CDPL::Chem::FragmentGenerator Class Reference

Generic rule-based molecule fragmentation engine that splits a molecular graph along bonds matching user-defined SMARTS fragmentation rules. More...

#include <FragmentGenerator.hpp>

Inheritance diagram for CDPL::Chem::FragmentGenerator:

Classes
class	ExcludePattern
	A pattern overriding a fragmentation rule: bonds matching the pattern are not cleaved. More...
class	FragmentationRule
	A single fragmentation rule, consisting of a SMARTS match pattern and a numeric rule ID. More...
class	FragmentLink
	Records the connectivity between two fragments produced by a single bond cleavage. More...

Public Types
typedef std::shared_ptr< FragmentGenerator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated FragmentGenerator instances. More...
typedef std::function< bool(const MolecularGraph &)>	FragmentFilterFunction
	Type of a predicate accepting/rejecting a generated fragment. More...
typedef FragmentationRuleList::const_iterator	ConstFragmentationRuleIterator
	A constant iterator over the registered fragmentation rules. More...
typedef FragmentationRuleList::iterator	FragmentationRuleIterator
	A mutable iterator over the registered fragmentation rules. More...
typedef ExcludePatternList::const_iterator	ConstExcludePatternIterator
	A constant iterator over the registered exclude patterns. More...
typedef ExcludePatternList::iterator	ExcludePatternIterator
	A mutable iterator over the registered exclude patterns. More...
typedef FragmentLinkList::const_iterator	ConstFragmentLinkIterator
	A constant iterator over the generated fragment links. More...

Public Member Functions
	FragmentGenerator ()
	Constructs the FragmentGenerator instance. More...
	FragmentGenerator (const FragmentGenerator &gen)
	Constructs a copy of the FragmentGenerator instance gen. More...
virtual	~FragmentGenerator ()
	Virtual destructor. More...
FragmentGenerator &	operator= (const FragmentGenerator &gen)
	Replaces the state of this generator by a copy of the state of gen. More...
void	addFragmentationRule (const MolecularGraph::SharedPointer &match_ptn, unsigned int rule_id)
	Registers a new fragmentation rule by its SMARTS match pattern and rule ID. More...
void	addFragmentationRule (const FragmentationRule &rule)
	Appends a copy of the pre-built fragmentation rule rule. More...
const FragmentationRule &	getFragmentationRule (std::size_t idx) const
	Returns the fragmentation rule at index idx. More...
FragmentationRule &	getFragmentationRule (std::size_t idx)
	Returns the fragmentation rule at index idx. More...
ConstFragmentationRuleIterator	getFragmentationRulesBegin () const
	Returns a constant iterator pointing to the first registered fragmentation rule. More...
ConstFragmentationRuleIterator	getFragmentationRulesEnd () const
	Returns a constant iterator pointing one past the last registered fragmentation rule. More...
FragmentationRuleIterator	getFragmentationRulesBegin ()
	Returns a mutable iterator pointing to the first registered fragmentation rule. More...
FragmentationRuleIterator	getFragmentationRulesEnd ()
	Returns a mutable iterator pointing one past the last registered fragmentation rule. More...
void	removeFragmentationRule (std::size_t idx)
	Removes the fragmentation rule at index idx. More...
std::size_t	getNumFragmentationRules () const
	Returns the number of registered fragmentation rules. More...
void	clearFragmentationRules ()
	Removes all registered fragmentation rules. More...
void	addExcludePattern (const MolecularGraph::SharedPointer &match_ptn, unsigned int rule_id)
	Registers a rule-specific exclude pattern. More...
void	addExcludePattern (const MolecularGraph::SharedPointer &match_ptn)
	Registers a generic exclude pattern (applies to all fragmentation rules). More...
void	addExcludePattern (const ExcludePattern &excl_ptn)
	Appends a copy of the pre-built exclude pattern excl_ptn. More...
const ExcludePattern &	getExcludePattern (std::size_t idx) const
	Returns the exclude pattern at index idx. More...
ExcludePattern &	getExcludePattern (std::size_t idx)
	Returns the exclude pattern at index idx. More...
ConstExcludePatternIterator	getExcludePatternsBegin () const
	Returns a constant iterator pointing to the first registered exclude pattern. More...
ConstExcludePatternIterator	getExcludePatternsEnd () const
	Returns a constant iterator pointing one past the last registered exclude pattern. More...
ExcludePatternIterator	getExcludePatternsBegin ()
	Returns a mutable iterator pointing to the first registered exclude pattern. More...
ExcludePatternIterator	getExcludePatternsEnd ()
	Returns a mutable iterator pointing one past the last registered exclude pattern. More...
void	removeExcludePattern (std::size_t idx)
	Removes the exclude pattern at index idx. More...
std::size_t	getNumExcludePatterns () const
	Returns the number of registered exclude patterns. More...
void	clearExcludePatterns ()
	Removes all registered exclude patterns. More...
bool	splitBondsIncluded () const
	Tells whether the split (cleaved) bonds are retained in the output fragments. More...
void	includeSplitBonds (bool include)
	Specifies whether the split (cleaved) bonds shall be retained in the output fragments. More...
const FragmentFilterFunction &	getFragmentFilterFunction () const
	Returns the predicate used to filter the generated fragments. More...
void	setFragmentFilterFunction (const FragmentFilterFunction &func)
	Sets the predicate used to filter the generated fragments (fragments for which the predicate returns false are discarded). More...
void	generate (const MolecularGraph &molgraph, FragmentList &frag_list, bool append=false)
	Performs the fragmentation of molgraph and writes the resulting fragments to frag_list. More...
std::size_t	getNumFragmentLinks () const
	Returns the number of fragment links produced by the most recent generate() call. More...
const FragmentLink &	getFragmentLink (std::size_t idx) const
	Returns the fragment link at index idx. More...
ConstFragmentLinkIterator	getFragmentLinksBegin () const
	Returns a constant iterator pointing to the first fragment link. More...
ConstFragmentLinkIterator	getFragmentLinksEnd () const
	Returns a constant iterator pointing one past the last fragment link. More...

