CDPL.Chem.BondOrderCalculator Class Reference

Perceives bond orders of a molecular graph from its 3D structure and atom connectivity. More...

Inheritance diagram for CDPL.Chem.BondOrderCalculator:

Public Member Functions
None	__init__ ()
	Constructs the BondOrderCalculator instance.
None	__init__ (MolecularGraph molgraph, Util.STArray orders, bool undef_only=True)
	Constructs the BondOrderCalculator instance and perceives the order of the bonds in the molecular graph molgraph. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	undefinedOnly (bool undef_only)
	Allows to specify whether already defined bond orders should be left unchanged. More...
bool	undefinedOnly ()
	Tells whether or not only undefined bond orders have to be perceived. More...
None	calculate (MolecularGraph molgraph, Util.STArray orders)
	Perceives the order of the bonds in the molecular graph molgraph from its 3D structure and atom connectivity. More...

Properties
	objectID = property(getObjectID)
	undefOnly = property(undefinedOnly, undefinedOnly)

Detailed Description

Perceives bond orders of a molecular graph from its 3D structure and atom connectivity.

The calculator combines per-atom geometry analysis (linear, trigonal-planar, tetrahedral, ...), functional-group substructure matching, conjugated π-system detection, and free-valence accounting to assign single, double, or triple bonds. By default only bonds whose order is currently undefined are assigned; this can be toggled via undefinedOnly().

Constructor & Destructor Documentation

__init__()

None CDPL.Chem.BondOrderCalculator.__init__	(	MolecularGraph	molgraph,
		Util.STArray	orders,
		bool	undef_only = True
	)

Constructs the BondOrderCalculator instance and perceives the order of the bonds in the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to perceive the bond orders.
orders	An array containing the perceived bond orders. The orders are stored in the same sequence as the bonds appear in the input molecular graph, i.e. the order of a particular bond is accessible via its index in the molecular graph.
undef_only	Specifies whether or not to perceive only undefined (= unset) bond orders.

Member Function Documentation

getObjectID()

int CDPL.Chem.BondOrderCalculator.getObjectID

(

)

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

Different Python BondOrderCalculator 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 BondOrderCalculator 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.

undefinedOnly() [1/2]

None CDPL.Chem.BondOrderCalculator.undefinedOnly

(

bool

undef_only

)

Allows to specify whether already defined bond orders should be left unchanged.

Parameters

undef_only

Specifies whether or not to perceive only undefined (= unset) bond orders.

Note

The default setting is to perceive only the order of undefined bonds.

undefinedOnly() [2/2]

bool CDPL.Chem.BondOrderCalculator.undefinedOnly

(

)

Tells whether or not only undefined bond orders have to be perceived.

Returns

True if only undefined (= unset) bond orders are perceived, and False otherwise.

calculate()

None CDPL.Chem.BondOrderCalculator.calculate	(	MolecularGraph	molgraph,
		Util.STArray	orders
	)

Perceives the order of the bonds in the molecular graph molgraph from its 3D structure and atom connectivity.

Parameters

molgraph	The molecular graph for which to perceive the bond orders.
orders	An array containing the perceived bond orders. The orders are stored in the same sequence as the bonds appear in the input molecular graph, i.e. the order of a particular bond is accessible via its index in the molecular graph.