Generation of atom-centered circular substructure fingerprints in the spirit of SciTegic's Extended Connectivity Fingerprints (ECFP). More...

#include <CircularFingerprintGenerator.hpp>

Classes
class	DefAtomIdentifierFunctor
	The functor for the generation of ECFP atom identifiers. More...

class	DefBondIdentifierFunctor
	The default functor for the generation of bond identifiers. More...

Public Types
typedef std::function< std::uint64_t(const Chem::Atom &, const Chem::MolecularGraph &)>	AtomIdentifierFunction
	Type of the generic functor class used to store user-defined functions or function objects for the generation of atom identifiers. More...

typedef std::function< std::uint64_t(const Chem::Bond &)>	BondIdentifierFunction
	Type of the generic functor class used to store user-defined functions or function objects for the generation of bond identifiers. More...

Public Member Functions
	CircularFingerprintGenerator ()
	Constructs the `CircularFingerprintGenerator` instance. More...

	CircularFingerprintGenerator (const Chem::MolecularGraph &molgraph)
	Constructs the `CircularFingerprintGenerator` instance and generates the atom-centered circular substructure fingerprint of the molecular graph molgraph. More...

void	setAtomIdentifierFunction (const AtomIdentifierFunction &func)
	Allows to specify a customized function for the generation of initial atom identifiers. More...

void	setBondIdentifierFunction (const BondIdentifierFunction &func)
	Allows to specify a customized function for the generation of initial bond identifiers. More...

void	setNumIterations (std::size_t num_iter)
	Allows to specify the desired number of feature substructure growing iterations. More...

std::size_t	getNumIterations () const
	Returns the number of feature substructure growing iterations. More...

void	includeHydrogens (bool include)
	Specifies whether hydrogens shall be included in the generated fingerprint. More...

bool	hydrogensIncluded () const
	Tells whether hydrogens are considered during fingerprint generation. More...

void	includeChirality (bool include)
	Specifies whether atom stereo configurations shall be incorporated into atom identifiers. More...

bool	chiralityIncluded () const
	Tells whether atom chirality is considered during fingerprint generation. More...

void	generate (const Chem::MolecularGraph &molgraph)
	Generates the atom-centered circular substructure fingerprint of the molecular graph molgraph. More...

void	setFeatureBits (Util::BitSet &bs, bool reset=true) const
	Maps previously generated feature identifiers to bit indices and sets the correponding bits of bs. More...

void	setFeatureBits (std::size_t atom_idx, Util::BitSet &bs, bool reset=true) const
	Maps previously generated identifiers of structural features involving the atom specified by atom_idx to bit indices and sets the correponding bits of bs. More...

std::size_t	getNumFeatures () const
	Returns the number of features generated by the most recent call to generate(). More...

std::uint64_t	getFeatureIdentifier (std::size_t ftr_idx) const
	Returns the identifier of the feature at index ftr_idx. More...

const Util::BitSet &	getFeatureSubstructure (std::size_t ftr_idx) const
	Returns the atom-bit mask describing the substructure covered by the feature at index ftr_idx. More...

void	getFeatureSubstructure (std::size_t ftr_idx, Chem::Fragment &frag, bool clear=true) const
	Extracts the substructure covered by the feature at index ftr_idx into frag. More...

void	getFeatureSubstructures (std::size_t bit_idx, std::size_t bs_size, Chem::FragmentList &frags, bool clear=true) const
	Extracts the substructures of every feature that, when folded into a bitset of size bs_size, maps to the bit index bit_idx. More...

Static Public Attributes
static constexpr unsigned int	DEF_ATOM_PROPERTY_FLAGS
	Specifies the default set of atomic properties considered in the generation of atom identifiers by DefAtomIdentifierFunctor. More...

static constexpr unsigned int	DEF_BOND_PROPERTY_FLAGS
	Specifies the default set of bond properties considered in the generation of bond identifiers by DefBondIdentifierFunctor. More...

Detailed Description

Generation of atom-centered circular substructure fingerprints in the spirit of SciTegic's Extended Connectivity Fingerprints (ECFP).

Starting from initial atom and bond identifiers (generated either by the built-in DefAtomIdentifierFunctor / DefBondIdentifierFunctor or by user-supplied functions) the generator runs a configurable number of growing iterations (see setNumIterations()). Each iteration produces a new set of feature identifiers from the identifiers of the previous iteration and the connecting bonds, capturing circular substructures of incrementing radius. The resulting feature identifiers can be folded into a bitset of any size via setFeatureBits().

See also: [STECFP]

Member Typedef Documentation

◆ AtomIdentifierFunction

typedef std::function<std::uint64_t(const Chem::Atom&, const Chem::MolecularGraph&)> CDPL::Descr::CircularFingerprintGenerator::AtomIdentifierFunction

Type of the generic functor class used to store user-defined functions or function objects for the generation of atom identifiers.

