CDPL::Chem::ResonanceStructureGenerator Class Reference

Enumerates the resonance structures of a molecular graph by redistributing π-electrons across conjugated bonds. More...

#include <ResonanceStructureGenerator.hpp>

Classes
class	StructureData
	Data structure storing formal atom charges and bond orders that define a single resonance structure. More...

Public Types
typedef std::shared_ptr< ResonanceStructureGenerator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated ResonanceStructureGenerator instances. More...
typedef boost::indirect_iterator< StructureDataList::const_iterator, const StructureData >	ConstStructureDataIterator
	A constant random access iterator used to iterate over the generated const StructureData records. More...

Public Member Functions
	ResonanceStructureGenerator ()
	Constructs the ResonanceStructureGenerator instance. More...
	ResonanceStructureGenerator (const ResonanceStructureGenerator &gen)
	Constructs a copy of the ResonanceStructureGenerator instance gen. More...
virtual	~ResonanceStructureGenerator ()
	Virtual destructor. More...
ResonanceStructureGenerator &	operator= (const ResonanceStructureGenerator &gen)
	Replaces the state of this generator by a copy of the state of gen. More...
Util::BitSet &	getOctetRuleCheckAtomTypes ()
	Returns the bit mask of atom types subjected to the octet rule check during violation minimization. More...
const Util::BitSet &	getOctetRuleCheckAtomTypes () const
	Returns the bit mask of atom types subjected to the octet rule check during violation minimization. More...
void	minimizeOctetRuleViolations (bool minimize)
	Specifies whether resonance structures violating the octet rule shall be filtered out. More...
bool	octetRuleViolationsMinimized () const
	Tells whether octet rule violations are minimized. More...
void	minimizeSP1GeometryViolations (bool minimize)
	Specifies whether resonance structures with sp-hybridization geometry violations shall be filtered out. More...
bool	sp1GeometryViolationsMinimized () const
	Tells whether sp-hybridization geometry violations are minimized. More...
void	minimizeCarbonBond12Charges (bool minimize)
	Specifies whether resonance structures with 1,2-charge separations on adjacent carbon atoms shall be filtered out. More...
bool	carbonBond12ChargesMinimized () const
	Tells whether 1,2-charge separations on adjacent carbon atoms are minimized. More...
void	setChargeCountWindow (std::size_t win_size)
	Sets the maximum allowed difference between the lowest and highest total absolute formal atom charge count of accepted resonance structures. More...
std::size_t	getChargeCountWindow () const
	Returns the configured total absolute formal atom charge count window size. More...
void	setMaxNumGeneratedStructures (std::size_t max_num)
	Sets the upper limit on the number of resonance structures generated per molecular graph. More...
std::size_t	getMaxNumGeneratedStructures () const
	Returns the upper limit on the number of resonance structures generated per molecular graph. More...
void	generate (const MolecularGraph &molgraph)
	Generates all unique resonance structures of the molecular graph molgraph. More...
std::size_t	getNumStructures () const
	Returns the number of generated resonance structures. More...
const StructureData &	getStructureData (std::size_t idx) const
	Returns the resonance structure record at index idx. More...
ConstStructureDataIterator	getStructureDataBegin () const
	Returns a constant iterator pointing to the beginning of the generated const StructureData records. More...
ConstStructureDataIterator	getStructureDataEnd () const
	Returns a constant iterator pointing to the end of the generated const StructureData records. More...
ConstStructureDataIterator	begin () const
	Returns a constant iterator pointing to the beginning of the generated const StructureData records. More...
ConstStructureDataIterator	end () const
	Returns a constant iterator pointing to the end of the generated const StructureData records. More...

Detailed Description

Enumerates the resonance structures of a molecular graph by redistributing π-electrons across conjugated bonds.

For each generated resonance structure the formal atom charges and bond orders are reported as a StructureData record. Optional postprocessing minimizes octet rule violations, sp-hybridization geometry violations, and 1,2-charge separations on adjacent carbon atoms.

Member Typedef Documentation

SharedPointer

typedef std::shared_ptr<ResonanceStructureGenerator> CDPL::Chem::ResonanceStructureGenerator::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated ResonanceStructureGenerator instances.

ConstStructureDataIterator

typedef boost::indirect_iterator<StructureDataList::const_iterator, const StructureData> CDPL::Chem::ResonanceStructureGenerator::ConstStructureDataIterator

A constant random access iterator used to iterate over the generated const StructureData records.

Constructor & Destructor Documentation

ResonanceStructureGenerator() [1/2]

CDPL::Chem::ResonanceStructureGenerator::ResonanceStructureGenerator

(

)

Constructs the ResonanceStructureGenerator instance.

ResonanceStructureGenerator() [2/2]

CDPL::Chem::ResonanceStructureGenerator::ResonanceStructureGenerator

(

const ResonanceStructureGenerator &

gen

)

Constructs a copy of the ResonanceStructureGenerator instance gen.

Parameters

gen	The generator to copy.

~ResonanceStructureGenerator()

virtual CDPL::Chem::ResonanceStructureGenerator::~ResonanceStructureGenerator ( )

inlinevirtual

Virtual destructor.

Member Function Documentation

operator=()

ResonanceStructureGenerator& CDPL::Chem::ResonanceStructureGenerator::operator=

(

const ResonanceStructureGenerator &

gen

)

Replaces the state of this generator by a copy of the state of gen.

Parameters

gen	The generator to copy.

