CDPL.Chem.ResonanceStructureGenerator Class Reference

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

Inheritance diagram for CDPL.Chem.ResonanceStructureGenerator:

Classes
class	StructureData
	Holds the per-atom formal charges and per-bond bond-orders that define a single resonance structure. More...

Public Member Functions
None	__init__ ()
	Constructs the ResonanceStructureGenerator instance.
None	__init__ (ResonanceStructureGenerator gen)
	Constructs a copy of the ResonanceStructureGenerator instance gen. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
ResonanceStructureGenerator	assign (ResonanceStructureGenerator gen)
	Replaces the state of this generator by a copy of the state of gen. More...
bool	octetRuleViolationsMinimized ()
	Tells whether octet-rule violations are minimized. More...
None	minimizeOctetRuleViolations (bool minimize)
	Specifies whether resonance structures violating the octet rule shall be filtered out. More...
bool	sp1GeometryViolationsMinimized ()
	Tells whether sp-hybridization-geometry violations are minimized. More...
None	minimizeSP1GeometryViolations (bool minimize)
	Specifies whether resonance structures with sp-hybridization-geometry violations shall be filtered out. More...
bool	carbonBond12ChargesMinimized ()
	Tells whether 1,2-charge separations on adjacent carbon atoms are minimized. More...
None	minimizeCarbonBond12Charges (bool minimize)
	Specifies whether resonance structures with 1,2-charge separations on adjacent carbon atoms shall be filtered out. More...
Util.BitSet	getOctetRuleCheckAtomTypes ()
	Returns the bit mask of atom types subjected to the octet-rule check during minimization. More...
int	getChargeCountWindow ()
	Returns the configured charge-count window size. More...
None	setChargeCountWindow (int win_size)
	Sets the maximum allowed difference between the lowest and highest formal charge count of accepted resonance structures. More...
int	getMaxNumGeneratedStructures ()
	Returns the upper limit on the number of resonance structures generated per molecule. More...
None	setMaxNumGeneratedStructures (int max_num)
	Sets the upper limit on the number of resonance structures generated per molecule. More...
None	generate (MolecularGraph molgraph)
	Generates all unique resonance structures of the molecular graph molgraph. More...
int	getNumStructures ()
	Returns the number of generated resonance structures. More...
StructureData	getStructureData (int idx)
	Returns the resonance-structure record at index idx. More...
StructureData	__getitem__ (int idx)
int	__len__ ()

Properties
	objectID = property(getObjectID)
	numStructures = property(getNumStructures)
	minOctetRuleViolations = property(octetRuleViolationsMinimized, minimizeOctetRuleViolations)
	minSP1GeometryViolations = property(sp1GeometryViolationsMinimized, minimizeSP1GeometryViolations)
	minCarbonBond12Charges = property(carbonBond12ChargesMinimized, minimizeCarbonBond12Charges)
	octetRuleCheckAtomTypes = property(getOctetRuleCheckAtomTypes)
	chargeCountWindow = property(getChargeCountWindow, setChargeCountWindow)
	maxNumGeneratedStructures = property(getMaxNumGeneratedStructures, setMaxNumGeneratedStructures)

Detailed Description

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

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

Constructor & Destructor Documentation

__init__()

None CDPL.Chem.ResonanceStructureGenerator.__init__

(

ResonanceStructureGenerator

gen

)

Constructs a copy of the ResonanceStructureGenerator instance gen.

Parameters

gen	The ResonanceStructureGenerator to copy.

Member Function Documentation

getObjectID()

int CDPL.Chem.ResonanceStructureGenerator.getObjectID

(

)

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python ResonanceStructureGenerator instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two ResonanceStructureGenerator instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns

The numeric ID of the internally referenced C++ class instance.

assign()

ResonanceStructureGenerator CDPL.Chem.ResonanceStructureGenerator.assign

(

ResonanceStructureGenerator

gen

)

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

Parameters

gen	The source ResonanceStructureGenerator.

Returns

self

octetRuleViolationsMinimized()

bool CDPL.Chem.ResonanceStructureGenerator.octetRuleViolationsMinimized

(

)

Tells whether octet-rule violations are minimized.

Returns

True if octet-rule violations are minimized, and False otherwise.

minimizeOctetRuleViolations()

None 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.

sp1GeometryViolationsMinimized()

bool CDPL.Chem.ResonanceStructureGenerator.sp1GeometryViolationsMinimized

(

)

Tells whether sp-hybridization-geometry violations are minimized.

Returns

True if sp-geometry violations are minimized, and False otherwise.

minimizeSP1GeometryViolations()

None 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.

carbonBond12ChargesMinimized()

bool CDPL.Chem.ResonanceStructureGenerator.carbonBond12ChargesMinimized

(

)

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

Returns

True if 1,2-charged C−C resonance forms are minimized, and False otherwise.

minimizeCarbonBond12Charges()

None 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 C−C resonance forms are minimized.

getOctetRuleCheckAtomTypes()

Util.BitSet CDPL.Chem.ResonanceStructureGenerator.getOctetRuleCheckAtomTypes

(

)

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

Returns

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

getChargeCountWindow()

int CDPL.Chem.ResonanceStructureGenerator.getChargeCountWindow

(

)

Returns the configured charge-count window size.

Returns

The charge-count window size.

setChargeCountWindow()

None CDPL.Chem.ResonanceStructureGenerator.setChargeCountWindow

(

int

win_size

)

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

Parameters

win_size

The new charge-count window size.

getMaxNumGeneratedStructures()

int CDPL.Chem.ResonanceStructureGenerator.getMaxNumGeneratedStructures

(

)

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

Returns

The output-structure limit.

setMaxNumGeneratedStructures()

None CDPL.Chem.ResonanceStructureGenerator.setMaxNumGeneratedStructures

(

int

max_num

)

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

Parameters

max_num

The new output-structure limit.

generate()

None CDPL.Chem.ResonanceStructureGenerator.generate

(

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()

int CDPL.Chem.ResonanceStructureGenerator.getNumStructures

(

)

Returns the number of generated resonance structures.

Returns

The resonance-structure count.

getStructureData()

StructureData CDPL.Chem.ResonanceStructureGenerator.getStructureData

(

int

idx

)

Returns the resonance-structure record at index idx.

Parameters

idx	The zero-based structure index.

Returns

A reference to the resonance-structure record.

Exceptions

Base.IndexError

if the number of resonance structures is zero or idx is not in the range [0, getNumStructures() - 1].

__getitem__()

StructureData CDPL.Chem.ResonanceStructureGenerator.__getitem__

(

int

idx

)

Parameters

idx

Returns

__len__()

int CDPL.Chem.ResonanceStructureGenerator.__len__

(

)

Returns