RDKit::Atom Class Reference

The class for representing atoms. More...

#include <Atom.h>

Inheritance diagram for RDKit::Atom:

List of all members.

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
	Atom (std::string what)
	construct an Atom with a particular symbol (looked up in the PeriodicTable)
	Atom (const Atom &other)
virtual	~Atom ()
virtual Atom *	copy () const
	makes a copy of this Atom and returns a pointer to it.
const 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)
ROMol &	getOwningMol () const
	returns a reference to the ROMol that owns this Atom
const unsigned int	getIdx () const
	returns our index within the ROMol
void	setIdx (unsigned int index)
	sets our index within the ROMol
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	getNumImplicitHs () const
	returns the number of implicit Hs this Atom is bound to
int	getExplicitValence () const
	returns the number of explicit Hs this Atom is bound to
int	getImplicitValence () const
	returns the implicit valence for this Atom
unsigned int	getNumRadicalElectrons () const
	returns the number of radical electrons for this Atom
void	setNumRadicalElectrons (unsigned int num)
const 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 explict Hs
unsigned int	getNumExplicitHs () const
	returns our number of explict Hs
void	setIsAromatic (bool what)
	sets our isAromatic flag, indicating whether or not we are aromatic
bool	getIsAromatic () const
	returns our isAromatic flag
void	setMass (double what)
	sets our mass (for isotopes)
double	getMass () const
	returns our mass
void	setDativeFlag (int what)
	sets our dativeFlag
int	getDativeFlag () const
	returns our dativeFlag
bool	hasDativeFlag (int what) const
void	clearDativeFlag ()
	clears our dativeFlag
void	setChiralTag (ChiralType what)
	sets our chiralTag
void	invertChirality ()
	inverts our chiralTag
ChiralType	getChiralTag () const
	returns our chiralTag
void	setHybridization (HybridizationType what)
	sets our hybridization
HybridizationType	getHybridization () const
	returns our hybridization
virtual bool	hasQuery () const
virtual void	setQuery (QUERYATOM_QUERY *what)
	NOT CALLABLE.
virtual QUERYATOM_QUERY *	getQuery () const
	NOT CALLABLE.
virtual void	expandQuery (QUERYATOM_QUERY *what, Queries::CompositeQueryType how=Queries::COMPOSITE_AND, bool maintainOrder=true)
	NOT CALLABLE.
virtual bool	Match (Atom const *what) const
	returns whether or not we match the argument
virtual bool	Match (const ATOM_SPTR what) const
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
int	getPerturbationOrder (INT_LIST probe) const
	returns the perturbation order for a list of integers
void	updatePropertyCache (bool strict=true)
	calculates any of our lazy properties
int	calcExplicitValence (bool strict=true)
	calculates and returns our explicit valence
int	calcImplicitValence (bool strict=true)
	calculates and returns our implicit valence
Protected Member Functions
void	setOwningMol (ROMol *other)
	sets our owning molecule
void	setOwningMol (ROMol &other)
	sets our owning molecule
void	initAtom ()
Protected Attributes
bool	df_isAromatic
bool	df_noImplicit
int	d_dativeFlag
unsigned int	d_numExplicitHs
int	d_formalCharge
unsigned int	d_atomicNum
unsigned int	d_index
int	d_implicitValence
int	d_explicitValence
unsigned int	d_numRadicalElectrons
ChiralType	d_chiralTag
HybridizationType	d_hybrid
double	d_mass
ROMol *	dp_mol
Dict *	dp_props
Friends
class	MolPickler
	the pickler needs access to our privates
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

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 represenation of chirality

Definition at line 56 of file Atom.h.

---

Member Typedef Documentation

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

Definition at line 62 of file Atom.h.

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

Definition at line 63 of file Atom.h.

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

Reimplemented in RDKit::QueryAtom.

Definition at line 65 of file Atom.h.

---

Member Enumeration Documentation

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 68 of file Atom.h.

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 80 of file Atom.h.

