CDPL::Chem::SubstructureHistogramCalculator Class Reference

Counts occurrences of registered SMARTS substructure queries in a molecular graph, emitting the per-pattern hit counts into a user-supplied histogram container. More...

#include <SubstructureHistogramCalculator.hpp>

Classes
class	Pattern
	Holds a single SMARTS query pattern, its histogram ID, its priority and match-handling flags. More...

Public Types
typedef std::shared_ptr< SubstructureHistogramCalculator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated SubstructureHistogramCalculator instances. More...
typedef PatternList::const_iterator	ConstPatternIterator
	A constant iterator over the registered patterns. More...
typedef PatternList::iterator	PatternIterator
	A mutable iterator over the registered patterns. More...

Public Member Functions
	SubstructureHistogramCalculator ()
	Constructs an empty SubstructureHistogramCalculator instance. More...
	SubstructureHistogramCalculator (const SubstructureHistogramCalculator &gen)
	Constructs a copy of the SubstructureHistogramCalculator instance gen. More...
void	addPattern (const MolecularGraph::SharedPointer &molgraph, std::size_t id, std::size_t priority=0, bool all_matches=true, bool unique_matches=true)
	Registers a new pattern by its query molecular graph and per-pattern settings. More...
void	addPattern (const Pattern &pattern)
	Appends a copy of the pre-built pattern pattern. More...
const Pattern &	getPattern (std::size_t idx) const
	Returns the registered pattern at index idx. More...
void	removePattern (std::size_t idx)
	Removes the registered pattern at index idx. More...
void	removePattern (const PatternIterator &it)
	Removes the registered pattern referenced by it. More...
void	clear ()
	Removes all registered patterns. More...
std::size_t	getNumPatterns () const
	Returns the number of registered patterns. More...
ConstPatternIterator	getPatternsBegin () const
	Returns a constant iterator pointing to the first registered pattern. More...
ConstPatternIterator	getPatternsEnd () const
	Returns a constant iterator pointing one past the last registered pattern. More...
PatternIterator	getPatternsBegin ()
	Returns a mutable iterator pointing to the first registered pattern. More...
PatternIterator	getPatternsEnd ()
	Returns a mutable iterator pointing one past the last registered pattern. More...
ConstPatternIterator	begin () const
	Returns a constant iterator pointing to the first registered pattern (range-based for support). More...
ConstPatternIterator	end () const
	Returns a constant iterator pointing one past the last registered pattern (range-based for support). More...
PatternIterator	begin ()
	Returns a mutable iterator pointing to the first registered pattern (range-based for support). More...
PatternIterator	end ()
	Returns a mutable iterator pointing one past the last registered pattern (range-based for support). More...
template<typename T >
void	calculate (const MolecularGraph &molgraph, T &histo)
	Counts substructure occurrences in molgraph and writes the per-pattern hit counts to histo. More...
SubstructureHistogramCalculator &	operator= (const SubstructureHistogramCalculator &gen)
	Replaces the state of this calculator by a copy of the state of gen. More...

Detailed Description

Counts occurrences of registered SMARTS substructure queries in a molecular graph, emitting the per-pattern hit counts into a user-supplied histogram container.

Patterns are added via addPattern() (each pattern carries a numeric ID, a priority and match-handling flags). On calculate() the registered patterns are run in priority order against the input molecular graph; matched atom/bond regions are masked so that subsequent lower-priority patterns cannot re-count overlapping substructures. The per-pattern hit count is then forwarded to the histogram via the expression histo[id]++ for every accepted match.

Member Typedef Documentation

SharedPointer

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

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

ConstPatternIterator

typedef PatternList::const_iterator CDPL::Chem::SubstructureHistogramCalculator::ConstPatternIterator

A constant iterator over the registered patterns.

PatternIterator

typedef PatternList::iterator CDPL::Chem::SubstructureHistogramCalculator::PatternIterator

A mutable iterator over the registered patterns.

Constructor & Destructor Documentation

SubstructureHistogramCalculator() [1/2]

CDPL::Chem::SubstructureHistogramCalculator::SubstructureHistogramCalculator

(

)

Constructs an empty SubstructureHistogramCalculator instance.

SubstructureHistogramCalculator() [2/2]

CDPL::Chem::SubstructureHistogramCalculator::SubstructureHistogramCalculator

(

const SubstructureHistogramCalculator &

gen

)

Constructs a copy of the SubstructureHistogramCalculator instance gen.

Parameters

gen	The SubstructureHistogramCalculator to copy.

Member Function Documentation

addPattern() [1/2]

void CDPL::Chem::SubstructureHistogramCalculator::addPattern	(	const MolecularGraph::SharedPointer &	molgraph,
		std::size_t	id,
		std::size_t	priority = 0,
		bool	all_matches = true,
		bool	unique_matches = true
	)

Registers a new pattern by its query molecular graph and per-pattern settings.

