class for representing a bond More...

#include <Bond.h>

Inheritance diagram for RDKit::Bond:

Public Types
enum	BondType { UNSPECIFIED = 0 , SINGLE , DOUBLE , TRIPLE , QUADRUPLE , QUINTUPLE , HEXTUPLE , ONEANDAHALF , TWOANDAHALF , THREEANDAHALF , FOURANDAHALF , FIVEANDAHALF , AROMATIC , IONIC , HYDROGEN , THREECENTER , DATIVEONE , DATIVE , DATIVEL , DATIVER , OTHER , ZERO }
	the type of Bond More...

enum	BondDir { NONE = 0 , BEGINWEDGE , BEGINDASH , ENDDOWNRIGHT , ENDUPRIGHT , EITHERDOUBLE , UNKNOWN }
	the bond's direction (for chirality) More...

enum	BondStereo { STEREONONE = 0 , STEREOANY , STEREOZ , STEREOE , STEREOCIS , STEREOTRANS , STEREOATROPCW , STEREOATROPCCW }
	the nature of the bond's stereochem (for cis/trans) More...

typedef Queries::Query< int, Bond const *, true >	QUERYBOND_QUERY

Public Member Functions
	Bond ()

	Bond (BondType bT)
	construct with a particular BondType

	Bond (const Bond &other)

virtual	~Bond ()

Bond &	operator= (const Bond &other)

	Bond (Bond &&o) noexcept

Bond &	operator= (Bond &&o) noexcept

virtual Bond *	copy () const
	returns a copy

BondType	getBondType () const
	returns our `bondType`

void	setBondType (BondType bT)
	sets our `bondType`

double	getBondTypeAsDouble () const
	returns our `bondType` as a double (e.g. SINGLE->1.0, AROMATIC->1.5, etc.)

virtual double	getValenceContrib (const Atom *at) const
	returns our contribution to the explicit valence of an Atom

void	setIsAromatic (bool what)
	sets our `isAromatic` flag

bool	getIsAromatic () const
	returns the status of our `isAromatic` flag

void	setIsConjugated (bool what)
	sets our `isConjugated` flag

bool	getIsConjugated () const
	returns the status of our `isConjugated` flag

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

void	setOwningMol (ROMol *other)
	sets our owning molecule

void	setOwningMol (ROMol &other)
	sets our owning molecule

bool	invertChirality ()

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

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

unsigned int	getBeginAtomIdx () const
	returns the index of our begin Atom

unsigned int	getEndAtomIdx () const
	returns the index of our end Atom

unsigned int	getOtherAtomIdx (unsigned int thisIdx) const
	given the index of one Atom, returns the index of the other

void	setBeginAtomIdx (unsigned int what)
	sets the index of our begin Atom

void	setEndAtomIdx (unsigned int what)
	sets the index of our end Atom

void	setBeginAtom (Atom *at)
	sets our begin Atom

void	setEndAtom (Atom *at)
	sets our end Atom

Atom *	getBeginAtom () const
	returns a pointer to our begin Atom

Atom *	getEndAtom () const
	returns a pointer to our end Atom

Atom *	getOtherAtom (Atom const *what) const
	returns a pointer to the other Atom

virtual bool	hasQuery () const

virtual void	setQuery (QUERYBOND_QUERY *what)
	NOT CALLABLE.

virtual QUERYBOND_QUERY *	getQuery () const
	NOT CALLABLE.

