CDPL::Descr::PathFingerprintGenerator Class Reference

PathFingerprintGenerator. 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	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

PathFingerprintGenerator.

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()

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

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

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

• PathFingerprintGenerator.hpp