Parameters

molgraph	The SMARTS query molecular graph.
id	The histogram-bin ID to which matches of this pattern contribute.
priority	The pattern's priority; higher-priority patterns are evaluated first.
all_matches	If true, every match of the query is processed; otherwise only the first.
unique_matches	If true, only one of multiple equivalent substructure mappings is processed per match.

addPattern() [2/2]

void CDPL::Chem::SubstructureHistogramCalculator::addPattern

(

const Pattern &

pattern

)

Appends a copy of the pre-built pattern pattern.

Parameters

pattern

The pattern to copy and register.

getPattern()

const Pattern& CDPL::Chem::SubstructureHistogramCalculator::getPattern

(

std::size_t

idx

)

const

Returns the registered pattern at index idx.

Parameters

idx	The zero-based pattern index.

Returns

A const reference to the pattern.

Exceptions

Base::IndexError

if the number of patterns is zero or idx is not in the range [0, getNumPatterns() - 1].

removePattern() [1/2]

void CDPL::Chem::SubstructureHistogramCalculator::removePattern

(

std::size_t

idx

)

Removes the registered pattern at index idx.

Parameters

idx	The zero-based pattern index.

Exceptions

Base::IndexError

if the number of patterns is zero or idx is not in the range [0, getNumPatterns() - 1].

removePattern() [2/2]

void CDPL::Chem::SubstructureHistogramCalculator::removePattern

(

const PatternIterator &

it

)

Removes the registered pattern referenced by it.

Parameters

it	Iterator referencing the pattern to remove.

Exceptions

Base::IndexError

if it is not in the range [getPatternsBegin(), getPatternsEnd() - 1].

clear()

void CDPL::Chem::SubstructureHistogramCalculator::clear

(

)

Removes all registered patterns.

getNumPatterns()

std::size_t CDPL::Chem::SubstructureHistogramCalculator::getNumPatterns

(

)

const

Returns the number of registered patterns.

Returns

The pattern count.

getPatternsBegin() [1/2]

ConstPatternIterator CDPL::Chem::SubstructureHistogramCalculator::getPatternsBegin

(

)

const

Returns a constant iterator pointing to the first registered pattern.

Returns

A constant iterator pointing to the first pattern.

getPatternsEnd() [1/2]

ConstPatternIterator CDPL::Chem::SubstructureHistogramCalculator::getPatternsEnd

(

)

const

Returns a constant iterator pointing one past the last registered pattern.

Returns

A constant iterator pointing one past the last pattern.

getPatternsBegin() [2/2]

PatternIterator CDPL::Chem::SubstructureHistogramCalculator::getPatternsBegin

(

)

Returns a mutable iterator pointing to the first registered pattern.

Returns

A mutable iterator pointing to the first pattern.

getPatternsEnd() [2/2]

PatternIterator CDPL::Chem::SubstructureHistogramCalculator::getPatternsEnd

(

)

Returns a mutable iterator pointing one past the last registered pattern.

Returns

A mutable iterator pointing one past the last pattern.

begin() [1/2]

ConstPatternIterator CDPL::Chem::SubstructureHistogramCalculator::begin

(

)

const

Returns a constant iterator pointing to the first registered pattern (range-based for support).

Returns

A constant iterator pointing to the first pattern.

end() [1/2]

ConstPatternIterator CDPL::Chem::SubstructureHistogramCalculator::end

(

)

const

Returns a constant iterator pointing one past the last registered pattern (range-based for support).

Returns

A constant iterator pointing one past the last pattern.

begin() [2/2]

PatternIterator CDPL::Chem::SubstructureHistogramCalculator::begin

(

)

Returns a mutable iterator pointing to the first registered pattern (range-based for support).

Returns

A mutable iterator pointing to the first pattern.

end() [2/2]

PatternIterator CDPL::Chem::SubstructureHistogramCalculator::end

(

)

Returns a mutable iterator pointing one past the last registered pattern (range-based for support).

Returns

A mutable iterator pointing one past the last pattern.

calculate()

template<typename T >

void CDPL::Chem::SubstructureHistogramCalculator::calculate	(	const MolecularGraph &	molgraph,
		T &	histo
	)

Counts substructure occurrences in molgraph and writes the per-pattern hit counts to histo.

For every accepted match, the histogram is updated via histo[id] += 1 with the ID being the histogram-bin ID of the matching pattern.

Template Parameters

T	The histogram type (must support operator[] returning an arithmetic value).

Parameters

molgraph	The molecular graph to be analyzed.
histo	The histogram receiving the hit counts.

operator=()

SubstructureHistogramCalculator& CDPL::Chem::SubstructureHistogramCalculator::operator=

(

const SubstructureHistogramCalculator &

gen

)

Replaces the state of this calculator by a copy of the state of gen.

Parameters

gen	The source SubstructureHistogramCalculator.

Returns

A reference to itself.

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

• SubstructureHistogramCalculator.hpp