Driver for the systematic enumeration of conformers obtained by rotating around rotatable bonds of a molecular graph, using preferred torsion angles taken from configured ConfGen::TorsionLibrary instances. More...

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

	TorsionDriver (const TorsionDriver &)=delete

	~TorsionDriver ()
	Destructor. More...

TorsionDriver &	operator= (const TorsionDriver &)=delete

const TorsionDriverSettings &	getSettings () const
	Returns the current driver settings. More...

TorsionDriverSettings &	getSettings ()
	Returns the current driver settings (mutable). 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 driver. More...

const LogMessageCallbackFunction &	getLogMessageCallback () const
	Returns the currently configured log-message callback. More...

unsigned int	setup (const Chem::MolecularGraph &molgraph)
	Sets up the driver for molgraph with the default rotatable bond perception. More...

unsigned int	setup (const Chem::MolecularGraph &molgraph, const Util::BitSet &bond_mask)
	Sets up the driver for molgraph using only the bonds whose corresponding bit is set in bond_mask as rotatable. More...

void	clearInputCoordinates ()
	Removes all stored input coordinates. More...

void	clearInputCoordinates (std::size_t frag_idx)
	Removes all input coordinates of the fragment at index frag_idx. More...

void	addInputCoordinates (const Math::Vector3DArray &coords)
	Adds coords as a new starting conformation that the driver will torsion-drive. More...

void	addInputCoordinates (const Math::Vector3DArray &coords, std::size_t frag_idx)
	Adds coords as a new starting conformation restricted to the fragment at index frag_idx. More...

void	addInputCoordinates (const ConformerData &conf_data, std::size_t frag_idx)
	Adds the conformer data conf_data as a new starting conformation restricted to the fragment at index frag_idx. More...

void	addInputCoordinates (const ConformerData::SharedPointer &conf_data, std::size_t frag_idx)
	Adds the conformer data shared pointer conf_data as a new starting conformation restricted to the fragment at index frag_idx. More...

std::size_t	getNumFragments () const
	Returns the number of fragments produced by the rotatable bond decomposition. More...

const Chem::Fragment &	getFragment (std::size_t idx) const
	Returns the fragment at index idx. More...

unsigned int	generateConformers ()
	Runs the torsion-driving conformer enumeration. 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

Driver for the systematic enumeration of conformers obtained by rotating around rotatable bonds of a molecular graph, using preferred torsion angles taken from configured ConfGen::TorsionLibrary instances.

Member Typedef Documentation

◆ ConstConformerIterator

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

A constant iterator over the generated conformers.

◆ ConformerIterator

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

A mutable iterator over the generated conformers.

Constructor & Destructor Documentation

◆ TorsionDriver() [1/2]

CDPL::ConfGen::TorsionDriver::TorsionDriver ( )

Constructs the TorsionDriver instance.

◆ TorsionDriver() [2/2]

CDPL::ConfGen::TorsionDriver::TorsionDriver ( const TorsionDriver & )

delete

◆ ~TorsionDriver()

CDPL::ConfGen::TorsionDriver::~TorsionDriver ( )

Destructor.

Member Function Documentation

◆ operator=()

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

delete

◆ getSettings() [1/2]

const TorsionDriverSettings& CDPL::ConfGen::TorsionDriver::getSettings ( ) const

Returns the current driver settings.

Returns: A const reference to the settings.

◆ getSettings() [2/2]

TorsionDriverSettings& CDPL::ConfGen::TorsionDriver::getSettings ( )

Returns the current driver settings (mutable).

Returns: A reference to the settings.

◆ clearTorsionLibraries()

void CDPL::ConfGen::TorsionDriver::clearTorsionLibraries ( )

Removes all configured torsion libraries.

◆ addTorsionLibrary()

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

Returns the currently configured abort-check callback.

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

◆ setTimeoutCallback()

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

Returns the currently configured timeout-check callback.

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

◆ setLogMessageCallback()

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

Sets the callback receiving log messages emitted by the driver.

Parameters

func	The log-message callback.

◆ getLogMessageCallback()

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

Returns the currently configured log-message callback.

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

◆ setup() [1/2]

unsigned int CDPL::ConfGen::TorsionDriver::setup ( const Chem::MolecularGraph & molgraph )

Sets up the driver for molgraph with the default rotatable bond perception.

Parameters

molgraph The input molecular graph.

Returns: A ConfGen::ReturnCode value reporting the outcome of the setup.