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

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

void	setBondDir (BondDir what)
	sets our direction

BondDir	getBondDir () const
	returns our direction

void	setStereo (BondStereo what)
	sets our stereo code

BondStereo	getStereo () const
	returns our stereo code

void	setStereoAtoms (unsigned int bgnIdx, unsigned int endIdx)
	sets the atoms to be considered as reference points for bond stereo

const INT_VECT &	getStereoAtoms () const
	returns the indices of our stereo atoms

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

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

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

Protected Member Functions
void	initBond ()

Protected Attributes
ROMol *	dp_mol

INT_VECT *	dp_stereoAtoms

atomindex_t	d_index

atomindex_t	d_beginAtomIdx

atomindex_t	d_endAtomIdx

bool	df_isAromatic

bool	df_isConjugated

std::uint8_t	d_bondType

std::uint8_t	d_dirTag

std::uint8_t	d_stereo

Protected Attributes inherited from RDKit::RDProps
Dict	d_props

Friends
class	RWMol

class	ROMol

Detailed Description

class for representing a bond

Notes:

many of the methods of Atom require that the Atom be associated with a molecule (an ROMol).
each Bond 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 Bond objects.

Definition at line 47 of file Bond.h.

Member Typedef Documentation

◆ QUERYBOND_QUERY

typedef Queries::Query<int, Bond const *, true> RDKit::Bond::QUERYBOND_QUERY

Definition at line 53 of file Bond.h.

Member Enumeration Documentation

◆ BondDir

enum RDKit::Bond::BondDir

the bond's direction (for chirality)

Enumerator
NONE	no special style
BEGINWEDGE	wedged: narrow at begin
BEGINDASH	dashed: narrow at begin
ENDDOWNRIGHT	for cis/trans
ENDUPRIGHT	ditto
EITHERDOUBLE	a "crossed" double bond
UNKNOWN	intentionally unspecified stereochemistry

Definition at line 83 of file Bond.h.

◆ BondStereo

enum RDKit::Bond::BondStereo

the nature of the bond's stereochem (for cis/trans)

Enumerator
STEREONONE
STEREOANY
STEREOZ
STEREOE
STEREOCIS
STEREOTRANS
STEREOATROPCW
STEREOATROPCCW

Definition at line 95 of file Bond.h.

◆ BondType

enum RDKit::Bond::BondType

the type of Bond

Enumerator
UNSPECIFIED
SINGLE
DOUBLE
TRIPLE
QUADRUPLE
QUINTUPLE
HEXTUPLE
ONEANDAHALF
TWOANDAHALF
THREEANDAHALF
FOURANDAHALF
FIVEANDAHALF
AROMATIC
IONIC
HYDROGEN
THREECENTER
DATIVEONE	one-electron dative (e.g. from a C in a Cp ring to a metal)
DATIVE	standard two-electron dative
DATIVEL	standard two-electron dative
DATIVER	standard two-electron dative
OTHER
ZERO	Zero-order bond (from.

Definition at line 56 of file Bond.h.

Constructor & Destructor Documentation

◆ Bond() [1/4]

RDKit::Bond::Bond ( )

◆ Bond() [2/4]

RDKit::Bond::Bond ( BondType bT )

explicit

construct with a particular BondType

◆ Bond() [3/4]

RDKit::Bond::Bond ( const Bond & other )

◆ ~Bond()

virtual RDKit::Bond::~Bond ( )

virtual

◆ Bond() [4/4]

RDKit::Bond::Bond ( Bond && o )

inlinenoexcept

Definition at line 115 of file Bond.h.

Member Function Documentation

◆ copy()

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

virtual

returns a copy

Note: the caller is responsible for deleteing the returned pointer.

Reimplemented in RDKit::QueryBond.

◆ expandQuery()

virtual void RDKit::Bond::expandQuery	(	QUERYBOND_QUERY *	what,
		Queries::CompositeQueryType	how = `Queries::COMPOSITE_AND`,
		bool	maintainOrder = `true`
	)

virtual

NOT CALLABLE.

Reimplemented in RDKit::QueryBond.

◆ getBeginAtom()

Atom * RDKit::Bond::getBeginAtom ( ) const

returns a pointer to our begin Atom

Notes:

requires an owning molecule

◆ getBeginAtomIdx()

unsigned int RDKit::Bond::getBeginAtomIdx ( ) const

inline

returns the index of our begin Atom

Notes:

this makes no sense if we do not have an owning molecule

Definition at line 218 of file Bond.h.

