CDPL::Chem::SubstructureEditor Class Reference

Pattern-driven editor that rewrites matched substructures of a molecule according to a given editing template. More...

#include <SubstructureEditor.hpp>

Public Types
typedef std::shared_ptr< SubstructureEditor >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated SubstructureEditor instances. More...
typedef boost::transform_iterator< GetMolGraphFunc, PatternList::const_iterator >	ConstPatternIterator
	A constant iterator used to iterate over the stored search/exclude pattern Chem::MolecularGraph objects. More...
typedef boost::transform_iterator< GetMolGraphFunc, PatternList::iterator >	PatternIterator
	A mutable iterator used to iterate over the stored search/exclude pattern Chem::MolecularGraph objects. More...

Public Member Functions
	SubstructureEditor ()
	Constructs the SubstructureEditor instance. More...
	SubstructureEditor (const SubstructureEditor &editor)
	Constructs a copy of the SubstructureEditor instance editor. More...
	~SubstructureEditor ()
	Destructor. More...
void	addSearchPattern (const MolecularGraph::SharedPointer &molgraph)
	Appends a new substructure search pattern to the current set of patterns. More...
std::size_t	getNumSearchPatterns () const
	Returns the number of stored substructure search patterns. More...
const MolecularGraph::SharedPointer &	getSearchPattern (std::size_t idx) const
	Returns the molecular graph of the substructure search pattern at index idx. More...
void	removeSearchPattern (std::size_t idx)
	Removes the substructure search pattern at index idx. More...
void	removeSearchPattern (const PatternIterator &it)
	Removes the substructure search pattern pointed to by it. More...
void	clearSearchPatterns ()
	Clears the current set of substructure search patterns. More...
PatternIterator	getSearchPatternsBegin ()
	Returns a mutable iterator pointing to the beginning of the stored search pattern Chem::MolecularGraph objects. More...
PatternIterator	getSearchPatternsEnd ()
	Returns a mutable iterator pointing to the end of the stored search pattern Chem::MolecularGraph objects. More...
ConstPatternIterator	getSearchPatternsBegin () const
	Returns a constant iterator pointing to the beginning of the stored search pattern const Chem::MolecularGraph objects. More...
ConstPatternIterator	getSearchPatternsEnd () const
	Returns a constant iterator pointing to the end of the stored search pattern const Chem::MolecularGraph objects. More...
void	addExcludePattern (const MolecularGraph::SharedPointer &molgraph)
	Appends a new substructure exclude pattern to the current set of patterns. More...
std::size_t	getNumExcludePatterns () const
	Returns the number of stored substructure exclude patterns. More...
const MolecularGraph::SharedPointer &	getExcludePattern (std::size_t idx) const
	Returns the molecular graph of the substructure exclude pattern at index idx. More...
void	removeExcludePattern (std::size_t idx)
	Removes the substructure exclude pattern at index idx. More...
void	removeExcludePattern (const PatternIterator &it)
	Removes the substructure exclude pattern pointed to by it. More...
void	clearExcludePatterns ()
	Clears the current set of substructure exclude patterns. More...
PatternIterator	getExcludePatternsBegin ()
	Returns a mutable iterator pointing to the beginning of the stored exclude pattern Chem::MolecularGraph objects. More...
PatternIterator	getExcludePatternsEnd ()
	Returns a mutable iterator pointing to the end of the stored exclude pattern Chem::MolecularGraph objects. More...
ConstPatternIterator	getExcludePatternsBegin () const
	Returns a constant iterator pointing to the beginning of the stored exclude pattern const Chem::MolecularGraph objects. More...
ConstPatternIterator	getExcludePatternsEnd () const
	Returns a constant iterator pointing to the end of the stored exclude pattern const Chem::MolecularGraph objects. More...
void	setResultPattern (const MolecularGraph::SharedPointer &pattern)
	Sets the result pattern that defines how each matched search pattern instance will be rewritten. More...
const MolecularGraph::SharedPointer &	getResultPattern () const
	Returns the currently set result pattern. More...
void	clear ()
	Clears the current editing result pattern and the sets of substructure search and exclude patterns. More...
std::size_t	edit (Molecule &mol)
	Edits the molecule mol in place by applying the result pattern at every search pattern match that is not covered by an exclude pattern. More...
std::size_t	edit (const MolecularGraph &molgraph, Molecule &res_mol)
	Copies the molecular graph molgraph into the molecule res_mol and then edits it by calling edit(Molecule&). More...
SubstructureEditor &	operator= (const SubstructureEditor &gen)
	Copies the state of the SubstructureEditor instance gen. More...

Detailed Description

Pattern-driven editor that rewrites matched substructures of a molecule according to a given editing template.

Search patterns supply the substructures the editor will look for. The (single) result pattern defines what each match is rewritten to and exclude patterns mark matches that must be skipped (a search match is discarded when its atoms/bonds form a subset of any exclude match). The editor iterates until no further matches can be transformed and returns the number of applied edits.

Since

1.3.0

Member Typedef Documentation

SharedPointer

typedef std::shared_ptr<SubstructureEditor> CDPL::Chem::SubstructureEditor::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated SubstructureEditor instances.

ConstPatternIterator

typedef boost::transform_iterator<GetMolGraphFunc, PatternList::const_iterator> CDPL::Chem::SubstructureEditor::ConstPatternIterator

A constant iterator used to iterate over the stored search/exclude pattern Chem::MolecularGraph objects.

PatternIterator

typedef boost::transform_iterator<GetMolGraphFunc, PatternList::iterator> CDPL::Chem::SubstructureEditor::PatternIterator

A mutable iterator used to iterate over the stored search/exclude pattern Chem::MolecularGraph objects.

Constructor & Destructor Documentation

SubstructureEditor() [1/2]

CDPL::Chem::SubstructureEditor::SubstructureEditor

(

)

Constructs the SubstructureEditor instance.

SubstructureEditor() [2/2]

CDPL::Chem::SubstructureEditor::SubstructureEditor

(

const SubstructureEditor &

editor

)

Constructs a copy of the SubstructureEditor instance editor.

Parameters

editor

The other editor instance to copy.

~SubstructureEditor()

CDPL::Chem::SubstructureEditor::~SubstructureEditor

(

)

Destructor.

Destroys the SubstructureEditor instance and frees all allocated resources.

Member Function Documentation

addSearchPattern()

void CDPL::Chem::SubstructureEditor::addSearchPattern

(

const MolecularGraph::SharedPointer &

molgraph

)

Appends a new substructure search pattern to the current set of patterns.

Parameters

molgraph

A smart pointer to the molecular graph of the substructure search pattern to add.

getNumSearchPatterns()

std::size_t CDPL::Chem::SubstructureEditor::getNumSearchPatterns

(

)

const

Returns the number of stored substructure search patterns.

Returns

The number of stored search patterns.

getSearchPattern()

const MolecularGraph::SharedPointer& CDPL::Chem::SubstructureEditor::getSearchPattern

(

std::size_t

idx

)

const

Returns the molecular graph of the substructure search pattern at index idx.

Parameters

idx	The zero-based search pattern index.

Returns

A smart pointer to the molecular graph of the search pattern at index idx.

Exceptions

Base::IndexError

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

removeSearchPattern() [1/2]

void CDPL::Chem::SubstructureEditor::removeSearchPattern

(

std::size_t

idx

)

Removes the substructure search pattern at index idx.

Parameters

idx	The zero-based search pattern index.

Exceptions

Base::IndexError

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

removeSearchPattern() [2/2]

void CDPL::Chem::SubstructureEditor::removeSearchPattern

(

const PatternIterator &

it

)

Removes the substructure search pattern pointed to by it.

Parameters

it	An iterator pointing to the search pattern.

Exceptions

Base::RangeError

if it is not in the range [getSearchPatternsBegin(), getSearchPatternsEnd()).

clearSearchPatterns()

void CDPL::Chem::SubstructureEditor::clearSearchPatterns

(

)

Clears the current set of substructure search patterns.

getSearchPatternsBegin() [1/2]

PatternIterator CDPL::Chem::SubstructureEditor::getSearchPatternsBegin

(

)

Returns a mutable iterator pointing to the beginning of the stored search pattern Chem::MolecularGraph objects.

Returns

A mutable iterator pointing to the beginning of the stored search pattern Chem::MolecularGraph objects.

getSearchPatternsEnd() [1/2]

PatternIterator CDPL::Chem::SubstructureEditor::getSearchPatternsEnd

(

)

Returns a mutable iterator pointing to the end of the stored search pattern Chem::MolecularGraph objects.

Returns

A mutable iterator pointing to the end of the stored search pattern Chem::MolecularGraph objects.

getSearchPatternsBegin() [2/2]

ConstPatternIterator CDPL::Chem::SubstructureEditor::getSearchPatternsBegin

(

)

const

Returns a constant iterator pointing to the beginning of the stored search pattern const Chem::MolecularGraph objects.

Returns

A constant iterator pointing to the beginning of the stored search pattern const Chem::MolecularGraph objects.

getSearchPatternsEnd() [2/2]

ConstPatternIterator CDPL::Chem::SubstructureEditor::getSearchPatternsEnd

(

)

const

Returns a constant iterator pointing to the end of the stored search pattern const Chem::MolecularGraph objects.

Returns

A constant iterator pointing to the end of the stored search pattern const Chem::MolecularGraph objects.

addExcludePattern()

void CDPL::Chem::SubstructureEditor::addExcludePattern

(

const MolecularGraph::SharedPointer &

molgraph

)

Appends a new substructure exclude pattern to the current set of patterns.

