Generation of Daylight-style path fingerprints of molecular graphs. More...

#include <PathFingerprintGenerator.hpp>

Classes
class	DefAtomDescriptorFunctor
	The default functor for the generation of atom descriptors. More...

class	DefBondDescriptorFunctor
	The default functor for the generation of bond descriptors. More...

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

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

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

	PathFingerprintGenerator (const Chem::MolecularGraph &molgraph, Util::BitSet &fp)
	Constructs the `PathFingerprintGenerator` instance and generates the fingerprint of the molecular graph molgraph. More...

void	setAtomDescriptorFunction (const AtomDescriptorFunction &func)
	Allows to specify a custom function for the generation of atom descriptors. More...

void	setBondDescriptorFunction (const BondDescriptorFunction &func)
	Allows to specify a custom function for the generation of bond descriptors. More...

void	setMinPathLength (std::size_t min_length)
	Allows to specify the minimum length a path must have to contribute to the generated fingerprint. More...

std::size_t	getMinPathLength () const
	Returns the minimum length a path must have to contribute to the generated fingerprint. More...

void	setMaxPathLength (std::size_t max_length)
	Allows to specify the maximum considered path length. More...

std::size_t	getMaxPathLength () const
	Returns the maximum considered path length. More...

void	includeHydrogens (bool include)
	Specifies whether hydrogens shall be considered during path enumeration. More...

bool	hydrogensIncluded () const
	Tells whether hydrogens are considered during path enumeration. More...

void	generate (const Chem::MolecularGraph &molgraph, Util::BitSet &fp)
	Generates the fingerprint of the molecular graph molgraph. 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 descriptors by PathFingerprintGenerator::DefAtomDescriptorFunction. More...

static constexpr unsigned int	DEF_BOND_PROPERTY_FLAGS
	Specifies the default set of bond properties considered in the generation of bond descriptors by PathFingerprintGenerator::DefBondDescriptorFunction. More...

Detailed Description

Generation of Daylight-style path fingerprints of molecular graphs.

The generator enumerates atom-bond-atom paths up to a configurable maximum length, derives a hash for each path from per-atom and per-bond descriptors (provided by the DefAtomDescriptorFunctor / DefBondDescriptorFunctor or user-supplied alternatives), and folds the hashes into a bitset of any size.

See also: [DTPFP]

Member Typedef Documentation

◆ AtomDescriptorFunction

typedef std::function<std::uint64_t(const Chem::Atom&)> CDPL::Descr::PathFingerprintGenerator::AtomDescriptorFunction

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

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

◆ BondDescriptorFunction

typedef std::function<std::uint64_t(const Chem::Bond&)> CDPL::Descr::PathFingerprintGenerator::BondDescriptorFunction

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

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

Constructor & Destructor Documentation

◆ PathFingerprintGenerator() [1/2]

CDPL::Descr::PathFingerprintGenerator::PathFingerprintGenerator ( )

Constructs the PathFingerprintGenerator instance.

◆ PathFingerprintGenerator() [2/2]

CDPL::Descr::PathFingerprintGenerator::PathFingerprintGenerator	(	const Chem::MolecularGraph &	molgraph,
		Util::BitSet &	fp
	)

Constructs the PathFingerprintGenerator instance and generates the fingerprint of the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to generate the fingerprint.
fp	The generated fingerprint.

Member Function Documentation

◆ setAtomDescriptorFunction()

void CDPL::Descr::PathFingerprintGenerator::setAtomDescriptorFunction ( const AtomDescriptorFunction & func )

Allows to specify a custom function for the generation of atom descriptors.

Parameters

func	A PathFingerprintGenerator::AtomDescriptorFunction instance that wraps the target function.

Note: By default, atom descriptors are generated by PathFingerprintGenerator::DefAtomDescriptorFunctor.

◆ setBondDescriptorFunction()

void CDPL::Descr::PathFingerprintGenerator::setBondDescriptorFunction ( const BondDescriptorFunction & func )

Allows to specify a custom function for the generation of bond descriptors.

