Driver for the fragment-based generation of 3D starting conformers. More...

#include <FragmentAssembler.hpp>

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

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

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

	FragmentAssembler (const FragmentAssembler &)=delete

	~FragmentAssembler ()
	Destructor. More...

FragmentAssembler &	operator= (const FragmentAssembler &)=delete

const FragmentAssemblerSettings &	getSettings () const
	Returns the current assembler settings. More...

FragmentAssemblerSettings &	getSettings ()
	Returns the current assembler settings (mutable). 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 assembly. More...

void	setAbortCallback (const CallbackFunction &func)
	Sets the callback invoked periodically to allow the processing 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 assembler. More...

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

unsigned int	assemble (const Chem::MolecularGraph &molgraph)
	Assembles 3D conformer(s) for molgraph from fragment building blocks. More...

unsigned int	assemble (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &fixed_substr, const Math::Vector3DArray &fixed_substr_coords)
	Assembles 3D conformer(s) for molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates. More...

std::size_t	getNumConformers () const
	Returns the number of assembled 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 fragment-based generation of 3D starting conformers.

The assembler decomposes a molecular graph into chain and ring fragments, looks up pre-built conformers from a ConfGen::FragmentLibrary for each fragment (generating them on the fly when no library entry is available) and reassembles them into full 3D structures. The conformers produced this way are intended to serve as starting conformers for subsequent torsion driving — they are not (in general) a final conformer ensemble.

See also: ConfGen::TorsionDriver, ConfGen::ConformerGenerator

Member Typedef Documentation

◆ ConstConformerIterator

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

A constant iterator over the assembled conformers.

◆ ConformerIterator

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

A mutable iterator over the assembled conformers.

Constructor & Destructor Documentation

◆ FragmentAssembler() [1/2]

CDPL::ConfGen::FragmentAssembler::FragmentAssembler ( )

Constructs the FragmentAssembler instance.

◆ FragmentAssembler() [2/2]

CDPL::ConfGen::FragmentAssembler::FragmentAssembler ( const FragmentAssembler & )

delete

◆ ~FragmentAssembler()

CDPL::ConfGen::FragmentAssembler::~FragmentAssembler ( )

Destructor.

Member Function Documentation

◆ operator=()

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

delete

◆ getSettings() [1/2]

const FragmentAssemblerSettings& CDPL::ConfGen::FragmentAssembler::getSettings ( ) const

Returns the current assembler settings.

Returns: A const reference to the settings.

◆ getSettings() [2/2]

FragmentAssemblerSettings& CDPL::ConfGen::FragmentAssembler::getSettings ( )

Returns the current assembler settings (mutable).

Returns: A reference to the settings.

◆ clearFragmentLibraries()

void CDPL::ConfGen::FragmentAssembler::clearFragmentLibraries ( )

Removes all configured fragment libraries.

◆ addFragmentLibrary()

void CDPL::ConfGen::FragmentAssembler::addFragmentLibrary ( const FragmentLibrary::SharedPointer & lib )

Adds lib to the list of fragment libraries consulted during assembly.

Parameters

lib	The fragment library to add.

◆ setAbortCallback()

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

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

Parameters

func	The abort-check callback.

◆ getAbortCallback()

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

Returns the currently configured abort-check callback.

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

◆ setTimeoutCallback()

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

Returns the currently configured timeout-check callback.

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

◆ setLogMessageCallback()

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

Sets the callback receiving log messages emitted by the assembler.

Parameters

func	The log-message callback.

◆ getLogMessageCallback()

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

Returns the currently configured log-message callback.

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

◆ assemble() [1/2]

unsigned int CDPL::ConfGen::FragmentAssembler::assemble ( const Chem::MolecularGraph & molgraph )

Assembles 3D conformer(s) for molgraph from fragment building blocks.

Parameters

molgraph The input molecular graph.

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

◆ assemble() [2/2]

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

Assembles 3D conformer(s) for molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates.

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 assembly.

Since: 1.1

◆ getNumConformers()

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

Returns the number of assembled conformers.

Returns: The conformer count.

◆ getConformer() [1/2]

const ConformerData& CDPL::ConfGen::FragmentAssembler::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::FragmentAssembler::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::FragmentAssembler::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::FragmentAssembler::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::FragmentAssembler::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::FragmentAssembler::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::FragmentAssembler::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::FragmentAssembler::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::FragmentAssembler::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::FragmentAssembler::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:

FragmentAssembler.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstConformerIterator

◆ ConformerIterator

Constructor & Destructor Documentation

◆ FragmentAssembler() [1/2]

◆ FragmentAssembler() [2/2]

◆ ~FragmentAssembler()

Member Function Documentation

◆ operator=()

◆ getSettings() [1/2]

◆ getSettings() [2/2]

◆ clearFragmentLibraries()

◆ addFragmentLibrary()

◆ setAbortCallback()

◆ getAbortCallback()

◆ setTimeoutCallback()

◆ getTimeoutCallback()

◆ setLogMessageCallback()

◆ getLogMessageCallback()

◆ assemble() [1/2]

◆ assemble() [2/2]

◆ 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]