Functions or function objects for the generation of atom identifiers are required to take the atom (as a const reference to Chem::Atom) and containing molecular graph (as a const reference to Chem::MolecularGraph) as argument and return the identifier as an integer of type std::uint64_t (see [FUNWRP]).

◆ BondIdentifierFunction

typedef std::function<std::uint64_t(const Chem::Bond&)> CDPL::Descr::CircularFingerprintGenerator::BondIdentifierFunction

Type of the generic functor class used to store user-defined functions or function objects for the generation of bond identifiers.

Functions or function objects for the generation of bond identifiers are required to take the bond (as a const reference to Chem::Bond) as argument and return the identifier as an integer of type std::uint64_t (see [FUNWRP]).

Constructor & Destructor Documentation

◆ CircularFingerprintGenerator() [1/2]

CDPL::Descr::CircularFingerprintGenerator::CircularFingerprintGenerator ( )

Constructs the CircularFingerprintGenerator instance.

◆ CircularFingerprintGenerator() [2/2]

CDPL::Descr::CircularFingerprintGenerator::CircularFingerprintGenerator ( const Chem::MolecularGraph & molgraph )

Constructs the CircularFingerprintGenerator instance and generates the atom-centered circular substructure fingerprint of the molecular graph molgraph.

Parameters

molgraph The molecular graph to process.

Member Function Documentation

◆ setAtomIdentifierFunction()

void CDPL::Descr::CircularFingerprintGenerator::setAtomIdentifierFunction ( const AtomIdentifierFunction & func )

Allows to specify a customized function for the generation of initial atom identifiers.

Parameters

func	A CircularFingerprintGenerator::AtomIdentifierFunction instance that wraps the target function.

Note: By default, atom identifiers are generated by a CircularFingerprintGenerator::DefAtomIdentifierFunctor instance. If the generated initial identifier for an atom is 0, the atom is regarded as not being present in the processed molecular graph.

◆ setBondIdentifierFunction()

void CDPL::Descr::CircularFingerprintGenerator::setBondIdentifierFunction ( const BondIdentifierFunction & func )

Allows to specify a customized function for the generation of initial bond identifiers.

Parameters

func	A CircularFingerprintGenerator::BondIdentifierFunction instance that wraps the target function.

Note: By default, bond identifiers are generated by a CircularFingerprintGenerator::DefBondIdentifierFunctor instance. If the generated initial identifier for a bond is 0, the bond is regarded as not being present in the processed molecular graph.

◆ setNumIterations()

void CDPL::Descr::CircularFingerprintGenerator::setNumIterations ( std::size_t num_iter )

Allows to specify the desired number of feature substructure growing iterations.

Parameters

num_iter The number of iterations.

Note: The default number of iterations is 2.

◆ getNumIterations()

std::size_t CDPL::Descr::CircularFingerprintGenerator::getNumIterations ( ) const

Returns the number of feature substructure growing iterations.

Returns: The number of iterations.

◆ includeHydrogens()

void CDPL::Descr::CircularFingerprintGenerator::includeHydrogens ( bool include )

Specifies whether hydrogens shall be included in the generated fingerprint.

Parameters

include If true, hydrogens are considered as regular atoms during fingerprint generation.

◆ hydrogensIncluded()

bool CDPL::Descr::CircularFingerprintGenerator::hydrogensIncluded ( ) const

Tells whether hydrogens are considered during fingerprint generation.

Returns: true if hydrogens are considered, and false otherwise.

◆ includeChirality()

void CDPL::Descr::CircularFingerprintGenerator::includeChirality ( bool include )

Specifies whether atom stereo configurations shall be incorporated into atom identifiers.

Parameters

include If true, atom chirality is considered during fingerprint generation.

◆ chiralityIncluded()

bool CDPL::Descr::CircularFingerprintGenerator::chiralityIncluded ( ) const

Tells whether atom chirality is considered during fingerprint generation.

Returns: true if atom chirality is considered, and false otherwise.

◆ generate()

void CDPL::Descr::CircularFingerprintGenerator::generate ( const Chem::MolecularGraph & molgraph )

Generates the atom-centered circular substructure fingerprint of the molecular graph molgraph.

Parameters

molgraph The molecular graph to process.

◆ setFeatureBits() [1/2]

void CDPL::Descr::CircularFingerprintGenerator::setFeatureBits	(	Util::BitSet &	bs,
		bool	reset = `true`
	)		const

Maps previously generated feature identifiers to bit indices and sets the correponding bits of bs.

Parameters

bs	The target bitset.
reset	If true, bs will be cleared before any feature bits are set.

Note: The binary fingerprint size is specified implicitly via the size of bs.

See also: generate()

◆ setFeatureBits() [2/2]

void CDPL::Descr::CircularFingerprintGenerator::setFeatureBits	(	std::size_t	atom_idx,
		Util::BitSet &	bs,
		bool	reset = `true`
	)		const

Maps previously generated identifiers of structural features involving the atom specified by atom_idx to bit indices and sets the correponding bits of bs.