Detailed Description

Generic rule-based molecule fragmentation engine that splits a molecular graph along bonds matching user-defined SMARTS fragmentation rules.

Fragmentation rules are added via addFragmentationRule() (each rule has a SMARTS pattern matching a bond plus a numeric rule ID). Bonds matching any registered rule are scheduled for splitting, unless a registered exclude pattern overrides the split. The optional fragment filter rejects generated fragments based on a user-supplied predicate. The connectivity between the resulting fragments is exposed via the FragmentLink list, recording for each cleaved bond the two adjacent fragment indices, the cleaved bond, the matching rule and per-side atom labels.

Member Typedef Documentation

SharedPointer

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

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

FragmentFilterFunction

typedef std::function<bool(const MolecularGraph&)> CDPL::Chem::FragmentGenerator::FragmentFilterFunction

Type of a predicate accepting/rejecting a generated fragment.

ConstFragmentationRuleIterator

typedef FragmentationRuleList::const_iterator CDPL::Chem::FragmentGenerator::ConstFragmentationRuleIterator

A constant iterator over the registered fragmentation rules.

FragmentationRuleIterator

typedef FragmentationRuleList::iterator CDPL::Chem::FragmentGenerator::FragmentationRuleIterator

A mutable iterator over the registered fragmentation rules.

ConstExcludePatternIterator

typedef ExcludePatternList::const_iterator CDPL::Chem::FragmentGenerator::ConstExcludePatternIterator

A constant iterator over the registered exclude patterns.

ExcludePatternIterator

typedef ExcludePatternList::iterator CDPL::Chem::FragmentGenerator::ExcludePatternIterator

A mutable iterator over the registered exclude patterns.

ConstFragmentLinkIterator

typedef FragmentLinkList::const_iterator CDPL::Chem::FragmentGenerator::ConstFragmentLinkIterator

A constant iterator over the generated fragment links.

Constructor & Destructor Documentation

FragmentGenerator() [1/2]

CDPL::Chem::FragmentGenerator::FragmentGenerator

(

)

Constructs the FragmentGenerator instance.

FragmentGenerator() [2/2]

CDPL::Chem::FragmentGenerator::FragmentGenerator

(

const FragmentGenerator &

gen

)

Constructs a copy of the FragmentGenerator instance gen.

Parameters

gen	The FragmentGenerator to copy.

~FragmentGenerator()

virtual CDPL::Chem::FragmentGenerator::~FragmentGenerator ( )

inlinevirtual

Virtual destructor.

Member Function Documentation

operator=()

FragmentGenerator& CDPL::Chem::FragmentGenerator::operator=

(

const FragmentGenerator &

gen

)

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

Parameters

gen	The source FragmentGenerator.

