CircularFingerprintGenerator.
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#include <CircularFingerprintGenerator.hpp>
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static constexpr unsigned int | DEF_ATOM_PROPERTY_FLAGS |
| Specifies the default set of atomic properties considered in the generation of atom identifiers by CircularFingerprintGenerator::DefAtomIdentifierFunction. More...
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static constexpr unsigned int | DEF_BOND_PROPERTY_FLAGS |
| Specifies the default set of bond properties considered in the generation of bond identifiers by CircularFingerprintGenerator::DefBondIdentifierFunction. More...
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◆ 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
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]).
◆ CircularFingerprintGenerator() [1/2]
CDPL::Descr::CircularFingerprintGenerator::CircularFingerprintGenerator |
( |
| ) |
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Constructs the CircularFingerprintGenerator
instance.
◆ CircularFingerprintGenerator() [2/2]
CDPL::Descr::CircularFingerprintGenerator::CircularFingerprintGenerator |
( |
const Chem::MolecularGraph & |
molgraph | ) |
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Constructs the CircularFingerprintGenerator
instance and generates the atom-centered circular substructure fingerprint of the molecular graph molgraph.
- Parameters
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molgraph | The molecular graph to process. |
◆ setAtomIdentifierFunction()
void CDPL::Descr::CircularFingerprintGenerator::setAtomIdentifierFunction |
( |
const AtomIdentifierFunction & |
func | ) |
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Allows to specify a customized function for the generation of initial atom identifiers.
- Parameters
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- 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 | ) |
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Allows to specify a customized function for the generation of initial bond identifiers.
- Parameters
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- 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 | ) |
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Allows to specify the desired number of feature substructure growing iterations.
- Parameters
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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 | ) |
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◆ hydrogensIncluded()
bool CDPL::Descr::CircularFingerprintGenerator::hydrogensIncluded |
( |
| ) |
const |
◆ includeChirality()
void CDPL::Descr::CircularFingerprintGenerator::includeChirality |
( |
bool |
include | ) |
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◆ chiralityIncluded()
bool CDPL::Descr::CircularFingerprintGenerator::chiralityIncluded |
( |
| ) |
const |
◆ generate()
Generates the atom-centered circular substructure fingerprint of the molecular graph molgraph.
- Parameters
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molgraph | The molecular graph to process. |
◆ setFeatureBits() [1/2]
void CDPL::Descr::CircularFingerprintGenerator::setFeatureBits |
( |
Util::BitSet & |
bs, |
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bool |
reset = true |
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) |
| const |
Maps previously generated feature identifiers to bit indices and sets the correponding bits of bs.
- Parameters
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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, |
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Util::BitSet & |
bs, |
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bool |
reset = true |
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) |
| 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
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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 |
◆ getFeatureIdentifier()
std::uint64_t CDPL::Descr::CircularFingerprintGenerator::getFeatureIdentifier |
( |
std::size_t |
ftr_idx | ) |
const |
◆ getFeatureSubstructure() [1/2]
const Util::BitSet& CDPL::Descr::CircularFingerprintGenerator::getFeatureSubstructure |
( |
std::size_t |
ftr_idx | ) |
const |
◆ getFeatureSubstructure() [2/2]
void CDPL::Descr::CircularFingerprintGenerator::getFeatureSubstructure |
( |
std::size_t |
ftr_idx, |
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Chem::Fragment & |
frag, |
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bool |
clear = true |
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) |
| const |
◆ getFeatureSubstructures()
void CDPL::Descr::CircularFingerprintGenerator::getFeatureSubstructures |
( |
std::size_t |
bit_idx, |
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std::size_t |
bs_size, |
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Chem::FragmentList & |
frags, |
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bool |
clear = true |
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) |
| const |
◆ DEF_ATOM_PROPERTY_FLAGS
constexpr unsigned int CDPL::Descr::CircularFingerprintGenerator::DEF_ATOM_PROPERTY_FLAGS |
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staticconstexpr |
Initial value:
Specifies the default set of atomic properties considered in the generation of atom identifiers by CircularFingerprintGenerator::DefAtomIdentifierFunction.
◆ DEF_BOND_PROPERTY_FLAGS
constexpr unsigned int CDPL::Descr::CircularFingerprintGenerator::DEF_BOND_PROPERTY_FLAGS |
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staticconstexpr |
Initial value:
Specifies the default set of bond properties considered in the generation of bond identifiers by CircularFingerprintGenerator::DefBondIdentifierFunction.
The documentation for this class was generated from the following file: