CDPL::ConfGen::TorsionDriver Class Reference

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. 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.

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 idx is not in the range [0, getNumFragments()).

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 idx is not in the range [0, getNumConformers()).

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 idx is not in the range [0, getNumConformers()).

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