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 }
	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 }
	the nature of the bond's stereochem (for cis/trans) More...
typedef boost::shared_ptr< Bond >	BOND_SPTR
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)
virtual Bond *	copy () const
	returns a copy
const 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.)
double	getValenceContrib (const Atom *at) const
	returns our contribution to the explicit valence of an Atom
double	getValenceContrib (ATOM_SPTR at) const
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
ROMol &	getOwningMol () const
	returns a reference to the ROMol that owns this Bond
void	setOwningMol (ROMol *other)
	sets our owning molecule
void	setOwningMol (ROMol &other)
	sets our owning molecule
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	setBeginAtom (ATOM_SPTR at)
void	setEndAtom (Atom *at)
	sets our end Atom
void	setEndAtom (ATOM_SPTR at)
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
virtual bool	Match (const Bond::BOND_SPTR what) const
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
const INT_VECT &	getStereoAtoms () const
	returns the indices of our stereo atoms
INT_VECT &	getStereoAtoms ()
STR_VECT	getPropList () const
	returns a list with the names of our `properties`
template<typename T >
void	setProp (const char *key, T val, bool computed=false) const
	sets a `property` value
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
template<typename T >
void	getProp (const std::string key, T &res) const
bool	hasProp (const char *key) const
	returns whether or not we have a `property` with name `key`
bool	hasProp (const std::string key) const
void	clearProp (const char *key) const
	clears the value of a `property`
void	clearProp (const std::string key) const
void	clearComputedProps () const
	clears all of our `computed` `properties`
void	updatePropertyCache (bool strict=true)
	calculates any of our lazy `properties`
Protected Member Functions
void	initBond ()
Protected Attributes
BondType	d_bondType
ROMol *	dp_mol
bool	df_isAromatic
bool	df_isConjugated
unsigned int	d_index
unsigned int	d_beginAtomIdx
unsigned int	d_endAtomIdx
BondDir	d_dirTag
BondStereo	d_stereo
INT_VECT	d_stereoAtoms
Dict *	dp_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 44 of file Bond.h.

Member Typedef Documentation

typedef boost::shared_ptr<Bond> RDKit::Bond::BOND_SPTR

Definition at line 48 of file Bond.h.

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

Reimplemented in RDKit::QueryBond.

Definition at line 50 of file Bond.h.

Member Enumeration Documentation

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 78 of file Bond.h.

enum RDKit::Bond::BondStereo

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

Enumerator:

STEREONONE
STEREOANY
STEREOZ
STEREOE

Definition at line 90 of file Bond.h.

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

Definition at line 53 of file Bond.h.

Constructor & Destructor Documentation

RDKit::Bond::Bond ( )

RDKit::Bond::Bond ( BondType bT ) [explicit]

construct with a particular BondType

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

virtual RDKit::Bond::~Bond ( ) [virtual]

Member Function Documentation

void RDKit::Bond::clearComputedProps ( ) const [inline]

clears all of our computed properties

Definition at line 382 of file Bond.h.

References RDKit::Dict::clearVal(), dp_props, getProp(), hasProp(), and RDKit::Dict::setVal().

void RDKit::Bond::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 363 of file Bond.h.

void RDKit::Bond::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 368 of file Bond.h.

References RDKit::Dict::clearVal(), dp_props, getProp(), hasProp(), and RDKit::Dict::setVal().

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

returns a copy

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

Reimplemented in RDKit::QueryBond.

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

NOT CALLABLE.

Reimplemented in RDKit::QueryBond.

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

returns a pointer to our begin Atom

Notes:

requires an owning molecule

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 167 of file Bond.h.

References d_beginAtomIdx.

BondDir RDKit::Bond::getBondDir ( ) const [inline]

returns our direction

Definition at line 266 of file Bond.h.

References d_dirTag.

Referenced by RDKit::queryBondDir().

const BondType RDKit::Bond::getBondType ( ) const [inline]

returns our bondType

Definition at line 114 of file Bond.h.

References d_bondType.

