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; 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() - 1].

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() - 1].

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() - 1].

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() - 1].

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