Parameters

molgraph

A smart pointer to the molecular graph of the substructure exclude pattern to add.

getNumExcludePatterns()

std::size_t CDPL::Chem::SubstructureEditor::getNumExcludePatterns

(

)

const

Returns the number of stored substructure exclude patterns.

Returns

The number of stored exclude patterns.

getExcludePattern()

const MolecularGraph::SharedPointer& CDPL::Chem::SubstructureEditor::getExcludePattern

(

std::size_t

idx

)

const

Returns the molecular graph of the substructure exclude pattern at index idx.

Parameters

idx	The zero-based exclude pattern index.

Returns

A smart pointer to the molecular graph of the exclude pattern at index idx.

Exceptions

Base::IndexError

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

removeExcludePattern() [1/2]

void CDPL::Chem::SubstructureEditor::removeExcludePattern

(

std::size_t

idx

)

Removes the substructure exclude pattern at index idx.

Parameters

idx	The zero-based exclude pattern index.

Exceptions

Base::IndexError

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

removeExcludePattern() [2/2]

void CDPL::Chem::SubstructureEditor::removeExcludePattern

(

const PatternIterator &

it

)

Removes the substructure exclude pattern pointed to by it.

Parameters

it	An iterator pointing to the exclude pattern.

Exceptions

Base::RangeError

if it is not in the range [getExcludePatternsBegin(), getExcludePatternsEnd()).

clearExcludePatterns()

void CDPL::Chem::SubstructureEditor::clearExcludePatterns

(

)

Clears the current set of substructure exclude patterns.

getExcludePatternsBegin() [1/2]

PatternIterator CDPL::Chem::SubstructureEditor::getExcludePatternsBegin

(

)

Returns a mutable iterator pointing to the beginning of the stored exclude pattern Chem::MolecularGraph objects.

Returns

A mutable iterator pointing to the beginning of the stored exclude pattern Chem::MolecularGraph objects.

getExcludePatternsEnd() [1/2]

PatternIterator CDPL::Chem::SubstructureEditor::getExcludePatternsEnd

(

)

Returns a mutable iterator pointing to the end of the stored exclude pattern Chem::MolecularGraph objects.

Returns

A mutable iterator pointing to the end of the stored exclude pattern Chem::MolecularGraph objects.

getExcludePatternsBegin() [2/2]

ConstPatternIterator CDPL::Chem::SubstructureEditor::getExcludePatternsBegin

(

)

const

Returns a constant iterator pointing to the beginning of the stored exclude pattern const Chem::MolecularGraph objects.

Returns

A constant iterator pointing to the beginning of the stored exclude pattern const Chem::MolecularGraph objects.

getExcludePatternsEnd() [2/2]

ConstPatternIterator CDPL::Chem::SubstructureEditor::getExcludePatternsEnd

(

)

const

Returns a constant iterator pointing to the end of the stored exclude pattern const Chem::MolecularGraph objects.

Returns

A constant iterator pointing to the end of the stored exclude pattern const Chem::MolecularGraph objects.

setResultPattern()

void CDPL::Chem::SubstructureEditor::setResultPattern

(

const MolecularGraph::SharedPointer &

pattern

)

Sets the result pattern that defines how each matched search pattern instance will be rewritten.

Parameters

pattern

A smart pointer to the molecular graph of the result pattern.

getResultPattern()

const MolecularGraph::SharedPointer& CDPL::Chem::SubstructureEditor::getResultPattern

(

)

const

Returns the currently set result pattern.

Returns

A smart pointer to the molecular graph of the currently set result pattern, or a null pointer if none has been set.

clear()

void CDPL::Chem::SubstructureEditor::clear

(

)

Clears the current editing result pattern and the sets of substructure search and exclude patterns.

edit() [1/2]

std::size_t CDPL::Chem::SubstructureEditor::edit

(

Molecule &

mol

)

Edits the molecule mol in place by applying the result pattern at every search pattern match that is not covered by an exclude pattern.

Parameters

mol	The molecule to edit.

Returns

The number of applied transformations.

edit() [2/2]

std::size_t CDPL::Chem::SubstructureEditor::edit	(	const MolecularGraph &	molgraph,
		Molecule &	res_mol
	)

Copies the molecular graph molgraph into the molecule res_mol and then edits it by calling edit(Molecule&).

Parameters

molgraph	The source molecular graph.
res_mol	The molecule receiving the edited result.

Returns

The number of applied transformations.

operator=()

SubstructureEditor& CDPL::Chem::SubstructureEditor::operator=

(

const SubstructureEditor &

gen

)

Copies the state of the SubstructureEditor instance gen.

Parameters

gen	The other editor instance to copy.

Returns

A reference to itself.

---

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

• SubstructureEditor.hpp