Referenced by RDKit::queryBondOrder().

double RDKit::Bond::getBondTypeAsDouble ( ) const

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

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

returns a pointer to our end Atom

Notes:

requires an owning molecule

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 174 of file Bond.h.

References d_endAtomIdx.

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

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 153 of file Bond.h.

References d_index.

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

bool RDKit::Bond::getIsAromatic ( ) const [inline]

returns the status of our isAromatic flag

Definition at line 133 of file Bond.h.

References df_isAromatic.

bool RDKit::Bond::getIsConjugated ( ) const [inline]

returns the status of our isConjugated flag

Definition at line 138 of file Bond.h.

References df_isConjugated.

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

returns a pointer to the other Atom

Notes:

requires an owning molecule

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

ROMol& RDKit::Bond::getOwningMol ( ) const [inline]

returns a reference to the ROMol that owns this Bond

Definition at line 141 of file Bond.h.

References dp_mol.

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

template<typename T >

void RDKit::Bond::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 332 of file Bond.h.

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

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

template<typename T >

void RDKit::Bond::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 338 of file Bond.h.

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

STR_VECT RDKit::Bond::getPropList ( ) const [inline]

returns a list with the names of our properties

Definition at line 283 of file Bond.h.

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

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

NOT CALLABLE.

Reimplemented in RDKit::QueryBond.

BondStereo RDKit::Bond::getStereo ( ) const [inline]

returns our stereo code

Definition at line 271 of file Bond.h.

References d_stereo.

const INT_VECT& RDKit::Bond::getStereoAtoms ( ) const [inline]

returns the indices of our stereo atoms

Definition at line 274 of file Bond.h.

References d_stereoAtoms.

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 276 of file Bond.h.

References d_stereoAtoms.

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

returns our contribution to the explicit valence of an Atom

Notes:

requires an owning molecule

double RDKit::Bond::getValenceContrib ( ATOM_SPTR at ) const

bool RDKit::Bond::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 350 of file Bond.h.

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

bool RDKit::Bond::hasProp ( const char * key ) const [inline]

returns whether or not we have a property with name key

Definition at line 345 of file Bond.h.

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

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

virtual bool RDKit::Bond::hasQuery ( ) const [inline, virtual]

Reimplemented in RDKit::QueryBond.

Definition at line 239 of file Bond.h.

void RDKit::Bond::initBond ( ) [protected]

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.

virtual bool RDKit::Bond::Match ( const Bond::BOND_SPTR what ) const [virtual]

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::QueryBond.

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

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

sets our begin Atom

Notes:

requires an owning molecule

void RDKit::Bond::setBeginAtom ( ATOM_SPTR at )

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

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

sets the index of our begin Atom

Notes:

requires an owning molecule

void RDKit::Bond::setBondDir ( BondDir what ) [inline]

sets our direction

Reimplemented in RDKit::QueryBond.

Definition at line 264 of file Bond.h.

References d_dirTag.

void RDKit::Bond::setBondType ( BondType bT ) [inline]

sets our bondType

Reimplemented in RDKit::QueryBond.

Definition at line 116 of file Bond.h.

References d_bondType.

void RDKit::Bond::setEndAtom ( ATOM_SPTR at )

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

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

sets our end Atom

Notes:

requires an owning molecule

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

sets the index of our end Atom

Notes:

requires an owning molecule

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

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 160 of file Bond.h.

References d_index.

void RDKit::Bond::setIsAromatic ( bool what ) [inline]

sets our isAromatic flag

Definition at line 131 of file Bond.h.

References df_isAromatic.

void RDKit::Bond::setIsConjugated ( bool what ) [inline]

sets our isConjugated flag

Definition at line 136 of file Bond.h.

References df_isConjugated.

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

sets our owning molecule

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

void RDKit::Bond::setOwningMol ( ROMol & other ) [inline]

sets our owning molecule

Definition at line 145 of file Bond.h.

References setOwningMol().

Referenced by setOwningMol().

template<typename T >

void RDKit::Bond::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 304 of file Bond.h.

References dp_props, getProp(), hasProp(), and RDKit::Dict::setVal().

template<typename T >

void RDKit::Bond::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`.