CDPL::Chem::SubstructureEditor Class Reference

Pattern-driven editor that rewrites matched substructures of a Chem::Molecule using a result template, with optional exclude patterns guarding sites that must not be touched. 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 over the molecular graphs of the stored search/exclude patterns. More...
typedef boost::transform_iterator< GetMolGraphFunc, PatternList::iterator >	PatternIterator
	A mutable iterator over the molecular graphs of the stored search/exclude patterns. 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 search pattern at index idx. More...
void	removeSearchPattern (std::size_t idx)
	Removes the search pattern at index idx. More...
void	removeSearchPattern (const PatternIterator &it)
	Removes the search pattern pointed to by it. More...
void	clearSearchPatterns ()
	Clears the current set of substructuresearch patterns. More...
PatternIterator	getSearchPatternsBegin ()
	Returns a mutable iterator pointing to the beginning of the stored search patterns. More...
PatternIterator	getSearchPatternsEnd ()
	Returns a mutable iterator pointing to the end of the stored search patterns. More...
ConstPatternIterator	getSearchPatternsBegin () const
	Returns a constant iterator pointing to the beginning of the stored search patterns. More...
ConstPatternIterator	getSearchPatternsEnd () const
	Returns a constant iterator pointing to the end of the stored search patterns. 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 exclude pattern at index idx. More...
void	removeExcludePattern (std::size_t idx)
	Removes the exclude pattern at index idx. More...
void	removeExcludePattern (const PatternIterator &it)
	Removes the 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 patterns. More...
PatternIterator	getExcludePatternsEnd ()
	Returns a mutable iterator pointing to the end of the stored exclude patterns. More...
ConstPatternIterator	getExcludePatternsBegin () const
	Returns a constant iterator pointing to the beginning of the stored exclude patterns. More...
ConstPatternIterator	getExcludePatternsEnd () const
	Returns a constant iterator pointing to the end of the stored exclude patterns. 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 mol in place by applying the result pattern at every search-pattern match that is not covered by an exclude pattern; repeats until no further changes occur. More...
std::size_t	edit (const MolecularGraph &molgraph, Molecule &res_mol)
	Copies molgraph into res_mol and then edits res_mol via 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 Chem::Molecule using a result template, with optional exclude patterns guarding sites that must not be touched.

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 over the molecular graphs of the stored search/exclude patterns.

PatternIterator

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

A mutable iterator over the molecular graphs of the stored search/exclude patterns.

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 SubstructureEditor instance to copy.

~SubstructureEditor()

CDPL::Chem::SubstructureEditor::~SubstructureEditor

(

)

Destructor.

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

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 search pattern at index idx.

Parameters

idx	The zero-based search-pattern index.

Returns

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 search pattern at index idx.

Parameters

idx	The zero-based search-pattern index to remove.

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 search pattern pointed to by it.

Parameters

it	An iterator pointing to the search pattern to remove.

Exceptions

Base::RangeError

if it does not point into the current search-pattern range.

clearSearchPatterns()

void CDPL::Chem::SubstructureEditor::clearSearchPatterns

(

)

Clears the current set of substructuresearch patterns.

getSearchPatternsBegin() [1/2]

PatternIterator CDPL::Chem::SubstructureEditor::getSearchPatternsBegin

(

)

Returns a mutable iterator pointing to the beginning of the stored search patterns.

Returns

A mutable iterator pointing to the beginning of the stored search patterns.

getSearchPatternsEnd() [1/2]

PatternIterator CDPL::Chem::SubstructureEditor::getSearchPatternsEnd

(

)

Returns a mutable iterator pointing to the end of the stored search patterns.

Returns

A mutable iterator pointing to the end of the stored search patterns.

getSearchPatternsBegin() [2/2]

ConstPatternIterator CDPL::Chem::SubstructureEditor::getSearchPatternsBegin

(

)

const

Returns a constant iterator pointing to the beginning of the stored search patterns.

Returns

A constant iterator pointing to the beginning of the stored search patterns.

getSearchPatternsEnd() [2/2]

ConstPatternIterator CDPL::Chem::SubstructureEditor::getSearchPatternsEnd

(

)

const

Returns a constant iterator pointing to the end of the stored search patterns.

Returns

A constant iterator pointing to the end of the stored search patterns.

addExcludePattern()

void CDPL::Chem::SubstructureEditor::addExcludePattern

(

const MolecularGraph::SharedPointer &

molgraph

)

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

Parameters

molgraph

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 exclude pattern at index idx.

Parameters

idx	The zero-based exclude-pattern index.

Returns

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 exclude pattern at index idx.

Parameters

idx	The zero-based exclude-pattern index to remove.

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 exclude pattern pointed to by it.

Parameters

it	An iterator pointing to the exclude pattern to remove.

Exceptions

Base::RangeError

if it does not point into the current exclude-pattern range.

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 patterns.

Returns

A mutable iterator pointing to the beginning of the stored exclude patterns.

getExcludePatternsEnd() [1/2]

PatternIterator CDPL::Chem::SubstructureEditor::getExcludePatternsEnd

(

)

Returns a mutable iterator pointing to the end of the stored exclude patterns.

Returns

A mutable iterator pointing to the end of the stored exclude patterns.

getExcludePatternsBegin() [2/2]

ConstPatternIterator CDPL::Chem::SubstructureEditor::getExcludePatternsBegin

(

)

const

Returns a constant iterator pointing to the beginning of the stored exclude patterns.

Returns

A constant iterator pointing to the beginning of the stored exclude patterns.

getExcludePatternsEnd() [2/2]

ConstPatternIterator CDPL::Chem::SubstructureEditor::getExcludePatternsEnd

(

)

const

Returns a constant iterator pointing to the end of the stored exclude patterns.

Returns

A constant iterator pointing to the end of the stored exclude patterns.

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

The molecular graph of the result pattern.

getResultPattern()

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

(

)

const

Returns the currently set result pattern.

Returns

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 mol in place by applying the result pattern at every search-pattern match that is not covered by an exclude pattern; repeats until no further changes occur.

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 molgraph into res_mol and then edits res_mol via 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 SubstructureEditor instance to copy.

Returns

A reference to itself.

---

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

• SubstructureEditor.hpp