◆ getBondDir()

BondDir RDKit::Bond::getBondDir ( ) const

inline

returns our direction

Definition at line 311 of file Bond.h.

Referenced by RDKit::queryBondDir().

◆ getBondType()

BondType RDKit::Bond::getBondType ( ) const

inline

returns our bondType

Definition at line 158 of file Bond.h.

Referenced by RDKit::canHaveDirection(), RDKit::canSetDoubleBondStereo(), RDKit::isDative(), RDKit::queryBondIsDoubleOrAromatic(), RDKit::queryBondIsSingleOrAromatic(), RDKit::queryBondIsSingleOrDouble(), RDKit::queryBondIsSingleOrDoubleOrAromatic(), and RDKit::queryBondOrder().

◆ getBondTypeAsDouble()

double RDKit::Bond::getBondTypeAsDouble ( ) const

returns our bondType as a double (e.g. SINGLE->1.0, AROMATIC->1.5, etc.)

◆ getEndAtom()

Atom * RDKit::Bond::getEndAtom ( ) const

returns a pointer to our end Atom

Notes:

requires an owning molecule

◆ getEndAtomIdx()

unsigned int RDKit::Bond::getEndAtomIdx ( ) const

inline

returns the index of our end Atom

Notes:

this makes no sense if we do not have an owning molecule

Definition at line 225 of file Bond.h.

◆ getIdx()

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

inline

returns our index within the ROMol

Notes:

this makes no sense if we do not have an owning molecule

Definition at line 204 of file Bond.h.

Referenced by RDKit::queryBondIsInRingOfSize(), RDKit::queryBondMinRingSize(), RDKit::queryIsBondInNRings(), and RDKit::queryIsBondInRing().

◆ getIsAromatic()

bool RDKit::Bond::getIsAromatic ( ) const

inline

returns the status of our isAromatic flag

Definition at line 175 of file Bond.h.

◆ getIsConjugated()

bool RDKit::Bond::getIsConjugated ( ) const

inline

returns the status of our isConjugated flag

Definition at line 180 of file Bond.h.

◆ getOtherAtom()

Atom * RDKit::Bond::getOtherAtom ( Atom const * what ) const

returns a pointer to the other Atom

Notes:

requires an owning molecule

◆ getOtherAtomIdx()

unsigned int RDKit::Bond::getOtherAtomIdx ( unsigned int thisIdx ) const

given the index of one Atom, returns the index of the other

Notes:

this makes no sense if we do not have an owning molecule

◆ getOwningMol()

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

inline

returns a reference to the ROMol that owns this instance

Definition at line 186 of file Bond.h.

References PRECONDITION.

Referenced by RDKit::queryBondIsInRingOfSize(), RDKit::queryBondMinRingSize(), RDKit::queryIsBondInNRings(), and RDKit::queryIsBondInRing().

◆ getQuery()

virtual QUERYBOND_QUERY * RDKit::Bond::getQuery ( ) const

virtual

NOT CALLABLE.

Reimplemented in RDKit::QueryBond.

Referenced by RDKit::describeQuery(), RDKit::QueryOps::hasBondTypeQuery(), and RDKit::QueryOps::hasComplexBondTypeQuery().

◆ getStereo()

BondStereo RDKit::Bond::getStereo ( ) const

inline

returns our stereo code

Definition at line 333 of file Bond.h.

◆ getStereoAtoms() [1/2]

INT_VECT & RDKit::Bond::getStereoAtoms ( )

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 357 of file Bond.h.

◆ getStereoAtoms() [2/2]

const INT_VECT & RDKit::Bond::getStereoAtoms ( ) const

inline

returns the indices of our stereo atoms

Definition at line 350 of file Bond.h.

◆ getValenceContrib()

virtual double RDKit::Bond::getValenceContrib ( const Atom * at ) const

virtual

returns our contribution to the explicit valence of an Atom

Notes:

requires an owning molecule

Reimplemented in RDKit::QueryBond.