Returns

A reference to itself.

addFragmentationRule() [1/2]

void CDPL::Chem::FragmentGenerator::addFragmentationRule	(	const MolecularGraph::SharedPointer &	match_ptn,
		unsigned int	rule_id
	)

Registers a new fragmentation rule by its SMARTS match pattern and rule ID.

Parameters

match_ptn	The SMARTS match pattern (must match a single bond to be cleaved).
rule_id	The rule identifier.

addFragmentationRule() [2/2]

void CDPL::Chem::FragmentGenerator::addFragmentationRule

(

const FragmentationRule &

rule

)

Appends a copy of the pre-built fragmentation rule rule.

Parameters

rule	The rule to copy and register.

getFragmentationRule() [1/2]

const FragmentationRule& CDPL::Chem::FragmentGenerator::getFragmentationRule

(

std::size_t

idx

)

const

Returns the fragmentation rule at index idx.

Parameters

idx	The zero-based rule index.

Returns

A const reference to the rule.

Exceptions

Base::IndexError

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

getFragmentationRule() [2/2]

FragmentationRule& CDPL::Chem::FragmentGenerator::getFragmentationRule

(

std::size_t

idx

)

Returns the fragmentation rule at index idx.

Parameters

idx	The zero-based rule index.

Returns

A reference to the rule.

Exceptions

Base::IndexError

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

getFragmentationRulesBegin() [1/2]

ConstFragmentationRuleIterator CDPL::Chem::FragmentGenerator::getFragmentationRulesBegin

(

)

const

Returns a constant iterator pointing to the first registered fragmentation rule.

Returns

A constant iterator pointing to the first rule.

getFragmentationRulesEnd() [1/2]

ConstFragmentationRuleIterator CDPL::Chem::FragmentGenerator::getFragmentationRulesEnd

(

)

const

Returns a constant iterator pointing one past the last registered fragmentation rule.

Returns

A constant iterator pointing one past the last rule.

getFragmentationRulesBegin() [2/2]

FragmentationRuleIterator CDPL::Chem::FragmentGenerator::getFragmentationRulesBegin

(

)

Returns a mutable iterator pointing to the first registered fragmentation rule.

Returns

A mutable iterator pointing to the first rule.

getFragmentationRulesEnd() [2/2]

FragmentationRuleIterator CDPL::Chem::FragmentGenerator::getFragmentationRulesEnd

(

)

Returns a mutable iterator pointing one past the last registered fragmentation rule.

Returns

A mutable iterator pointing one past the last rule.

removeFragmentationRule()

void CDPL::Chem::FragmentGenerator::removeFragmentationRule

(

std::size_t

idx

)

Removes the fragmentation rule at index idx.

Parameters

idx	The zero-based rule index.

Exceptions

Base::IndexError

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

getNumFragmentationRules()

std::size_t CDPL::Chem::FragmentGenerator::getNumFragmentationRules

(

)

const

Returns the number of registered fragmentation rules.

Returns

The rule count.

clearFragmentationRules()

void CDPL::Chem::FragmentGenerator::clearFragmentationRules

(

)

Removes all registered fragmentation rules.

addExcludePattern() [1/3]

void CDPL::Chem::FragmentGenerator::addExcludePattern	(	const MolecularGraph::SharedPointer &	match_ptn,
		unsigned int	rule_id
	)

Registers a rule-specific exclude pattern.

Parameters

match_ptn	The SMARTS match pattern.
rule_id	The rule ID this exclusion applies to.

addExcludePattern() [2/3]

void CDPL::Chem::FragmentGenerator::addExcludePattern

(

const MolecularGraph::SharedPointer &

match_ptn

)

Registers a generic exclude pattern (applies to all fragmentation rules).

Parameters

match_ptn

The SMARTS match pattern.

addExcludePattern() [3/3]

void CDPL::Chem::FragmentGenerator::addExcludePattern

(

const ExcludePattern &

excl_ptn

)

Appends a copy of the pre-built exclude pattern excl_ptn.

Parameters

excl_ptn

The exclude pattern to copy and register.

getExcludePattern() [1/2]

const ExcludePattern& CDPL::Chem::FragmentGenerator::getExcludePattern

(

std::size_t

idx

)

const

Returns the exclude pattern at index idx.

Parameters

idx	The zero-based pattern index.

Returns

A const reference to the exclude pattern.

Exceptions

Base::IndexError

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

getExcludePattern() [2/2]

ExcludePattern& CDPL::Chem::FragmentGenerator::getExcludePattern

(

std::size_t

idx

)

Returns the exclude pattern at index idx.

