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...

#include <ProtonationStateStandardizer.hpp>

Public Types
enum	Flavor {   MIN_CHARGED_ATOM_COUNT ,   PHYSIOLOGICAL_CONDITION_STATE ,   MAX_CHARGE_COMPENSATION }
	Selects the objective driving the protonation-state adjustment. More...
typedef std::shared_ptr< ProtonationStateStandardizer >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated ProtonationStateStandardizer instances. More...

Public Member Functions
	ProtonationStateStandardizer ()
	Constructs the ProtonationStateStandardizer instance. More...
	ProtonationStateStandardizer (const ProtonationStateStandardizer &standardizer)
	Constructs a copy of the ProtonationStateStandardizer instance standardizer. More...
bool	standardize (Molecule &mol, Flavor flavor)
	Adjusts the protonation state of mol in place according to the selected flavor. More...
bool	standardize (const Molecule &mol, Molecule &std_mol, Flavor flavor)
	Writes a standardized copy of mol to std_mol without modifying mol. More...
ProtonationStateStandardizer &	operator= (const ProtonationStateStandardizer &standardizer)
	Replaces the state of this standardizer by a copy of the state of standardizer. More...

Friends
class	ChEMBLStandardizer

Detailed Description

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

Member Typedef Documentation

SharedPointer

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

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

Member Enumeration Documentation

Flavor

enum CDPL::Chem::ProtonationStateStandardizer::Flavor

Selects the objective driving the protonation-state adjustment.

Enumerator
MIN_CHARGED_ATOM_COUNT	Minimize the total number of formally charged atoms (neutralize where possible).
PHYSIOLOGICAL_CONDITION_STATE	Set the protonation state expected under physiological conditions (pH ~7.4).
MAX_CHARGE_COMPENSATION	Maximize the cancellation of opposite formal charges (neutralize zwitterion-like pairs).

Constructor & Destructor Documentation

ProtonationStateStandardizer() [1/2]

CDPL::Chem::ProtonationStateStandardizer::ProtonationStateStandardizer

(

)

Constructs the ProtonationStateStandardizer instance.

ProtonationStateStandardizer() [2/2]

CDPL::Chem::ProtonationStateStandardizer::ProtonationStateStandardizer

(

const ProtonationStateStandardizer &

standardizer

)

Constructs a copy of the ProtonationStateStandardizer instance standardizer.

Parameters

standardizer

The ProtonationStateStandardizer to copy.

Member Function Documentation

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	(	const 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.

operator=()

ProtonationStateStandardizer& CDPL::Chem::ProtonationStateStandardizer::operator=

(

const ProtonationStateStandardizer &

standardizer

)

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

Parameters

standardizer

The source ProtonationStateStandardizer.

Returns

A reference to itself.

Friends And Related Function Documentation

ChEMBLStandardizer

friend class ChEMBLStandardizer

friend

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

• ProtonationStateStandardizer.hpp