◆ setup() [2/2]

unsigned int CDPL::ConfGen::TorsionDriver::setup	(	const Chem::MolecularGraph &	molgraph,
		const Util::BitSet &	bond_mask
	)

Sets up the driver for molgraph using only the bonds whose corresponding bit is set in bond_mask as rotatable.

Parameters

molgraph	The input molecular graph.
bond_mask	The bit mask of rotatable bonds (one bit per bond of molgraph).

Returns: A ConfGen::ReturnCode value reporting the outcome of the setup.

◆ clearInputCoordinates() [1/2]

void CDPL::ConfGen::TorsionDriver::clearInputCoordinates ( )

Removes all stored input coordinates.

◆ clearInputCoordinates() [2/2]

void CDPL::ConfGen::TorsionDriver::clearInputCoordinates ( std::size_t frag_idx )

Removes all input coordinates of the fragment at index frag_idx.

Parameters

frag_idx The zero-based fragment index.

◆ addInputCoordinates() [1/4]

void CDPL::ConfGen::TorsionDriver::addInputCoordinates ( const Math::Vector3DArray & coords )

Adds coords as a new starting conformation that the driver will torsion-drive.

Parameters

coords The input 3D coordinates.

◆ addInputCoordinates() [2/4]

void CDPL::ConfGen::TorsionDriver::addInputCoordinates	(	const Math::Vector3DArray &	coords,
		std::size_t	frag_idx
	)

Adds coords as a new starting conformation restricted to the fragment at index frag_idx.

Parameters

coords	The input 3D coordinates of the fragment.
frag_idx	The zero-based fragment index.

◆ addInputCoordinates() [3/4]

void CDPL::ConfGen::TorsionDriver::addInputCoordinates	(	const ConformerData &	conf_data,
		std::size_t	frag_idx
	)

Adds the conformer data conf_data as a new starting conformation restricted to the fragment at index frag_idx.

Parameters

conf_data	The input conformer data.
frag_idx	The zero-based fragment index.

◆ addInputCoordinates() [4/4]

void CDPL::ConfGen::TorsionDriver::addInputCoordinates	(	const ConformerData::SharedPointer &	conf_data,
		std::size_t	frag_idx
	)

Adds the conformer data shared pointer conf_data as a new starting conformation restricted to the fragment at index frag_idx.

Parameters

conf_data	The input conformer data.
frag_idx	The zero-based fragment index.

◆ getNumFragments()

std::size_t CDPL::ConfGen::TorsionDriver::getNumFragments ( ) const

Returns the number of fragments produced by the rotatable bond decomposition.

Returns: The fragment count.

◆ getFragment()

const Chem::Fragment& CDPL::ConfGen::TorsionDriver::getFragment ( std::size_t idx ) const

Returns the fragment at index idx.

Parameters

idx	The zero-based fragment index.

Returns: A const reference to the fragment.

Exceptions

Base::IndexError if the number of fragments is zero or idx is not in the range [0, getNumFragments() - 1].

◆ generateConformers()

unsigned int CDPL::ConfGen::TorsionDriver::generateConformers ( )

Runs the torsion-driving conformer enumeration.

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

◆ getNumConformers()

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

Returns the number of generated conformers.

Returns: The conformer count.

◆ getConformer() [1/2]

const ConformerData& CDPL::ConfGen::TorsionDriver::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::TorsionDriver::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::TorsionDriver::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::TorsionDriver::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::TorsionDriver::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::TorsionDriver::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::TorsionDriver::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::TorsionDriver::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::TorsionDriver::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::TorsionDriver::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:

TorsionDriver.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstConformerIterator

◆ ConformerIterator

Constructor & Destructor Documentation

◆ TorsionDriver() [1/2]

◆ TorsionDriver() [2/2]

◆ ~TorsionDriver()

Member Function Documentation

◆ operator=()

◆ getSettings() [1/2]

◆ getSettings() [2/2]

◆ clearTorsionLibraries()

◆ addTorsionLibrary()

◆ setAbortCallback()

◆ getAbortCallback()

◆ setTimeoutCallback()

◆ getTimeoutCallback()

◆ setLogMessageCallback()

◆ getLogMessageCallback()

◆ setup() [1/2]

◆ setup() [2/2]

◆ clearInputCoordinates() [1/2]

◆ clearInputCoordinates() [2/2]

◆ addInputCoordinates() [1/4]

◆ addInputCoordinates() [2/4]

◆ addInputCoordinates() [3/4]

◆ addInputCoordinates() [4/4]

◆ getNumFragments()

◆ getFragment()

◆ generateConformers()

◆ 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]