Parameters

atom_idx	The index of the atom that has to be involved in the structural features.
bs	The target bitset.
reset	If true, bs will be cleared before any feature bits are set.

Note: The binary fingerprint size is specified implicitly via the size of bs.

See also: generate()

◆ getNumFeatures()

std::size_t CDPL::Descr::CircularFingerprintGenerator::getNumFeatures ( ) const

Returns the number of features generated by the most recent call to generate().

Returns: The number of features.

◆ getFeatureIdentifier()

std::uint64_t CDPL::Descr::CircularFingerprintGenerator::getFeatureIdentifier ( std::size_t ftr_idx ) const

Returns the identifier of the feature at index ftr_idx.

Parameters

ftr_idx The zero-based feature index.

Returns: The feature identifier.

◆ getFeatureSubstructure() [1/2]

const Util::BitSet& CDPL::Descr::CircularFingerprintGenerator::getFeatureSubstructure ( std::size_t ftr_idx ) const

Returns the atom-bit mask describing the substructure covered by the feature at index ftr_idx.

In the returned bitset, the bit at position i is set if the atom with index i is part of the feature substructure.

Parameters

ftr_idx The zero-based feature index.

Returns: A const reference to the atom-bit mask.

◆ getFeatureSubstructure() [2/2]

void CDPL::Descr::CircularFingerprintGenerator::getFeatureSubstructure	(	std::size_t	ftr_idx,
		Chem::Fragment &	frag,
		bool	clear = `true`
	)		const

Extracts the substructure covered by the feature at index ftr_idx into frag.

Parameters

ftr_idx	The zero-based feature index.
frag	The output fragment.
clear	If `true`, frag is cleared before atoms and bonds are added.

◆ getFeatureSubstructures()

void CDPL::Descr::CircularFingerprintGenerator::getFeatureSubstructures	(	std::size_t	bit_idx,
		std::size_t	bs_size,
		Chem::FragmentList &	frags,
		bool	clear = `true`
	)		const

Extracts the substructures of every feature that, when folded into a bitset of size bs_size, maps to the bit index bit_idx.

Parameters

bit_idx	The target bit index.
bs_size	The bitset size used for the folding.
frags	The output fragment list.
clear	If `true`, frags is cleared before any fragments are appended.

Member Data Documentation

◆ DEF_ATOM_PROPERTY_FLAGS

constexpr unsigned int CDPL::Descr::CircularFingerprintGenerator::DEF_ATOM_PROPERTY_FLAGS

staticconstexpr

Initial value:

=
                Chem::AtomPropertyFlag::HEAVY_BOND_COUNT | Chem::AtomPropertyFlag::VALENCE | Chem::AtomPropertyFlag::TYPE |
                Chem::AtomPropertyFlag::FORMAL_CHARGE | Chem::AtomPropertyFlag::H_COUNT | Chem::AtomPropertyFlag::TOPOLOGY |
                Chem::AtomPropertyFlag::ISOTOPE

Specifies the default set of atomic properties considered in the generation of atom identifiers by DefAtomIdentifierFunctor.

◆ DEF_BOND_PROPERTY_FLAGS

constexpr unsigned int CDPL::Descr::CircularFingerprintGenerator::DEF_BOND_PROPERTY_FLAGS

staticconstexpr

Initial value:

=

Chem::BondPropertyFlag::ORDER | Chem::BondPropertyFlag::AROMATICITY

CDPL::Chem::BondPropertyFlag::AROMATICITY

constexpr unsigned int AROMATICITY

Specifies the membership of a bond in aromatic rings.

Definition: BondPropertyFlag.hpp:73

CDPL::Chem::BondPropertyFlag::ORDER

constexpr unsigned int ORDER

Specifies the order of a bond.

Definition: BondPropertyFlag.hpp:63

Specifies the default set of bond properties considered in the generation of bond identifiers by DefBondIdentifierFunctor.

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

CircularFingerprintGenerator.hpp

Classes

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ AtomIdentifierFunction

◆ BondIdentifierFunction

Constructor & Destructor Documentation

◆ CircularFingerprintGenerator() [1/2]

◆ CircularFingerprintGenerator() [2/2]

Member Function Documentation

◆ setAtomIdentifierFunction()

◆ setBondIdentifierFunction()

◆ setNumIterations()

◆ getNumIterations()

◆ includeHydrogens()

◆ hydrogensIncluded()

◆ includeChirality()

◆ chiralityIncluded()

◆ generate()

◆ setFeatureBits() [1/2]

◆ setFeatureBits() [2/2]

◆ getNumFeatures()

◆ getFeatureIdentifier()

◆ getFeatureSubstructure() [1/2]

◆ getFeatureSubstructure() [2/2]

◆ getFeatureSubstructures()

Member Data Documentation

◆ DEF_ATOM_PROPERTY_FLAGS

◆ DEF_BOND_PROPERTY_FLAGS