CDPL.Chem.ProtonationStateStandardizer Class Reference

Adjusts the protonation state of a molecule (atom formal charges and bonded hydrogen counts) according to one of several pre-defined objectives. More...

Inheritance diagram for CDPL.Chem.ProtonationStateStandardizer:

Classes
class	Flavor
	Selects the objective driving the protonation-state adjustment. More...

Public Member Functions
None	__init__ ()
	Constructs the ProtonationStateStandardizer instance.
None	__init__ (ProtonationStateStandardizer standardizer)
	Constructs a copy of the ProtonationStateStandardizer instance standardizer. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
ProtonationStateStandardizer	assign (ProtonationStateStandardizer standardizer)
	Replaces the state of this standardizer by a copy of the state of standardizer. More...
bool	standardize (Molecule mol, Flavor flavor)
	Adjusts the protonation state of mol in place according to the selected flavor. More...
bool	standardize (Molecule mol, Molecule std_mol, Flavor flavor)
	Writes a standardized copy of mol to std_mol without modifying mol. More...

Properties
	objectID = property(getObjectID)

Detailed Description

Adjusts the protonation state of a molecule (atom formal charges and bonded hydrogen counts) according to one of several pre-defined objectives.

Constructor & Destructor Documentation

__init__()

None CDPL.Chem.ProtonationStateStandardizer.__init__

(

ProtonationStateStandardizer

standardizer

)

Constructs a copy of the ProtonationStateStandardizer instance standardizer.

Parameters

standardizer

The ProtonationStateStandardizer to copy.

Member Function Documentation

getObjectID()

int CDPL.Chem.ProtonationStateStandardizer.getObjectID

(

)

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

Different Python ProtonationStateStandardizer 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 ProtonationStateStandardizer 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()

ProtonationStateStandardizer CDPL.Chem.ProtonationStateStandardizer.assign

(

ProtonationStateStandardizer

standardizer

)

Replaces the state of this standardizer by a copy of the state of standardizer.

Parameters

standardizer

The source ProtonationStateStandardizer.

Returns

self

standardize() [1/2]

bool CDPL.Chem.ProtonationStateStandardizer.standardize	(	Molecule	mol,
		Flavor	flavor
	)

Adjusts the protonation state of mol in place according to the selected flavor.

Parameters

mol	The molecule to standardize (modified in place).
flavor	The protonation-state objective.

Returns

True if the molecule was modified, and False otherwise.

standardize() [2/2]

bool CDPL.Chem.ProtonationStateStandardizer.standardize	(	Molecule	mol,
		Molecule	std_mol,
		Flavor	flavor
	)

Writes a standardized copy of mol to std_mol without modifying mol.

Parameters

mol	The input molecule.
std_mol	The output molecule receiving the standardized copy.
flavor	The protonation-state objective.

Returns

True if the output differs from the input, and False otherwise.