◆ hasOwningMol()

bool RDKit::Bond::hasOwningMol ( ) const

inline

returns whether or not this instance belongs to a molecule

Definition at line 183 of file Bond.h.

◆ hasQuery()

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

inlinevirtual

Reimplemented in RDKit::QueryBond.

Definition at line 285 of file Bond.h.

Referenced by RDKit::describeQuery(), RDKit::QueryOps::hasBondTypeQuery(), and RDKit::QueryOps::hasComplexBondTypeQuery().

◆ initBond()

void RDKit::Bond::initBond ( )

protected

◆ invertChirality()

bool RDKit::Bond::invertChirality ( )

◆ Match()

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

virtual

returns whether or not we match the argument

Notes:

for Bond objects, "match" means that either one of the Bonds has bondType Bond::UNSPECIFIED or both Bonds have the same bondType.

Reimplemented in RDKit::QueryBond.

◆ operator=() [1/2]

Bond & RDKit::Bond::operator= ( Bond && o )

inlinenoexcept

Definition at line 129 of file Bond.h.

◆ operator=() [2/2]

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

◆ setBeginAtom()

void RDKit::Bond::setBeginAtom ( Atom * at )

sets our begin Atom

Notes:

requires an owning molecule

◆ setBeginAtomIdx()

void RDKit::Bond::setBeginAtomIdx ( unsigned int what )

sets the index of our begin Atom

Notes:

requires an owning molecule

◆ setBondDir()

void RDKit::Bond::setBondDir ( BondDir what )

inline

sets our direction

Definition at line 309 of file Bond.h.

◆ setBondType()

void RDKit::Bond::setBondType ( BondType bT )

inline

sets our bondType

Definition at line 160 of file Bond.h.

◆ setEndAtom()

void RDKit::Bond::setEndAtom ( Atom * at )

sets our end Atom

Notes:

requires an owning molecule

◆ setEndAtomIdx()

void RDKit::Bond::setEndAtomIdx ( unsigned int what )

sets the index of our end Atom

Notes:

requires an owning molecule

◆ setIdx()

void RDKit::Bond::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()->getNumBonds()

Definition at line 211 of file Bond.h.

◆ setIsAromatic()

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

inline

sets our isAromatic flag

Definition at line 173 of file Bond.h.

◆ setIsConjugated()

void RDKit::Bond::setIsConjugated ( bool what )

inline

sets our isConjugated flag

Definition at line 178 of file Bond.h.

◆ setOwningMol() [1/2]

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

inline

sets our owning molecule

Definition at line 193 of file Bond.h.

References setOwningMol().

Referenced by setOwningMol().

◆ setOwningMol() [2/2]

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

sets our owning molecule

◆ setQuery()

virtual void RDKit::Bond::setQuery ( QUERYBOND_QUERY * what )

virtual

NOT CALLABLE.

Reimplemented in RDKit::QueryBond.

◆ setStereo()

void RDKit::Bond::setStereo ( BondStereo what )

inline

sets our stereo code

STEREONONE, STEREOANY, STEREOE and STEREOZ can be set without neighboring atoms specified in getStereoAtoms since they are defined by the topology of the molecular graph. In order to set STEREOCIS or STEREOTRANS the neighboring atoms must be set first (using setStereoBonds()) to know what atoms are being considered.

Notes:

MolOps::findPotentialStereoBonds can be used to set getStereoAtoms before setting CIS/TRANS

Definition at line 325 of file Bond.h.

References PRECONDITION.

◆ setStereoAtoms()

void RDKit::Bond::setStereoAtoms	(	unsigned int	bgnIdx,
		unsigned int	endIdx
	)

sets the atoms to be considered as reference points for bond stereo

These do not necessarily need to be the highest 'ranking' atoms like CIP stereo requires. They can be any arbitrary atoms neighboring the begin and end atoms of this bond respectively. STEREOCIS or STEREOTRANS is then set relative to only these atoms.