Returns

A reference to itself.

getOctetRuleCheckAtomTypes() [1/2]

Util::BitSet& CDPL::Chem::ResonanceStructureGenerator::getOctetRuleCheckAtomTypes

(

)

Returns the bit mask of atom types subjected to the octet rule check during violation minimization.

Returns

A reference to the bit mask (indexed by Chem::AtomType value).

getOctetRuleCheckAtomTypes() [2/2]

const Util::BitSet& CDPL::Chem::ResonanceStructureGenerator::getOctetRuleCheckAtomTypes

(

)

const

Returns the bit mask of atom types subjected to the octet rule check during violation minimization.

Returns

A const reference to the bit mask (indexed by Chem::AtomType value).

minimizeOctetRuleViolations()

void CDPL::Chem::ResonanceStructureGenerator::minimizeOctetRuleViolations

(

bool

minimize

)

Specifies whether resonance structures violating the octet rule shall be filtered out.

Parameters

minimize

If true, structures with octet rule violations on the configured atom types are minimized.

octetRuleViolationsMinimized()

bool CDPL::Chem::ResonanceStructureGenerator::octetRuleViolationsMinimized

(

)

const

Tells whether octet rule violations are minimized.

Returns

true if octet rule violations are minimized, and false otherwise.

minimizeSP1GeometryViolations()

void CDPL::Chem::ResonanceStructureGenerator::minimizeSP1GeometryViolations

(

bool

minimize

)

Specifies whether resonance structures with sp-hybridization geometry violations shall be filtered out.

Parameters

minimize

If true, sp-hybridization geometry violations are minimized.

sp1GeometryViolationsMinimized()

bool CDPL::Chem::ResonanceStructureGenerator::sp1GeometryViolationsMinimized

(

)

const

Tells whether sp-hybridization geometry violations are minimized.

Returns

true if sp-geometry violations are minimized, and false otherwise.

minimizeCarbonBond12Charges()

void CDPL::Chem::ResonanceStructureGenerator::minimizeCarbonBond12Charges

(

bool

minimize

)

Specifies whether resonance structures with 1,2-charge separations on adjacent carbon atoms shall be filtered out.

Parameters

minimize

If true, 1,2-charged carbon-carbon bonds are minimized.

carbonBond12ChargesMinimized()

bool CDPL::Chem::ResonanceStructureGenerator::carbonBond12ChargesMinimized

(

)

const

Tells whether 1,2-charge separations on adjacent carbon atoms are minimized.

Returns

true if 1,2-charged carbon-carbon bonds are minimized, and false otherwise.

setChargeCountWindow()

void CDPL::Chem::ResonanceStructureGenerator::setChargeCountWindow

(

std::size_t

win_size

)

Sets the maximum allowed difference between the lowest and highest total absolute formal atom charge count of accepted resonance structures.

Parameters

win_size

The new total absolute formal atom charge count window size.

getChargeCountWindow()

std::size_t CDPL::Chem::ResonanceStructureGenerator::getChargeCountWindow

(

)

const

Returns the configured total absolute formal atom charge count window size.

Returns

The total absolute formal atom charge count window size.

setMaxNumGeneratedStructures()

void CDPL::Chem::ResonanceStructureGenerator::setMaxNumGeneratedStructures

(

std::size_t

max_num

)

Sets the upper limit on the number of resonance structures generated per molecular graph.

Parameters

max_num

The new output structure limit.

getMaxNumGeneratedStructures()

std::size_t CDPL::Chem::ResonanceStructureGenerator::getMaxNumGeneratedStructures

(

)

const

Returns the upper limit on the number of resonance structures generated per molecular graph.

Returns

The output structure limit.

generate()

void CDPL::Chem::ResonanceStructureGenerator::generate

(

const MolecularGraph &

molgraph

)

Generates all unique resonance structures of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to generate the resonance structures.

getNumStructures()

std::size_t CDPL::Chem::ResonanceStructureGenerator::getNumStructures

(

)

const

Returns the number of generated resonance structures.

Returns

The resonance structure count.

getStructureData()

const StructureData& CDPL::Chem::ResonanceStructureGenerator::getStructureData

(

std::size_t

idx

)

const

Returns the resonance structure record at index idx.

Parameters

idx	The zero-based structure index.

Returns

A const reference to the resonance structure record.

Exceptions

Base::IndexError

if idx is not in the range [0, getNumStructures()).

getStructureDataBegin()

ConstStructureDataIterator CDPL::Chem::ResonanceStructureGenerator::getStructureDataBegin

(

)

const

Returns a constant iterator pointing to the beginning of the generated const StructureData records.

Returns

A constant iterator pointing to the beginning of the generated const StructureData records.

getStructureDataEnd()

ConstStructureDataIterator CDPL::Chem::ResonanceStructureGenerator::getStructureDataEnd

(

)

const

Returns a constant iterator pointing to the end of the generated const StructureData records.

Returns

A constant iterator pointing to the end of the generated const StructureData records.

begin()

ConstStructureDataIterator CDPL::Chem::ResonanceStructureGenerator::begin

(

)

const

Returns a constant iterator pointing to the beginning of the generated const StructureData records.

Returns

A constant iterator pointing to the beginning of the generated const StructureData records.

end()

ConstStructureDataIterator CDPL::Chem::ResonanceStructureGenerator::end

(

)

const

Returns a constant iterator pointing to the end of the generated const StructureData records.

Returns

A constant iterator pointing to the end of the generated const StructureData records.

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

• ResonanceStructureGenerator.hpp