Parameters

idx	The zero-based pattern index.

Returns

A reference to the exclude pattern.

Exceptions

Base::IndexError

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

getExcludePatternsBegin() [1/2]

ConstExcludePatternIterator CDPL::Chem::FragmentGenerator::getExcludePatternsBegin

(

)

const

Returns a constant iterator pointing to the first registered exclude pattern.

Returns

A constant iterator pointing to the first exclude pattern.

getExcludePatternsEnd() [1/2]

ConstExcludePatternIterator CDPL::Chem::FragmentGenerator::getExcludePatternsEnd

(

)

const

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

Returns

A constant iterator pointing one past the last exclude pattern.

getExcludePatternsBegin() [2/2]

ExcludePatternIterator CDPL::Chem::FragmentGenerator::getExcludePatternsBegin

(

)

Returns a mutable iterator pointing to the first registered exclude pattern.

Returns

A mutable iterator pointing to the first exclude pattern.

getExcludePatternsEnd() [2/2]

ExcludePatternIterator CDPL::Chem::FragmentGenerator::getExcludePatternsEnd

(

)

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

Returns

A mutable iterator pointing one past the last exclude pattern.

removeExcludePattern()

void CDPL::Chem::FragmentGenerator::removeExcludePattern

(

std::size_t

idx

)

Removes the exclude pattern at index idx.

Parameters

idx	The zero-based pattern index.

Exceptions

Base::IndexError

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

getNumExcludePatterns()

std::size_t CDPL::Chem::FragmentGenerator::getNumExcludePatterns

(

)

const

Returns the number of registered exclude patterns.

Returns

The exclude-pattern count.

clearExcludePatterns()

void CDPL::Chem::FragmentGenerator::clearExcludePatterns

(

)

Removes all registered exclude patterns.

splitBondsIncluded()

bool CDPL::Chem::FragmentGenerator::splitBondsIncluded

(

)

const

Tells whether the split (cleaved) bonds are retained in the output fragments.

Returns

true if split bonds are retained, and false otherwise.

includeSplitBonds()

void CDPL::Chem::FragmentGenerator::includeSplitBonds

(

bool

include

)

Specifies whether the split (cleaved) bonds shall be retained in the output fragments.

Parameters

include

If true, the cleaved bonds remain part of the adjacent output fragments.

getFragmentFilterFunction()

const FragmentFilterFunction& CDPL::Chem::FragmentGenerator::getFragmentFilterFunction

(

)

const

Returns the predicate used to filter the generated fragments.

Returns

A const reference to the fragment-filter function.

setFragmentFilterFunction()

void CDPL::Chem::FragmentGenerator::setFragmentFilterFunction

(

const FragmentFilterFunction &

func

)

Sets the predicate used to filter the generated fragments (fragments for which the predicate returns false are discarded).

Parameters

func	The new fragment-filter function.

generate()

void CDPL::Chem::FragmentGenerator::generate	(	const MolecularGraph &	molgraph,
		FragmentList &	frag_list,
		bool	append = false
	)

Performs the fragmentation of molgraph and writes the resulting fragments to frag_list.

Parameters

molgraph	The molecular graph to fragment.
frag_list	The output fragment list.
append	If true, new fragments are appended to frag_list; otherwise the list is cleared first.

getNumFragmentLinks()

std::size_t CDPL::Chem::FragmentGenerator::getNumFragmentLinks

(

)

const

Returns the number of fragment links produced by the most recent generate() call.

Returns

The fragment-link count.

getFragmentLink()

const FragmentLink& CDPL::Chem::FragmentGenerator::getFragmentLink

(

std::size_t

idx

)

const

Returns the fragment link at index idx.

Parameters

idx	The zero-based link index.

Returns

A const reference to the fragment link.

Exceptions

Base::IndexError

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

getFragmentLinksBegin()

ConstFragmentLinkIterator CDPL::Chem::FragmentGenerator::getFragmentLinksBegin

(

)

const

Returns a constant iterator pointing to the first fragment link.

Returns

A constant iterator pointing to the first fragment link.

getFragmentLinksEnd()

ConstFragmentLinkIterator CDPL::Chem::FragmentGenerator::getFragmentLinksEnd

(

)

const

Returns a constant iterator pointing one past the last fragment link.

Returns

A constant iterator pointing one past the last fragment link.

---

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

• FragmentGenerator.hpp