CDPL::ConfGen::StructureGenerator Class Reference

High-level driver for the generation of a single low-energy 3D structure from a molecular graph. More...

#include <StructureGenerator.hpp>

Public Member Functions
	StructureGenerator ()
	Constructs the StructureGenerator instance. More...
	StructureGenerator (const StructureGenerator &)=delete
	~StructureGenerator ()
	Destructor. More...
StructureGenerator &	operator= (const StructureGenerator &)=delete
const StructureGeneratorSettings &	getSettings () const
	Returns the current generator settings. More...
StructureGeneratorSettings &	getSettings ()
	Returns the current generator settings. More...
void	clearFragmentLibraries ()
	Removes all configured fragment libraries. More...
void	addFragmentLibrary (const FragmentLibrary::SharedPointer &lib)
	Adds lib to the list of fragment libraries consulted during fragment-based 3D structure generation. More...
void	clearTorsionLibraries ()
	Removes all configured torsion libraries. More...
void	addTorsionLibrary (const TorsionLibrary::SharedPointer &lib)
	Adds lib to the list of torsion libraries consulted during torsion driving. More...
void	setAbortCallback (const CallbackFunction &func)
	Sets the callback invoked periodically to allow the generation to be aborted by the user. More...
const CallbackFunction &	getAbortCallback () const
	Returns the currently configured abort-check callback. More...
void	setTimeoutCallback (const CallbackFunction &func)
	Sets the callback invoked periodically to check whether the configured timeout has elapsed. More...
const CallbackFunction &	getTimeoutCallback () const
	Returns the currently configured timeout-check callback. More...
void	setLogMessageCallback (const LogMessageCallbackFunction &func)
	Sets the callback receiving log messages emitted by the generator. More...
const LogMessageCallbackFunction &	getLogMessageCallback () const
	Returns the currently configured log-message callback. More...
unsigned int	generate (const Chem::MolecularGraph &molgraph)
	Generates a single 3D structure for molgraph. More...
unsigned int	generate (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &fixed_substr)
	Generates a single 3D structure for molgraph while keeping the substructure fixed_substr at its current 3D coordinates. More...
unsigned int	generate (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &fixed_substr, const Math::Vector3DArray &fixed_substr_coords)
	Generates a single 3D structure for molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates fixed_substr_coords. More...
void	setCoordinates (Chem::MolecularGraph &molgraph) const
	Transfers the generated 3D coordinates onto the atoms of molgraph (via Chem::set3DCoordinates). More...
const ConformerData &	getCoordinates () const
	Returns the conformer data produced by the most recent generate() call. More...

Detailed Description

High-level driver for the generation of a single low-energy 3D structure from a molecular graph.

Internally delegates to the same pipeline as class ConfGen::ConformerGenerator but stops after the first acceptable conformer has been produced.

Constructor & Destructor Documentation

StructureGenerator() [1/2]

CDPL::ConfGen::StructureGenerator::StructureGenerator

(

)

Constructs the StructureGenerator instance.

StructureGenerator() [2/2]

CDPL::ConfGen::StructureGenerator::StructureGenerator ( const StructureGenerator &  )

delete

~StructureGenerator()

CDPL::ConfGen::StructureGenerator::~StructureGenerator

(

)

Destructor.

Member Function Documentation

operator=()

StructureGenerator& CDPL::ConfGen::StructureGenerator::operator= ( const StructureGenerator &  )

delete

getSettings() [1/2]

const StructureGeneratorSettings& CDPL::ConfGen::StructureGenerator::getSettings

(

)

const

Returns the current generator settings.

Returns

A const reference to the settings.

getSettings() [2/2]

StructureGeneratorSettings& CDPL::ConfGen::StructureGenerator::getSettings

(

)

Returns the current generator settings.

Returns

A reference to the settings.

clearFragmentLibraries()

void CDPL::ConfGen::StructureGenerator::clearFragmentLibraries

(

)

Removes all configured fragment libraries.

addFragmentLibrary()

void CDPL::ConfGen::StructureGenerator::addFragmentLibrary

(

const FragmentLibrary::SharedPointer &

lib

)

Adds lib to the list of fragment libraries consulted during fragment-based 3D structure generation.