---

Constructor & Destructor Documentation

RDKit::Atom::Atom

(

)

RDKit::Atom::Atom

(

unsigned int

num

)

[explicit]

construct an Atom with a particular atomic number

RDKit::Atom::Atom

(

std::string

what

)

[explicit]

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

RDKit::Atom::Atom

(

const Atom &

other

)

virtual RDKit::Atom::~Atom

(

)

[virtual]

---

Member Function Documentation

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.

const int RDKit::Atom::getAtomicNum

(

)

const [inline]

returns our atomic number

Definition at line 102 of file Atom.h.

References d_atomicNum.

Referenced by RDKit::queryAtomNum().

void RDKit::Atom::setAtomicNum

(

int

newNum

)

[inline]

sets our atomic number

Definition at line 104 of file Atom.h.

References d_atomicNum.

std::string RDKit::Atom::getSymbol

(

)

const

returns our symbol (determined by our atomic number)

ROMol& RDKit::Atom::getOwningMol

(

)

const [inline]

returns a reference to the ROMol that owns this Atom

Definition at line 110 of file Atom.h.

References dp_mol.

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

const unsigned int RDKit::Atom::getIdx

(

)

const [inline]

returns our index within the ROMol

Definition at line 113 of file Atom.h.

References d_index.

Referenced by RDKit::SLNParse::addAtomToMol(), RDKit::RecursiveStructureQuery::getAtIdx(), RDKit::queryAtomIsInRingOfSize(), RDKit::queryAtomMinRingSize(), RDKit::queryAtomRingMembership(), RDKit::queryIsAtomInNRings(), and RDKit::queryIsAtomInRing().

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 120 of file Atom.h.

References d_index.

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 RDKit::queryAtomExplicitDegree(), RDKit::queryAtomHeavyAtomDegree(), RDKit::queryAtomTotalDegree(), and RDKit::queryAtomUnsaturated().

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

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::queryAtomHCount().

unsigned int RDKit::Atom::getNumImplicitHs

(

)

const

returns the number of implicit Hs this Atom is bound to

Notes:

• requires an owning molecule

int RDKit::Atom::getExplicitValence

(

)

const

returns the number of explicit Hs this Atom is bound to

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

int RDKit::Atom::getImplicitValence

(

)

const

returns the implicit valence for this Atom

Notes:

• requires an owning molecule

Referenced by RDKit::queryAtomImplicitValence(), RDKit::queryAtomTotalDegree(), and RDKit::queryAtomTotalValence().

unsigned int RDKit::Atom::getNumRadicalElectrons

(

)

const [inline]

returns the number of radical electrons for this Atom

Notes:

• requires an owning molecule

Definition at line 168 of file Atom.h.

References d_numRadicalElectrons.

void RDKit::Atom::setNumRadicalElectrons

(

unsigned int

num

)

[inline]

Definition at line 169 of file Atom.h.

References d_numRadicalElectrons.

const int RDKit::Atom::getFormalCharge

(

)

const [inline]

returns the formal charge of this atom

Definition at line 173 of file Atom.h.

References d_formalCharge.

Referenced by RDKit::queryAtomFormalCharge().

void RDKit::Atom::setFormalCharge

(

int

what

)

[inline]

set's the formal charge of this atom

Definition at line 175 of file Atom.h.

References d_formalCharge.

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 179 of file Atom.h.

References df_noImplicit.

bool RDKit::Atom::getNoImplicit

(

)

const [inline]

returns the noImplicit flag

Definition at line 181 of file Atom.h.

References df_noImplicit.

void RDKit::Atom::setNumExplicitHs

(

unsigned int

what

)

[inline]

sets our number of explict Hs

Definition at line 184 of file Atom.h.

References d_numExplicitHs.

unsigned int RDKit::Atom::getNumExplicitHs

(

)

const [inline]

returns our number of explict Hs

Definition at line 186 of file Atom.h.

References d_numExplicitHs.