Parameters

func	A PathFingerprintGenerator::BondDescriptorFunction instance that wraps the target function.

Note: By default, bond descriptors are generated by PathFingerprintGenerator::DefBondDescriptorFunctor.

◆ setMinPathLength()

void CDPL::Descr::PathFingerprintGenerator::setMinPathLength ( std::size_t min_length )

Allows to specify the minimum length a path must have to contribute to the generated fingerprint.

Any path whose length (in number of bonds) is lower than the specified minimum length will not be represented by a corresponding bit in the generated fingerprint.

Parameters

min_length The minimum path length in number of bonds.

Note: By default, the minimum path length is set to 0.

◆ getMinPathLength()

std::size_t CDPL::Descr::PathFingerprintGenerator::getMinPathLength ( ) const

Returns the minimum length a path must have to contribute to the generated fingerprint.

Returns: The minimum path length in number of bonds.

See also: setMinPathLength()

◆ setMaxPathLength()

void CDPL::Descr::PathFingerprintGenerator::setMaxPathLength ( std::size_t max_length )

Allows to specify the maximum considered path length.

Any path whose length (in number of bonds) is greater than the specified maximum length will not be represented by a corresponding bit in the generated fingerprint.

Parameters

max_length The maximum path length in number of bonds.

Note: By default, the maximum considered path length is 5.

◆ getMaxPathLength()

std::size_t CDPL::Descr::PathFingerprintGenerator::getMaxPathLength ( ) const

Returns the maximum considered path length.

Returns: The maximum path length in number of bonds.

See also: setMaxPathLength()

◆ includeHydrogens()

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

Specifies whether hydrogens shall be considered during path enumeration.

Parameters

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

Since: 1.3

◆ hydrogensIncluded()

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

Tells whether hydrogens are considered during path enumeration.

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

Since: 1.3

◆ generate()

void CDPL::Descr::PathFingerprintGenerator::generate	(	const Chem::MolecularGraph &	molgraph,
		Util::BitSet &	fp
	)

Generates the fingerprint of the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to generate the fingerprint.
fp	The generated fingerprint.

Member Data Documentation

◆ DEF_ATOM_PROPERTY_FLAGS

constexpr unsigned int CDPL::Descr::PathFingerprintGenerator::DEF_ATOM_PROPERTY_FLAGS

staticconstexpr

Initial value:

=
                Chem::AtomPropertyFlag::TYPE | Chem::AtomPropertyFlag::ISOTOPE | Chem::AtomPropertyFlag::FORMAL_CHARGE |
                Chem::AtomPropertyFlag::AROMATICITY

Specifies the default set of atomic properties considered in the generation of atom descriptors by PathFingerprintGenerator::DefAtomDescriptorFunction.

◆ DEF_BOND_PROPERTY_FLAGS

constexpr unsigned int CDPL::Descr::PathFingerprintGenerator::DEF_BOND_PROPERTY_FLAGS

staticconstexpr

Initial value:

=

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

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

CDPL::Chem::BondPropertyFlag::TOPOLOGY

constexpr unsigned int TOPOLOGY

Specifies the ring/chain topology of a bond.

Definition: BondPropertyFlag.hpp:68

Specifies the default set of bond properties considered in the generation of bond descriptors by PathFingerprintGenerator::DefBondDescriptorFunction.

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

PathFingerprintGenerator.hpp

Classes

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ AtomDescriptorFunction

◆ BondDescriptorFunction

Constructor & Destructor Documentation

◆ PathFingerprintGenerator() [1/2]

◆ PathFingerprintGenerator() [2/2]

Member Function Documentation

◆ setAtomDescriptorFunction()

◆ setBondDescriptorFunction()

◆ setMinPathLength()

◆ getMinPathLength()

◆ setMaxPathLength()

◆ getMaxPathLength()

◆ includeHydrogens()

◆ hydrogensIncluded()

◆ generate()

Member Data Documentation

◆ DEF_ATOM_PROPERTY_FLAGS

◆ DEF_BOND_PROPERTY_FLAGS