High-level driver for the generation of low-energy conformer ensembles of molecular graphs. More...

#include <ConformerGenerator.hpp>

Public Types
typedef boost::indirect_iterator< ConformerDataArray::const_iterator, const ConformerData >	ConstConformerIterator
	A constant iterator over the generated conformers. More...

typedef boost::indirect_iterator< ConformerDataArray::const_iterator, ConformerData >	ConformerIterator
	A mutable iterator over the generated conformers. More...

Public Member Functions
	ConformerGenerator ()
	Constructs the `ConformerGenerator` instance. More...

	ConformerGenerator (const ConformerGenerator &)=delete

	~ConformerGenerator ()
	Destructor. More...

ConformerGenerator &	operator= (const ConformerGenerator &)=delete

const ConformerGeneratorSettings &	getSettings () const
	Returns the current generator settings. More...

ConformerGeneratorSettings &	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 conformer ensemble for molgraph. More...

unsigned int	generate (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &fixed_substr)
	Generates a conformer ensemble 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 conformer ensemble for molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates fixed_substr_coords. More...

void	setConformers (Chem::MolecularGraph &molgraph) const
	Transfers the generated conformer ensemble onto molgraph. More...

std::size_t	getNumConformers () const
	Returns the number of generated conformers. More...

const ConformerData &	getConformer (std::size_t idx) const
	Returns the conformer at index idx. More...

ConformerData &	getConformer (std::size_t idx)
	Returns the conformer at index idx. More...

ConstConformerIterator	getConformersBegin () const
	Returns a constant iterator pointing to the first conformer. More...

ConstConformerIterator	getConformersEnd () const
	Returns a constant iterator pointing one past the last conformer. More...

ConformerIterator	getConformersBegin ()
	Returns a mutable iterator pointing to the first conformer. More...

ConformerIterator	getConformersEnd ()
	Returns a mutable iterator pointing one past the last conformer. More...

ConstConformerIterator	begin () const
	Returns a constant iterator pointing to the first conformer (range-based for support). More...

ConstConformerIterator	end () const
	Returns a constant iterator pointing one past the last conformer (range-based for support). More...

ConformerIterator	begin ()
	Returns a mutable iterator pointing to the first conformer (range-based for support). More...

ConformerIterator	end ()
	Returns a mutable iterator pointing one past the last conformer (range-based for support). More...

Detailed Description

High-level driver for the generation of low-energy conformer ensembles of molecular graphs.

The generator implements two complementary sampling strategies for producing the conformer ensemble:

a systematic strategy that performs a fragment-based 3D structure generation followed by exhaustive torsion-driving of all rotatable bonds, and
a stochastic strategy that picks conformations randomly from the conformational space of the molecule (by default used only for flexible macrocyclic molecules).

Both strategies share a common downstream pipeline of MMFF94-based energy minimization, RMSD-based clustering and energy window filtering. Behaviour is controlled by the embedded conformer generation settings instance, the configured fragment and torsion libraries and the optional abort/timeout/log callbacks.

See also: [CFRG]

Member Typedef Documentation

◆ ConstConformerIterator

typedef boost::indirect_iterator<ConformerDataArray::const_iterator, const ConformerData> CDPL::ConfGen::ConformerGenerator::ConstConformerIterator

A constant iterator over the generated conformers.

◆ ConformerIterator

typedef boost::indirect_iterator<ConformerDataArray::const_iterator, ConformerData> CDPL::ConfGen::ConformerGenerator::ConformerIterator

A mutable iterator over the generated conformers.

Constructor & Destructor Documentation

◆ ConformerGenerator() [1/2]

CDPL::ConfGen::ConformerGenerator::ConformerGenerator ( )

Constructs the ConformerGenerator instance.

◆ ConformerGenerator() [2/2]

CDPL::ConfGen::ConformerGenerator::ConformerGenerator ( const ConformerGenerator & )

delete

◆ ~ConformerGenerator()

CDPL::ConfGen::ConformerGenerator::~ConformerGenerator ( )

Destructor.

Member Function Documentation

◆ operator=()

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

delete

◆ getSettings() [1/2]

const ConformerGeneratorSettings& CDPL::ConfGen::ConformerGenerator::getSettings ( ) const

Returns the current generator settings.

Returns: A const reference to the settings.

◆ getSettings() [2/2]

ConformerGeneratorSettings& CDPL::ConfGen::ConformerGenerator::getSettings ( )

Returns the current generator settings.

Returns: A reference to the settings.

◆ clearFragmentLibraries()

void CDPL::ConfGen::ConformerGenerator::clearFragmentLibraries ( )

Removes all configured fragment libraries.

◆ addFragmentLibrary()

void CDPL::ConfGen::ConformerGenerator::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::ConformerGenerator::clearTorsionLibraries ( )

Removes all configured torsion libraries.

◆ addTorsionLibrary()

void CDPL::ConfGen::ConformerGenerator::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::ConformerGenerator::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::ConformerGenerator::getAbortCallback ( ) const

Returns the currently configured abort-check callback.

Returns: A const reference to the abort-check callback.

◆ setTimeoutCallback()

void CDPL::ConfGen::ConformerGenerator::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::ConformerGenerator::getTimeoutCallback ( ) const

Returns the currently configured timeout-check callback.