If CIP rankings are desired, use MolOps::findPotentialStereoBonds, but this is a more costly function as it takes the whole molecule topology into account.

◆ updatePropertyCache()

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

inline

calculates any of our lazy properties

Notes:

requires an owning molecule

Definition at line 369 of file Bond.h.

Friends And Related Symbol Documentation

◆ ROMol

friend class ROMol

friend

Definition at line 49 of file Bond.h.

◆ RWMol

friend class RWMol

friend

Definition at line 48 of file Bond.h.

Member Data Documentation

◆ d_beginAtomIdx

atomindex_t RDKit::Bond::d_beginAtomIdx

protected

Definition at line 379 of file Bond.h.

◆ d_bondType

std::uint8_t RDKit::Bond::d_bondType

protected

Definition at line 382 of file Bond.h.

◆ d_dirTag

std::uint8_t RDKit::Bond::d_dirTag

protected

Definition at line 383 of file Bond.h.

◆ d_endAtomIdx

atomindex_t RDKit::Bond::d_endAtomIdx

protected

Definition at line 379 of file Bond.h.

◆ d_index

atomindex_t RDKit::Bond::d_index

protected

Definition at line 378 of file Bond.h.

◆ d_stereo

std::uint8_t RDKit::Bond::d_stereo

protected

Definition at line 384 of file Bond.h.

◆ df_isAromatic

bool RDKit::Bond::df_isAromatic

protected

Definition at line 380 of file Bond.h.

◆ df_isConjugated

bool RDKit::Bond::df_isConjugated

protected

Definition at line 381 of file Bond.h.

◆ dp_mol

ROMol* RDKit::Bond::dp_mol

protected

sets our owning molecule void setOwningMol(ROMol *other); sets our owning molecule void setOwningMol(ROMol &other) { setOwningMol(&other); }

Definition at line 376 of file Bond.h.

◆ dp_stereoAtoms

INT_VECT* RDKit::Bond::dp_stereoAtoms

protected

Definition at line 377 of file Bond.h.

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

Bond.h

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ QUERYBOND_QUERY

Member Enumeration Documentation

◆ BondDir

◆ BondStereo

◆ BondType

Constructor & Destructor Documentation

◆ Bond() [1/4]

◆ Bond() [2/4]

◆ Bond() [3/4]

◆ ~Bond()

◆ Bond() [4/4]

Member Function Documentation

◆ copy()

◆ expandQuery()

◆ getBeginAtom()

◆ getBeginAtomIdx()

◆ getBondDir()

◆ getBondType()

◆ getBondTypeAsDouble()

◆ getEndAtom()

◆ getEndAtomIdx()

◆ getIdx()

◆ getIsAromatic()

◆ getIsConjugated()

◆ getOtherAtom()

◆ getOtherAtomIdx()

◆ getOwningMol()

◆ getQuery()

◆ getStereo()

◆ getStereoAtoms() [1/2]

◆ getStereoAtoms() [2/2]

◆ getValenceContrib()

◆ hasOwningMol()

◆ hasQuery()

◆ initBond()

◆ invertChirality()

◆ Match()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ setBeginAtom()

◆ setBeginAtomIdx()

◆ setBondDir()

◆ setBondType()

◆ setEndAtom()

◆ setEndAtomIdx()

◆ setIdx()

◆ setIsAromatic()

◆ setIsConjugated()

◆ setOwningMol() [1/2]

◆ setOwningMol() [2/2]

◆ setQuery()

◆ setStereo()

◆ setStereoAtoms()

◆ updatePropertyCache()

Friends And Related Symbol Documentation

◆ ROMol

◆ RWMol

Member Data Documentation

◆ d_beginAtomIdx

◆ d_bondType

◆ d_dirTag

◆ d_endAtomIdx

◆ d_index

◆ d_stereo

◆ df_isAromatic

◆ df_isConjugated

◆ dp_mol

◆ dp_stereoAtoms