Referenced by getIsotope().

◆ d_numExplicitHs

boost::uint8_t RDKit::Atom::d_numExplicitHs

protected

Definition at line 504 of file Atom.h.

Referenced by getNumExplicitHs(), and setNumExplicitHs().

◆ d_numRadicalElectrons

boost::uint8_t RDKit::Atom::d_numRadicalElectrons

protected

Definition at line 511 of file Atom.h.

Referenced by getNumRadicalElectrons(), and setNumRadicalElectrons().

◆ df_isAromatic

bool RDKit::Atom::df_isAromatic

protected

Definition at line 500 of file Atom.h.

Referenced by getIsAromatic(), setIsAromatic(), and setOwningMol().

◆ df_noImplicit

bool RDKit::Atom::df_noImplicit

protected

Definition at line 503 of file Atom.h.

Referenced by getNoImplicit(), and setNoImplicit().

◆ dp_mol

ROMol* RDKit::Atom::dp_mol

protected

Definition at line 518 of file Atom.h.

Referenced by getOwningMol().

◆ dp_monomerInfo

AtomMonomerInfo* RDKit::Atom::dp_monomerInfo

protected

Definition at line 520 of file Atom.h.

Referenced by getMonomerInfo(), and setMonomerInfo().

◆ dp_props

Dict* RDKit::Atom::dp_props

protected

Definition at line 519 of file Atom.h.

Referenced by clearComputedProps(), clearProp(), getProp(), getPropIfPresent(), getPropList(), hasProp(), and setProp().

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

◆ ATOM_SPTR

◆ C_ATOM_SPTR

◆ QUERYATOM_QUERY

Member Enumeration Documentation

◆ ChiralType

◆ HybridizationType

Constructor & Destructor Documentation

◆ Atom() [1/4]

◆ Atom() [2/4]

◆ Atom() [3/4]

◆ Atom() [4/4]

◆ ~Atom()

Member Function Documentation

◆ calcExplicitValence()

◆ calcImplicitValence()

◆ clearComputedProps()

◆ clearProp() [1/2]

◆ clearProp() [2/2]

◆ copy()

◆ expandQuery()

◆ getAtomicNum()

◆ getChiralTag()

◆ getDegree()

◆ getExplicitValence()

◆ getFormalCharge()

◆ getHybridization()

◆ getIdx()

◆ getImplicitValence()

◆ getIsAromatic()

◆ getIsotope()

◆ getMass()

◆ getMonomerInfo() [1/2]

◆ getMonomerInfo() [2/2]

◆ getNoImplicit()

◆ getNumExplicitHs()

◆ getNumImplicitHs()

◆ getNumRadicalElectrons()

◆ getOwningMol()

◆ getPerturbationOrder()

◆ getProp() [1/4]

◆ getProp() [2/4]

◆ getProp() [3/4]

◆ getProp() [4/4]

◆ getPropIfPresent() [1/2]

◆ getPropIfPresent() [2/2]

◆ getPropList()

◆ getQuery()

◆ getSymbol()

◆ getTotalDegree()

◆ getTotalNumHs()

◆ getTotalValence()

◆ hasProp() [1/2]

◆ hasProp() [2/2]

◆ hasQuery()

◆ initAtom()

◆ invertChirality()

◆ Match() [1/2]

◆ Match() [2/2]

◆ needsUpdatePropertyCache()

◆ setAtomicNum()

◆ setChiralTag()

◆ setFormalCharge()

◆ setHybridization()

◆ setIdx() [1/2]

◆ setIdx() [2/2]

◆ setIsAromatic()

◆ setIsotope()

◆ setMonomerInfo()

◆ setNoImplicit()

◆ setNumExplicitHs()

◆ setNumRadicalElectrons()

◆ setOwningMol() [1/2]

◆ setOwningMol() [2/2]