Driver for the generation of low-energy conformer ensembles for single molecular fragments (chain, small ring system or macrocycle) More...

#include <FragmentConformerGenerator.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
	FragmentConformerGenerator ()
	Constructs the `FragmentConformerGenerator` instance. More...

	FragmentConformerGenerator (const FragmentConformerGenerator &)=delete

	~FragmentConformerGenerator ()
	Destructor. More...

FragmentConformerGenerator &	operator= (const FragmentConformerGenerator &)=delete

FragmentConformerGeneratorSettings &	getSettings ()
	Returns the current generator settings (mutable). More...

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

void	setAbortCallback (const CallbackFunction &func)
	Sets the callback invoked periodically to allow conformer 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 that receives log messages produced during conformer generation. 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 the fragment molgraph (the fragment type is perceived automatically). More...

unsigned int	generate (const Chem::MolecularGraph &molgraph, unsigned int frag_type)
	Generates a conformer ensemble for the fragment molgraph using the fragment-type-specific settings selected by frag_type. More...

unsigned int	generate (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &fixed_substr, const Math::Vector3DArray &fixed_substr_coords)
	Generates a conformer ensemble for the fragment molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates. More...

unsigned int	generate (const Chem::MolecularGraph &molgraph, unsigned int frag_type, const Chem::MolecularGraph &fixed_substr, const Math::Vector3DArray &fixed_substr_coords)
	Generates a conformer ensemble for the fragment molgraph using the fragment-type-specific settings selected by frag_type while keeping the substructure fixed_substr at the supplied 3D coordinates. 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 generated conformer. More...

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

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

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

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

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

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

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

Detailed Description

Driver for the generation of low-energy conformer ensembles for single molecular fragments (chain, small ring system or macrocycle)

Conformer sampling is done in a stochastic manner using distance-geometry-based raw coordinates generation, MMFF94 energy minimization and conformer RMSD clustering.

See also: [CFRG]

Member Typedef Documentation

◆ ConstConformerIterator

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

A constant iterator over the generated conformers.

◆ ConformerIterator

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

A mutable iterator over the generated conformers.

Constructor & Destructor Documentation

◆ FragmentConformerGenerator() [1/2]

CDPL::ConfGen::FragmentConformerGenerator::FragmentConformerGenerator ( )

Constructs the FragmentConformerGenerator instance.

◆ FragmentConformerGenerator() [2/2]

CDPL::ConfGen::FragmentConformerGenerator::FragmentConformerGenerator ( const FragmentConformerGenerator & )

delete

◆ ~FragmentConformerGenerator()

CDPL::ConfGen::FragmentConformerGenerator::~FragmentConformerGenerator ( )

Destructor.

Member Function Documentation

◆ operator=()

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

delete

◆ getSettings() [1/2]

FragmentConformerGeneratorSettings& CDPL::ConfGen::FragmentConformerGenerator::getSettings ( )

Returns the current generator settings (mutable).

Returns: A reference to the settings.

◆ getSettings() [2/2]

const FragmentConformerGeneratorSettings& CDPL::ConfGen::FragmentConformerGenerator::getSettings ( ) const

Returns the current generator settings.

Returns: A const reference to the settings.

◆ setAbortCallback()

void CDPL::ConfGen::FragmentConformerGenerator::setAbortCallback ( const CallbackFunction & func )

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

Parameters

func	The abort-check callback.

◆ getAbortCallback()

const CallbackFunction& CDPL::ConfGen::FragmentConformerGenerator::getAbortCallback ( ) const

Returns the currently configured abort-check callback.

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

◆ setTimeoutCallback()

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

Returns the currently configured timeout-check callback.

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

◆ setLogMessageCallback()

void CDPL::ConfGen::FragmentConformerGenerator::setLogMessageCallback ( const LogMessageCallbackFunction & func )

Sets the callback that receives log messages produced during conformer generation.

Parameters

func	The log-message callback.

◆ getLogMessageCallback()

const LogMessageCallbackFunction& CDPL::ConfGen::FragmentConformerGenerator::getLogMessageCallback ( ) const

Returns the currently configured log-message callback.

Returns: A const reference to the log-message callback.

