CDPL.Chem.SymmetryClassCalculator Class Reference

SymmetryClassCalculator. More...

Inheritance diagram for CDPL.Chem.SymmetryClassCalculator:

Public Member Functions
None	__init__ ()
	Constructs the SymmetryClassCalculator instance.
None	__init__ (MolecularGraph molgraph, Util.STArray class_ids)
	Constructs the SymmetryClassCalculator instance and perceives the topological symmetry classes of the atoms in the molecular graph molgraph. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	setAtomPropertyFlags (int flags)
	Allows to specify the set of atomic properties that has to be considered in the perception of topological symmetry classes. More...
None	setBondPropertyFlags (int flags)
	Allows to specify the set of bond properties that has to be considered in the perception of topological symmetry classes. More...
None	includeImplicitHydrogens (bool include)
	Allows to specify whether implicit hydrogen atoms shall be ignored or treated in the same way as explicit ones. More...
int	getAtomPropertyFlags ()
	Returns the set of atomic properties that gets considered in the perception of topological symmetry classes. More...
int	getBondPropertyFlags ()
	Returns the set of bond properties that gets considered in the perception of topological symmetry classes. More...
bool	implicitHydrogensIncluded ()
	Tells whether implicit hydrogen atoms are ignored or treated in the same way as explicit ones. More...
None	calculate (MolecularGraph molgraph, Util.STArray class_ids)
	Perceives the topological symmetry classes of the atoms in the molecular graph molgraph. More...

Static Public Attributes
int	DEF_ATOM_PROPERTY_FLAGS = 158
	Specifies the default set of atomic properties considered in the perception of topological symmetry classes.
int	DEF_BOND_PROPERTY_FLAGS = 10
	Specifies the default set of bond properties considered in the perception of topological symmetry classes.

Properties
	objectID = property(getObjectID)
	atomPropertyFlags = property(getAtomPropertyFlags, setAtomPropertyFlags)
	bondPropertyFlags = property(getBondPropertyFlags, setBondPropertyFlags)
	hydrogenComplete = property(implicitHydrogensIncluded, includeImplicitHydrogens)

Detailed Description

SymmetryClassCalculator.

See also

[TOPSY]

Constructor & Destructor Documentation

__init__()

None CDPL.Chem.SymmetryClassCalculator.__init__	(	MolecularGraph	molgraph,
		Util.STArray	class_ids
	)

Constructs the SymmetryClassCalculator instance and perceives the topological symmetry classes of the atoms in the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to perceive the symmetry classes.
class_ids	An array containing the perceived symmetry class IDs. The class IDs are stored in the same order as the atoms appear in the atom list of the molecular graph (i.e. the symmetry class of an atom is accessible via its index).

Member Function Documentation

getObjectID()

int CDPL.Chem.SymmetryClassCalculator.getObjectID

(

)

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

Different Python SymmetryClassCalculator 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 SymmetryClassCalculator 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.

setAtomPropertyFlags()

None CDPL.Chem.SymmetryClassCalculator.setAtomPropertyFlags

(

int

flags

)

Allows to specify the set of atomic properties that has to be considered in the perception of topological symmetry classes.

The flags argument is an OR combination of the constants defined in namespace Chem.AtomPropertyFlag. Supported property flags are:

• Chem.AtomPropertyFlag.TYPE
• Chem.AtomPropertyFlag.ISOTOPE
• Chem.AtomPropertyFlag.FORMAL_CHARGE
• Chem.AtomPropertyFlag.AROMATICITY
• and Chem.AtomPropertyFlag.H_COUNT

Parameters

flags

The set of atomic properties to consider.

Note

The default set of atomic properties is specified by SymmetryClassCalculator.DEF_ATOM_PROPERTY_FLAGS.

setBondPropertyFlags()

None CDPL.Chem.SymmetryClassCalculator.setBondPropertyFlags

(

int

flags

)

Allows to specify the set of bond properties that has to be considered in the perception of topological symmetry classes.

The flags argument is an OR combination of the constants defined in namespace Chem.BondPropertyFlag. Supported property flags are:

• Chem.BondPropertyFlag.ORDER
• and Chem.BondPropertyFlag.AROMATICITY

Parameters

flags

The set of bond properties to consider.

Note

The default set of bond properties is specified by SymmetryClassCalculator.DEF_BOND_PROPERTY_FLAGS.

includeImplicitHydrogens()

None CDPL.Chem.SymmetryClassCalculator.includeImplicitHydrogens

(

bool

include

)

Allows to specify whether implicit hydrogen atoms shall be ignored or treated in the same way as explicit ones.

Parameters

include

If True, implicit hydrogen atoms are treated as if they were explicit and are ignored otherwise.

Note

By default, implicit hydrogen atoms are treated in the same way as explicit ones.

getAtomPropertyFlags()

int CDPL.Chem.SymmetryClassCalculator.getAtomPropertyFlags

(

)

Returns the set of atomic properties that gets considered in the perception of topological symmetry classes.

Returns

The set of considered atomic properties.

See also

setAtomPropertyFlags()

getBondPropertyFlags()

int CDPL.Chem.SymmetryClassCalculator.getBondPropertyFlags

(

)

Returns the set of bond properties that gets considered in the perception of topological symmetry classes.

Returns

The set of considered bond properties.

See also

setBondPropertyFlags()

implicitHydrogensIncluded()

bool CDPL.Chem.SymmetryClassCalculator.implicitHydrogensIncluded

(

)

Tells whether implicit hydrogen atoms are ignored or treated in the same way as explicit ones.

Returns

True if implicit hydrogen atoms are treated in the same way as explicit ones, and False if they are ignored.

calculate()

None CDPL.Chem.SymmetryClassCalculator.calculate	(	MolecularGraph	molgraph,
		Util.STArray	class_ids
	)

Perceives the topological symmetry classes of the atoms in the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to perceive the symmetry classes.
class_ids	An array containing the perceived symmetry class IDs. The class IDs are stored in the same order as the atoms appear in the atom list of the molecular graph (i.e. the symmetry class of an atom is accessible via its index).