Returns: A const reference to the timeout-check callback.

◆ setLogMessageCallback()

void CDPL::ConfGen::ConformerGenerator::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::ConformerGenerator::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::ConformerGenerator::generate ( const Chem::MolecularGraph & molgraph )

Generates a conformer ensemble 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::ConformerGenerator::generate	(	const Chem::MolecularGraph &	molgraph,
		const Chem::MolecularGraph &	fixed_substr
	)

Generates a conformer ensemble 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::ConformerGenerator::generate	(	const Chem::MolecularGraph &	molgraph,
		const Chem::MolecularGraph &	fixed_substr,
		const Math::Vector3DArray &	fixed_substr_coords
	)

Generates a conformer ensemble 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

◆ setConformers()

void CDPL::ConfGen::ConformerGenerator::setConformers ( Chem::MolecularGraph & molgraph ) const

Transfers the generated conformer ensemble onto molgraph.

The per-conformer 3D coordinates are written to each atom's 3D coordinates array (via Chem::set3DCoordinatesArray) and the corresponding per-conformer energies are attached to the molecular graph (via Chem::setConformerEnergies).

Parameters

molgraph The molecular graph that receives the conformer coordinates and energies.

◆ getNumConformers()

std::size_t CDPL::ConfGen::ConformerGenerator::getNumConformers ( ) const

Returns the number of generated conformers.

Returns: The conformer count.

◆ getConformer() [1/2]

const ConformerData& CDPL::ConfGen::ConformerGenerator::getConformer ( std::size_t idx ) const

Returns the conformer at index idx.

Parameters

idx	The zero-based conformer index.

Returns: A const reference to the conformer data.

Exceptions

Base::IndexError if idx is not in the range [0, getNumConformers()).

◆ getConformer() [2/2]

ConformerData& CDPL::ConfGen::ConformerGenerator::getConformer ( std::size_t idx )

Returns the conformer at index idx.

Parameters

idx	The zero-based conformer index.

Returns: A reference to the conformer data.

Exceptions

Base::IndexError if idx is not in the range [0, getNumConformers()).

◆ getConformersBegin() [1/2]

ConstConformerIterator CDPL::ConfGen::ConformerGenerator::getConformersBegin ( ) const

Returns a constant iterator pointing to the first conformer.

Returns: A constant iterator pointing to the first conformer.

◆ getConformersEnd() [1/2]

ConstConformerIterator CDPL::ConfGen::ConformerGenerator::getConformersEnd ( ) const

Returns a constant iterator pointing one past the last conformer.

Returns: A constant iterator pointing one past the last conformer.

◆ getConformersBegin() [2/2]

ConformerIterator CDPL::ConfGen::ConformerGenerator::getConformersBegin ( )

Returns a mutable iterator pointing to the first conformer.

Returns: A mutable iterator pointing to the first conformer.

◆ getConformersEnd() [2/2]

ConformerIterator CDPL::ConfGen::ConformerGenerator::getConformersEnd ( )

Returns a mutable iterator pointing one past the last conformer.

Returns: A mutable iterator pointing one past the last conformer.

◆ begin() [1/2]

ConstConformerIterator CDPL::ConfGen::ConformerGenerator::begin ( ) const

Returns a constant iterator pointing to the first conformer (range-based for support).

Returns: A constant iterator pointing to the first conformer.

◆ end() [1/2]

ConstConformerIterator CDPL::ConfGen::ConformerGenerator::end ( ) const

Returns a constant iterator pointing one past the last conformer (range-based for support).

Returns: A constant iterator pointing one past the last conformer.

◆ begin() [2/2]

ConformerIterator CDPL::ConfGen::ConformerGenerator::begin ( )

Returns a mutable iterator pointing to the first conformer (range-based for support).

Returns: A mutable iterator pointing to the first conformer.

◆ end() [2/2]

ConformerIterator CDPL::ConfGen::ConformerGenerator::end ( )

Returns a mutable iterator pointing one past the last conformer (range-based for support).

Returns: A mutable iterator pointing one past the last conformer.

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

ConformerGenerator.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstConformerIterator

◆ ConformerIterator

Constructor & Destructor Documentation

◆ ConformerGenerator() [1/2]

◆ ConformerGenerator() [2/2]

◆ ~ConformerGenerator()

Member Function Documentation

◆ operator=()

◆ getSettings() [1/2]

◆ getSettings() [2/2]

◆ clearFragmentLibraries()

◆ addFragmentLibrary()

◆ clearTorsionLibraries()

◆ addTorsionLibrary()

◆ setAbortCallback()

◆ getAbortCallback()

◆ setTimeoutCallback()

◆ getTimeoutCallback()

◆ setLogMessageCallback()

◆ getLogMessageCallback()

◆ generate() [1/3]

◆ generate() [2/3]

◆ generate() [3/3]

◆ setConformers()

◆ getNumConformers()

◆ getConformer() [1/2]

◆ getConformer() [2/2]

◆ getConformersBegin() [1/2]

◆ getConformersEnd() [1/2]

◆ getConformersBegin() [2/2]

◆ getConformersEnd() [2/2]

◆ begin() [1/2]

◆ end() [1/2]

◆ begin() [2/2]

◆ end() [2/2]