◆ generate() [1/4]

unsigned int CDPL::ConfGen::FragmentConformerGenerator::generate ( const Chem::MolecularGraph & molgraph )

Generates a conformer ensemble for the fragment molgraph (the fragment type is perceived automatically).

Parameters

molgraph The fragment to process.

Returns: A status code defined in ConfGen::ReturnCode.

◆ generate() [2/4]

unsigned int CDPL::ConfGen::FragmentConformerGenerator::generate	(	const Chem::MolecularGraph &	molgraph,
		unsigned int	frag_type
	)

Generates a conformer ensemble for the fragment molgraph using the fragment-type-specific settings selected by frag_type.

Parameters

molgraph	The fragment to process.
frag_type	One of the ConfGen::FragmentType values selecting the per-fragment-class settings.

Returns: A status code defined in ConfGen::ReturnCode.

◆ generate() [3/4]

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

Generates a conformer ensemble for the fragment molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates.

Parameters

molgraph	The fragment to process.
fixed_substr	The substructure that must retain the supplied 3D coordinates.
fixed_substr_coords	The 3D coordinates assigned to fixed_substr.

Returns: A status code defined in ConfGen::ReturnCode.

Since: 1.1

◆ generate() [4/4]

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

Generates a conformer ensemble for the fragment molgraph using the fragment-type-specific settings selected by frag_type while keeping the substructure fixed_substr at the supplied 3D coordinates.

Parameters

molgraph	The fragment to process.
frag_type	One of the ConfGen::FragmentType values selecting the per-fragment-class settings.
fixed_substr	The substructure that must retain the supplied 3D coordinates.
fixed_substr_coords	The 3D coordinates assigned to fixed_substr.

Returns: A status code defined in ConfGen::ReturnCode.

Since: 1.1

◆ setConformers()

void CDPL::ConfGen::FragmentConformerGenerator::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::FragmentConformerGenerator::getNumConformers ( ) const

Returns the number of generated conformers.

Returns: The conformer count.

◆ getConformer() [1/2]

const ConformerData& CDPL::ConfGen::FragmentConformerGenerator::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 the number of conformers is zero or idx is not in the range [0, getNumConformers() - 1].

◆ getConformer() [2/2]

ConformerData& CDPL::ConfGen::FragmentConformerGenerator::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 the number of conformers is zero or idx is not in the range [0, getNumConformers() - 1].

◆ getConformersBegin() [1/2]

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

Returns a constant iterator pointing to the first generated conformer.

Returns: A constant iterator pointing to the first conformer.

◆ getConformersEnd() [1/2]

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

Returns a constant iterator pointing one past the last generated conformer.

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

◆ getConformersBegin() [2/2]

ConformerIterator CDPL::ConfGen::FragmentConformerGenerator::getConformersBegin ( )

Returns a mutable iterator pointing to the first generated conformer.

Returns: A mutable iterator pointing to the first conformer.

◆ getConformersEnd() [2/2]

ConformerIterator CDPL::ConfGen::FragmentConformerGenerator::getConformersEnd ( )

Returns a mutable iterator pointing one past the last generated conformer.

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

◆ begin() [1/2]

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

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

Returns: A constant iterator pointing to the first conformer.

◆ end() [1/2]

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

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

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

◆ begin() [2/2]

ConformerIterator CDPL::ConfGen::FragmentConformerGenerator::begin ( )

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

Returns: A mutable iterator pointing to the first conformer.

◆ end() [2/2]

ConformerIterator CDPL::ConfGen::FragmentConformerGenerator::end ( )

Returns a mutable iterator pointing one past the last generated 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:

FragmentConformerGenerator.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstConformerIterator

◆ ConformerIterator

Constructor & Destructor Documentation

◆ FragmentConformerGenerator() [1/2]

◆ FragmentConformerGenerator() [2/2]

◆ ~FragmentConformerGenerator()

Member Function Documentation

◆ operator=()

◆ getSettings() [1/2]

◆ getSettings() [2/2]

◆ setAbortCallback()

◆ getAbortCallback()

◆ setTimeoutCallback()

◆ getTimeoutCallback()

◆ setLogMessageCallback()

◆ getLogMessageCallback()

◆ generate() [1/4]

◆ generate() [2/4]

◆ generate() [3/4]

◆ generate() [4/4]

◆ 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]