RDKit::Bond Class Reference

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
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

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
std::uint64_t	d_flags = 0
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 46 of file Bond.h.

Member Typedef Documentation

QUERYBOND_QUERY

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

Definition at line 52 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 82 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 94 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 55 of file Bond.h.

Constructor & Destructor Documentation

Bond() [1/4]

RDKit::Bond::Bond

(

)

Referenced by Bond(), Bond(), copy(), RDKit::QueryBond::copy(), getStereoAtoms(), Match(), RDKit::QueryBond::Match(), operator=(), operator=(), RDKit::QueryBond::QueryBond(), RDKit::QueryBond::QueryBond(), RDKit::QueryBond::QueryBond(), and RDKit::QueryBond::QueryBond().

Bond() [2/4]

RDKit::Bond::Bond ( BondType bT )

explicit

construct with a particular BondType

Bond() [3/4]

RDKit::Bond::Bond

(

const Bond &

other

)

References Bond().

~Bond()

virtual RDKit::Bond::~Bond ( )

virtual

Bond() [4/4]

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

inlinenoexcept

Definition at line 114 of file Bond.h.

References Bond(), d_beginAtomIdx, d_bondType, d_dirTag, d_endAtomIdx, d_flags, d_index, d_stereo, df_isAromatic, df_isConjugated, dp_mol, dp_stereoAtoms, and RDKit::RDProps::RDProps().

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.

References Bond().

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.

References Queries::COMPOSITE_AND.

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 219 of file Bond.h.

References d_beginAtomIdx.

getBondDir()

BondDir RDKit::Bond::getBondDir ( ) const

inline

returns our direction

Definition at line 312 of file Bond.h.

References d_dirTag.

Referenced by RDKit::queryBondDir().

getBondType()

BondType RDKit::Bond::getBondType ( ) const

inline

returns our bondType

Definition at line 159 of file Bond.h.

References d_bondType.

Referenced by RDKit::canHaveDirection(), RDKit::canSetDoubleBondStereo(), RDKit::isDative(), RDKit::QueryBond::QueryBond(), 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 226 of file Bond.h.

References d_endAtomIdx.

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

getFlags() [1/2]

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

inline

Definition at line 378 of file Bond.h.

References d_flags.

getFlags() [2/2]

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

inline

Definition at line 377 of file Bond.h.

References d_flags.

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 205 of file Bond.h.

References d_index.

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 176 of file Bond.h.

References df_isAromatic.

getIsConjugated()

bool RDKit::Bond::getIsConjugated ( ) const

inline

returns the status of our isConjugated flag

Definition at line 181 of file Bond.h.

References df_isConjugated.

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 187 of file Bond.h.

References dp_mol, PRECONDITION, and ROMol.

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 334 of file Bond.h.

References d_stereo.

Referenced by RDKit::queryBondHasStereo().

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 358 of file Bond.h.

References dp_stereoAtoms.

getStereoAtoms() [2/2]

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

inline

returns the indices of our stereo atoms

Definition at line 351 of file Bond.h.

References Bond(), and dp_stereoAtoms.

Referenced by setStereo().

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 184 of file Bond.h.

References dp_mol.

hasQuery()

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

inlinevirtual

Reimplemented in RDKit::QueryBond.

Definition at line 286 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.

References Bond().

operator=() [1/2]

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

inlinenoexcept

Definition at line 129 of file Bond.h.

References Bond(), d_beginAtomIdx, d_bondType, d_dirTag, d_endAtomIdx, d_flags, d_index, d_stereo, df_isAromatic, df_isConjugated, dp_mol, dp_stereoAtoms, and RDKit::RDProps::operator=().

operator=() [2/2]

Bond & RDKit::Bond::operator=

(

const Bond &

other

)

References Bond().

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 310 of file Bond.h.

References d_dirTag.

setBondType()

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

inline

sets our bondType

Definition at line 161 of file Bond.h.

References d_bondType.

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

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

setFlags()

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

inline

Flags that can be used by to store information on bonds. 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 376 of file Bond.h.

References d_flags.

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 212 of file Bond.h.

References d_index.

setIsAromatic()

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

inline

sets our isAromatic flag

Definition at line 174 of file Bond.h.

References df_isAromatic.

setIsConjugated()

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

inline

sets our isConjugated flag

Definition at line 179 of file Bond.h.

References df_isConjugated.

setOwningMol() [1/2]

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

inline

sets our owning molecule

Definition at line 194 of file Bond.h.

References ROMol, and setOwningMol().

Referenced by setOwningMol().

setOwningMol() [2/2]

void RDKit::Bond::setOwningMol

(

ROMol *

other

)

sets our owning molecule

References ROMol.

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

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 326 of file Bond.h.

References d_stereo, getStereoAtoms(), PRECONDITION, STEREOCIS, and STEREOTRANS.

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 370 of file Bond.h.

Friends And Related Symbol Documentation

ROMol

friend class ROMol

friend

Definition at line 48 of file Bond.h.

References ROMol.

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

RWMol

friend class RWMol

friend

Definition at line 47 of file Bond.h.

References RWMol.

Referenced by RWMol.

Member Data Documentation

d_beginAtomIdx

atomindex_t RDKit::Bond::d_beginAtomIdx

protected

Definition at line 388 of file Bond.h.

Referenced by Bond(), getBeginAtomIdx(), and operator=().

d_bondType

std::uint8_t RDKit::Bond::d_bondType

protected

Definition at line 391 of file Bond.h.

Referenced by Bond(), getBondType(), operator=(), and setBondType().

d_dirTag

std::uint8_t RDKit::Bond::d_dirTag

protected

Definition at line 392 of file Bond.h.

Referenced by Bond(), getBondDir(), operator=(), and setBondDir().

d_endAtomIdx

atomindex_t RDKit::Bond::d_endAtomIdx

protected

Definition at line 388 of file Bond.h.

Referenced by Bond(), getEndAtomIdx(), and operator=().

d_flags

std::uint64_t RDKit::Bond::d_flags = 0

protected

Definition at line 394 of file Bond.h.

Referenced by Bond(), getFlags(), getFlags(), operator=(), and setFlags().

d_index

atomindex_t RDKit::Bond::d_index

protected

Definition at line 387 of file Bond.h.

Referenced by Bond(), getIdx(), operator=(), and setIdx().

d_stereo

std::uint8_t RDKit::Bond::d_stereo

protected

Definition at line 393 of file Bond.h.

Referenced by Bond(), getStereo(), operator=(), and setStereo().

df_isAromatic

bool RDKit::Bond::df_isAromatic

protected

Definition at line 389 of file Bond.h.

Referenced by Bond(), getIsAromatic(), operator=(), and setIsAromatic().

df_isConjugated

bool RDKit::Bond::df_isConjugated

protected

Definition at line 390 of file Bond.h.

Referenced by Bond(), getIsConjugated(), operator=(), and setIsConjugated().

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 385 of file Bond.h.

Referenced by Bond(), getOwningMol(), hasOwningMol(), and operator=().

dp_stereoAtoms

INT_VECT* RDKit::Bond::dp_stereoAtoms

protected

Definition at line 386 of file Bond.h.

Referenced by Bond(), getStereoAtoms(), getStereoAtoms(), and operator=().

---

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

• Bond.h