Referenced by RDKit::queryAtomExplicitValence().

void RDKit::Atom::setIsAromatic

(

bool

what

)

[inline]

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

Definition at line 189 of file Atom.h.

References df_isAromatic.

bool RDKit::Atom::getIsAromatic

(

)

const [inline]

returns our isAromatic flag

Definition at line 191 of file Atom.h.

References df_isAromatic.

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

void RDKit::Atom::setMass

(

double

what

)

[inline]

sets our mass (for isotopes)

Definition at line 194 of file Atom.h.

References d_mass.

double RDKit::Atom::getMass

(

)

const [inline]

returns our mass

Definition at line 196 of file Atom.h.

References d_mass.

Referenced by RDKit::queryAtomMass().

void RDKit::Atom::setDativeFlag

(

int

what

)

[inline]

sets our dativeFlag

Definition at line 201 of file Atom.h.

References d_dativeFlag.

int RDKit::Atom::getDativeFlag

(

)

const [inline]

returns our dativeFlag

Definition at line 206 of file Atom.h.

References d_dativeFlag.

bool RDKit::Atom::hasDativeFlag

(

int

what

)

const [inline]

Definition at line 209 of file Atom.h.

References d_dativeFlag.

void RDKit::Atom::clearDativeFlag

(

)

[inline]

clears our dativeFlag

Definition at line 214 of file Atom.h.

References d_dativeFlag.

void RDKit::Atom::setChiralTag

(

ChiralType

what

)

[inline]

sets our chiralTag

Definition at line 217 of file Atom.h.

References d_chiralTag.

void RDKit::Atom::invertChirality

(

)

inverts our chiralTag

ChiralType RDKit::Atom::getChiralTag

(

)

const [inline]

returns our chiralTag

Definition at line 221 of file Atom.h.

References d_chiralTag.

void RDKit::Atom::setHybridization

(

HybridizationType

what

)

[inline]

sets our hybridization

Definition at line 224 of file Atom.h.

References d_hybrid.

HybridizationType RDKit::Atom::getHybridization

(

)

const [inline]

returns our hybridization

Definition at line 226 of file Atom.h.

References d_hybrid.

Referenced by RDKit::queryAtomHybridization().

virtual bool RDKit::Atom::hasQuery

(

)

const [inline, virtual]

Reimplemented in RDKit::QueryAtom.

Definition at line 241 of file Atom.h.

virtual void RDKit::Atom::setQuery

(

QUERYATOM_QUERY *

what

)

[virtual]

NOT CALLABLE.

Reimplemented in RDKit::QueryAtom.

virtual QUERYATOM_QUERY* RDKit::Atom::getQuery

(

)

const [virtual]

NOT CALLABLE.

Reimplemented in RDKit::QueryAtom.

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

NOT CALLABLE.

Reimplemented in RDKit::QueryAtom.

virtual bool RDKit::Atom::Match

(

Atom const *

what

)

const [virtual]

returns whether or not we match the argument

Notes:

• for Atom objects, "match" means that atomic numbers are the same.

Reimplemented in RDKit::QueryAtom.

virtual bool RDKit::Atom::Match

(

const ATOM_SPTR

what

)

const [virtual]

Reimplemented in RDKit::QueryAtom.

STR_VECT RDKit::Atom::getPropList

(

)

const [inline]

returns a list with the names of our properties

Definition at line 269 of file Atom.h.

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

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 283 of file Atom.h.

template<typename T>

void RDKit::Atom::setProp	(	const std::string	key,
		T	val,
		bool	computed = false
	)			const [inline]

Definition at line 292 of file Atom.h.

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

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 320 of file Atom.h.

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

Referenced by RDKit::SLNParse::bookmarkAtomID(), clearComputedProps(), clearProp(), and setProp().

template<typename T>

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

Definition at line 326 of file Atom.h.

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

bool RDKit::Atom::hasProp

(

const char *

key

)

const [inline]

returns whether or not we have a property with name key

Definition at line 332 of file Atom.h.

