RDKit::ResonanceMolSupplier Class Reference

#include <Resonance.h>

Public Types
enum	ResonanceFlags {   ALLOW_INCOMPLETE_OCTETS = (1 << 0), ALLOW_CHARGE_SEPARATION = (1 << 1), KEKULE_ALL = (1 << 2), UNCONSTRAINED_CATIONS = (1 << 3),   UNCONSTRAINED_ANIONS = (1 << 4) }

Public Member Functions
	ResonanceMolSupplier (ROMol &mol, unsigned int flags=0, unsigned int maxStructs=1000)
	~ResonanceMolSupplier ()
const ROMol &	mol () const
unsigned int	flags () const
unsigned int	getNumConjGrps () const
int	getBondConjGrpIdx (unsigned int bi) const
int	getAtomConjGrpIdx (unsigned int ai) const
void	setNumThreads (int numThreads=1)
void	enumerate ()
bool	getIsEnumerated ()
unsigned int	length ()
void	reset ()
bool	atEnd ()
ROMol *	next ()
void	moveTo (unsigned int idx)
ROMol *	operator[] (unsigned int idx)

Detailed Description

Definition at line 32 of file Resonance.h.

Member Enumeration Documentation

ResonanceFlags

enum RDKit::ResonanceMolSupplier::ResonanceFlags

Enumerator
ALLOW_INCOMPLETE_OCTETS	include resonance structures whose octets are less complete than the the most octet-complete structure
ALLOW_CHARGE_SEPARATION	include resonance structures featuring charge separation also when uncharged resonance structures exist
KEKULE_ALL	enumerate all possible degenerate Kekule resonance structures (the default is to include just one)
UNCONSTRAINED_CATIONS	if the UNCONSTRAINED_CATIONS flag is not set, positively charged atoms left and right of N with an incomplete octet are acceptable only if the conjugated group has a positive total formal charge
UNCONSTRAINED_ANIONS	if the UNCONSTRAINED_ANIONS flag is not set, negatively charged atoms left of N are acceptable only if the conjugated group has a negative total formal charge

Definition at line 34 of file Resonance.h.

Constructor & Destructor Documentation

ResonanceMolSupplier()

RDKit::ResonanceMolSupplier::ResonanceMolSupplier	(	ROMol &	mol,
		unsigned int	flags = 0,
		unsigned int	maxStructs = 1000
	)

Parameters

mol	- the starter molecule
flags	- flags which influence criteria to generate resonance structures
maxStructs	- maximum number of complete resonance structures generated
numThreads	- the number of threads used to carry out the resonance structure enumeration (defaults to 1; 0 selects the number of concurrent threads supported by the hardware; negative values are added to the number of concurrent threads supported by the hardware)

Referenced by getIsEnumerated().

~ResonanceMolSupplier()

RDKit::ResonanceMolSupplier::~ResonanceMolSupplier

(

)

Member Function Documentation

atEnd()

bool RDKit::ResonanceMolSupplier::atEnd

(

)

Returns true if there are no more resonance structures left

Referenced by getIsEnumerated().

enumerate()

void RDKit::ResonanceMolSupplier::enumerate

(

)

Ask ResonanceMolSupplier to enumerate resonance structures (automatically done as soon as any attempt to access them is made)

Referenced by getNumConjGrps().

flags()

unsigned int RDKit::ResonanceMolSupplier::flags ( ) const

inline

Returns the flags the ResonanceMolSupplier was initialized with

Definition at line 76 of file Resonance.h.

getAtomConjGrpIdx()

int RDKit::ResonanceMolSupplier::getAtomConjGrpIdx

(

unsigned int

ai

)

const

Given an atom index, it returns the index of the conjugated group the atom belongs to, or -1 if it is not conjugated

Referenced by getNumConjGrps().

getBondConjGrpIdx()

int RDKit::ResonanceMolSupplier::getBondConjGrpIdx

(

unsigned int

bi

)

const

Given a bond index, it returns the index of the conjugated group the bond belongs to, or -1 if it is not conjugated

Referenced by getNumConjGrps().

getIsEnumerated()

bool RDKit::ResonanceMolSupplier::getIsEnumerated ( )

inline

Returns true if resonance structure enumeration has already happened

Definition at line 98 of file Resonance.h.

References atEnd(), length(), mol(), moveTo(), next(), operator[](), reset(), and ResonanceMolSupplier().

getNumConjGrps()

unsigned int RDKit::ResonanceMolSupplier::getNumConjGrps ( ) const

inline

Returns the number of individual conjugated groups in the molecule

Definition at line 79 of file Resonance.h.

References enumerate(), getAtomConjGrpIdx(), getBondConjGrpIdx(), and setNumThreads().

length()

unsigned int RDKit::ResonanceMolSupplier::length

(

)

Returns the number of resonance structures in the ResonanceMolSupplier

Referenced by getIsEnumerated().

mol()

const ROMol& RDKit::ResonanceMolSupplier::mol ( ) const

inline

Returns a reference to the Kekulized form of the ROMol the ResonanceMolSupplier was initialized with

Definition at line 73 of file Resonance.h.

Referenced by getIsEnumerated().

moveTo()

void RDKit::ResonanceMolSupplier::moveTo

(

unsigned int

idx

)

Sets the ResonanceMolSupplier index to idx

Referenced by getIsEnumerated().

next()

ROMol* RDKit::ResonanceMolSupplier::next

(

)

Returns a pointer to the next resonance structure as a ROMol, or NULL if there are no more resonance structures left. The caller is responsible for freeing memory associated to the pointer

Referenced by getIsEnumerated().

operator[]()

ROMol* RDKit::ResonanceMolSupplier::operator[]

(

unsigned int

idx

)

Returns a pointer to the resonance structure with index idx as a ROMol. The index generates complete resonance structures by combining ConjElectrons objects for the respective conjugated groups in a breadth-first fashion, in order to return the most stable complete resonance structures first. The caller is responsible for freeing memory associated to the pointer

Referenced by getIsEnumerated().

reset()

void RDKit::ResonanceMolSupplier::reset

(

)

Resets the ResonanceMolSupplier index

Referenced by getIsEnumerated().

setNumThreads()

void RDKit::ResonanceMolSupplier::setNumThreads

(

int

numThreads = 1

)

Sets the number of threads to be used to enumerate resonance structures (defaults to 1; 0 selects the number of concurrent threads supported by the hardware; negative values are added to the number of concurrent threads supported by the hardware)

Referenced by getNumConjGrps().

---

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

• Resonance.h