Parameters

lib	The fragment library to add.

clearTorsionLibraries()

void CDPL::ConfGen::StructureGenerator::clearTorsionLibraries

(

)

Removes all configured torsion libraries.

addTorsionLibrary()

void CDPL::ConfGen::StructureGenerator::addTorsionLibrary

(

const TorsionLibrary::SharedPointer &

lib

)

Adds lib to the list of torsion libraries consulted during torsion driving.

Parameters

lib	The torsion library to add.

setAbortCallback()

void CDPL::ConfGen::StructureGenerator::setAbortCallback

(

const CallbackFunction &

func

)

Sets the callback invoked periodically to allow the generation to be aborted by the user.

Parameters

func	The abort-check callback.

getAbortCallback()

const CallbackFunction& CDPL::ConfGen::StructureGenerator::getAbortCallback

(

)

const

Returns the currently configured abort-check callback.

Returns

A const reference to the abort-check callback.

setTimeoutCallback()

void CDPL::ConfGen::StructureGenerator::setTimeoutCallback

(

const CallbackFunction &

func

)

Sets the callback invoked periodically to check whether the configured timeout has elapsed.

Parameters

func	The timeout-check callback.

getTimeoutCallback()

const CallbackFunction& CDPL::ConfGen::StructureGenerator::getTimeoutCallback

(

)

const

Returns the currently configured timeout-check callback.

Returns

A const reference to the timeout-check callback.

setLogMessageCallback()

void CDPL::ConfGen::StructureGenerator::setLogMessageCallback

(

const LogMessageCallbackFunction &

func

)

Sets the callback receiving log messages emitted by the generator.

Parameters

func	The log-message callback.

getLogMessageCallback()

const LogMessageCallbackFunction& CDPL::ConfGen::StructureGenerator::getLogMessageCallback

(

)

const

Returns the currently configured log-message callback.

Returns

A const reference to the log-message callback.

generate() [1/3]

unsigned int CDPL::ConfGen::StructureGenerator::generate

(

const Chem::MolecularGraph &

molgraph

)

Generates a single 3D structure for molgraph.

Parameters

molgraph

The input molecular graph.

Returns

A ConfGen::ReturnCode value reporting the outcome of the generation.

generate() [2/3]

unsigned int CDPL::ConfGen::StructureGenerator::generate	(	const Chem::MolecularGraph &	molgraph,
		const Chem::MolecularGraph &	fixed_substr
	)

Generates a single 3D structure for molgraph while keeping the substructure fixed_substr at its current 3D coordinates.

Parameters

molgraph	The input molecular graph.
fixed_substr	The substructure that must retain its current 3D coordinates.

Returns

A ConfGen::ReturnCode value reporting the outcome of the generation.

Since

1.1

generate() [3/3]

unsigned int CDPL::ConfGen::StructureGenerator::generate	(	const Chem::MolecularGraph &	molgraph,
		const Chem::MolecularGraph &	fixed_substr,
		const Math::Vector3DArray &	fixed_substr_coords
	)

Generates a single 3D structure for molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates fixed_substr_coords.

Parameters

molgraph	The input molecular graph.
fixed_substr	The substructure that must retain the supplied 3D coordinates.
fixed_substr_coords	The 3D coordinates assigned to fixed_substr.

Returns

A ConfGen::ReturnCode value reporting the outcome of the generation.

Since

1.1

setCoordinates()

void CDPL::ConfGen::StructureGenerator::setCoordinates

(

Chem::MolecularGraph &

molgraph

)

const

Transfers the generated 3D coordinates onto the atoms of molgraph (via Chem::set3DCoordinates).

Parameters

molgraph

The molecular graph receiving the 3D coordinates.

getCoordinates()

const ConformerData& CDPL::ConfGen::StructureGenerator::getCoordinates

(

)

const

Returns the conformer data produced by the most recent generate() call.

Returns

A const reference to the conformer data.

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

• StructureGenerator.hpp