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

Referenced by RDKit::SLNParse::bookmarkAtomID(), clearComputedProps(), clearProp(), and setProp().

bool RDKit::Atom::hasProp

(

const std::string

key

)

const [inline]

Definition at line 337 of file Atom.h.

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

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 351 of file Atom.h.

void RDKit::Atom::clearProp

(

const std::string

key

)

const [inline]

Definition at line 356 of file Atom.h.

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

void RDKit::Atom::clearComputedProps

(

)

const [inline]

clears all of our computed properties

Definition at line 370 of file Atom.h.

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

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

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

int RDKit::Atom::calcExplicitValence

(

bool

strict = true

)

calculates and returns our explicit valence

Notes:

• requires an owning molecule

int RDKit::Atom::calcImplicitValence

(

bool

strict = true

)

calculates and returns our implicit valence

Notes:

• requires an owning molecule

void RDKit::Atom::setOwningMol

(

ROMol *

other

)

[protected]

sets our owning molecule

Referenced by setOwningMol().

void RDKit::Atom::setOwningMol

(

ROMol &

other

)

[inline, protected]

sets our owning molecule

Definition at line 434 of file Atom.h.

References setOwningMol().

void RDKit::Atom::initAtom

(

)

[protected]

---

Friends And Related Function Documentation

friend class MolPickler [friend]

the pickler needs access to our privates

Definition at line 57 of file Atom.h.

friend class ROMol [friend]

Definition at line 58 of file Atom.h.

friend class RWMol [friend]

Definition at line 59 of file Atom.h.

---

Member Data Documentation

bool RDKit::Atom::df_isAromatic [protected]

Definition at line 434 of file Atom.h.

Referenced by getIsAromatic(), and setIsAromatic().

bool RDKit::Atom::df_noImplicit [protected]

Definition at line 437 of file Atom.h.

Referenced by getNoImplicit(), and setNoImplicit().

int RDKit::Atom::d_dativeFlag [protected]

Definition at line 438 of file Atom.h.

Referenced by clearDativeFlag(), getDativeFlag(), hasDativeFlag(), and setDativeFlag().

unsigned int RDKit::Atom::d_numExplicitHs [protected]

Definition at line 439 of file Atom.h.

Referenced by getNumExplicitHs(), and setNumExplicitHs().

int RDKit::Atom::d_formalCharge [protected]

Definition at line 440 of file Atom.h.

Referenced by getFormalCharge(), and setFormalCharge().

unsigned int RDKit::Atom::d_atomicNum [protected]

Definition at line 441 of file Atom.h.

Referenced by getAtomicNum(), and setAtomicNum().

unsigned int RDKit::Atom::d_index [protected]

Definition at line 442 of file Atom.h.

Referenced by getIdx(), and setIdx().

int RDKit::Atom::d_implicitValence [protected]

Definition at line 446 of file Atom.h.

int RDKit::Atom::d_explicitValence [protected]

Definition at line 446 of file Atom.h.

unsigned int RDKit::Atom::d_numRadicalElectrons [protected]

Definition at line 447 of file Atom.h.

Referenced by getNumRadicalElectrons(), and setNumRadicalElectrons().

ChiralType RDKit::Atom::d_chiralTag [protected]

Definition at line 448 of file Atom.h.

Referenced by getChiralTag(), and setChiralTag().

HybridizationType RDKit::Atom::d_hybrid [protected]

Definition at line 449 of file Atom.h.

Referenced by getHybridization(), and setHybridization().

double RDKit::Atom::d_mass [protected]

Definition at line 450 of file Atom.h.

Referenced by getMass(), and setMass().

ROMol* RDKit::Atom::dp_mol [protected]

Definition at line 451 of file Atom.h.

Referenced by getOwningMol().

Dict* RDKit::Atom::dp_props [protected]

Definition at line 452 of file Atom.h.

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

---

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

• Atom.h