Class for storing atomic queries. More...

#include <QueryAtom.h>

Inheritance diagram for RDKit::QueryAtom:

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

Public Types inherited from RDKit::Atom
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
	QueryAtom ()

	QueryAtom (int num)

	QueryAtom (const Atom &other)

	QueryAtom (const QueryAtom &other)

QueryAtom &	operator= (const QueryAtom &other)

	QueryAtom (QueryAtom &&other) noexcept

QueryAtom &	operator= (QueryAtom &&other) noexcept

	~QueryAtom () override

Atom *	copy () const override
	returns a copy of this query, owned by the caller

bool	hasQuery () const override

std::string	getQueryType () const override
	returns the label associated to this query

void	setQuery (QUERYATOM_QUERY *what) override
	replaces our current query with the value passed in

QUERYATOM_QUERY *	getQuery () const override
	returns our current query

void	expandQuery (QUERYATOM_QUERY *what, Queries::CompositeQueryType how=Queries::COMPOSITE_AND, bool maintainOrder=true) override
	expands our current query

bool	Match (Atom const *what) const override
	returns true if we match Atom `what`

bool	QueryMatch (QueryAtom const *what) const
	returns true if our query details match those of QueryAtom `what`

Public Member Functions inherited from RDKit::Atom
	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 ()

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

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

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

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

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

Additional Inherited Members
Protected Member Functions inherited from RDKit::Atom
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 inherited from RDKit::Atom
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

Detailed Description

Class for storing atomic queries.

QueryAtom objects are derived from Atom objects, so they can be added to molecules and the like, but they have much fancier querying capabilities.

Definition at line 28 of file QueryAtom.h.

Member Typedef Documentation

◆ QUERYATOM_QUERY

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

Definition at line 30 of file QueryAtom.h.

Constructor & Destructor Documentation

◆ QueryAtom() [1/5]

RDKit::QueryAtom::QueryAtom ( )

inline

Definition at line 32 of file QueryAtom.h.

◆ QueryAtom() [2/5]

RDKit::QueryAtom::QueryAtom ( int num )

inlineexplicit

Definition at line 33 of file QueryAtom.h.

References RDKit::makeAtomNumQuery().

◆ QueryAtom() [3/5]

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

inlineexplicit

Definition at line 34 of file QueryAtom.h.

References Queries::COMPOSITE_AND, RDKit::Atom::getFormalCharge(), RDKit::Atom::getIsotope(), RDKit::Atom::getNumRadicalElectrons(), RDKit::makeAtomFormalChargeQuery(), RDKit::makeAtomIsotopeQuery(), RDKit::makeAtomNumQuery(), and RDKit::makeAtomNumRadicalElectronsQuery().

◆ QueryAtom() [4/5]

RDKit::QueryAtom::QueryAtom ( const QueryAtom & other )

inline

Definition at line 50 of file QueryAtom.h.

References Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::copy().

◆ QueryAtom() [5/5]

RDKit::QueryAtom::QueryAtom ( QueryAtom && other )

inlinenoexcept

Definition at line 71 of file QueryAtom.h.

◆ ~QueryAtom()

RDKit::QueryAtom::~QueryAtom ( )

override

Member Function Documentation

◆ copy()

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

overridevirtual

returns a copy of this query, owned by the caller

Reimplemented from RDKit::Atom.

◆ expandQuery()

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

overridevirtual

expands our current query

Parameters

what	the Queries::Query to be added. The ownership of the query is passed to the current object, where it might be deleted, so that the pointer should not be used again in the calling code.
how	the operator to be used in the expansion
maintainOrder	(optional) flags whether the relative order of the queries needs to be maintained, if this is false, the order is reversed Notes: `what` should probably be constructed using one of the functions defined in QueryOps.h the `maintainOrder` option can be useful because the combination operators short circuit when possible.

Reimplemented from RDKit::Atom.

◆ getQuery()

QUERYATOM_QUERY * RDKit::QueryAtom::getQuery ( ) const

inlineoverridevirtual

returns our current query

Reimplemented from RDKit::Atom.

Definition at line 100 of file QueryAtom.h.

◆ getQueryType()

std::string RDKit::QueryAtom::getQueryType ( ) const

inlineoverridevirtual

returns the label associated to this query

Reimplemented from RDKit::Atom.

Definition at line 92 of file QueryAtom.h.

◆ hasQuery()

bool RDKit::QueryAtom::hasQuery ( ) const

inlineoverridevirtual

Reimplemented from RDKit::Atom.

Definition at line 89 of file QueryAtom.h.

◆ Match()

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

overridevirtual

returns true if we match Atom what

Reimplemented from RDKit::Atom.

◆ operator=() [1/2]

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

inline

Definition at line 57 of file QueryAtom.h.

References Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::copy().

◆ operator=() [2/2]

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

inlinenoexcept

Definition at line 74 of file QueryAtom.h.

◆ QueryMatch()

bool RDKit::QueryAtom::QueryMatch ( QueryAtom const * what ) const

returns true if our query details match those of QueryAtom what

◆ setQuery()

void RDKit::QueryAtom::setQuery ( QUERYATOM_QUERY * what )

inlineoverridevirtual

replaces our current query with the value passed in

Reimplemented from RDKit::Atom.

Definition at line 95 of file QueryAtom.h.

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

QueryAtom.h

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ QUERYATOM_QUERY

Constructor & Destructor Documentation

◆ QueryAtom() [1/5]

◆ QueryAtom() [2/5]

◆ QueryAtom() [3/5]

◆ QueryAtom() [4/5]

◆ QueryAtom() [5/5]

◆ ~QueryAtom()

Member Function Documentation

◆ copy()

◆ expandQuery()

◆ getQuery()

◆ getQueryType()

◆ hasQuery()

◆ Match()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ QueryMatch()

◆ setQuery()