12#ifndef RD_FINGERPRINTGEN_H_2018_05
13#define RD_FINGERPRINTGEN_H_2018_05
29 std::map<std::uint64_t,
30 std::vector<std::pair<std::uint32_t, std::uint32_t>>>;
31 using bitPathsType = std::map<std::uint64_t, std::vector<std::vector<int>>>;
51 atomToBits = atomToBitsHolder.get();
55 bitInfoMap = bitInfoMapHolder.get();
59 bitPaths = bitPathsHolder.get();
63 atomCounts = atomCountsHolder.get();
67 std::unique_ptr<atomToBitsType> atomToBitsHolder;
68 std::unique_ptr<bitInfoMapType> bitInfoMapHolder;
69 std::unique_ptr<bitPathsType> bitPathsHolder;
70 std::unique_ptr<atomCountsType> atomCountsHolder;
79template <
typename OutputType>
81 :
private boost::noncopyable {
84 const std::vector<std::uint32_t> countBounds,
86 std::uint32_t numBitsPerFeature = 1);
123template <
typename OutputType>
138 const std::vector<std::uint32_t> *atomInvariants,
139 const std::vector<std::uint32_t> *bondInvariants,
141 const bool hashResults =
false,
142 const std::uint64_t fpSize = 0)
const = 0;
151template <
typename OutputType>
153 :
private boost::noncopyable {
184 const std::vector<std::uint32_t> *fromAtoms =
nullptr,
185 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
187 const std::vector<std::uint32_t> *atomInvariants =
nullptr,
188 const std::vector<std::uint32_t> *bondInvariants =
nullptr,
189 const bool hashResults =
false)
const = 0;
207 :
private boost::noncopyable {
218 const ROMol &mol)
const = 0;
237 :
private boost::noncopyable {
248 const ROMol &mol)
const = 0;
267template <
typename OutputType>
269 :
private boost::noncopyable {
274 const bool df_ownsAtomInvGenerator;
275 const bool df_ownsBondInvGenerator;
278 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
279 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
281 const std::vector<std::uint32_t> *customAtomInvariants =
nullptr,
282 const std::vector<std::uint32_t> *customBondInvariants =
nullptr,
283 const std::uint64_t fpSize = 0)
const;
291 bool ownsAtomInvGenerator =
false,
bool ownsBondInvGenerator =
false);
296 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
297 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
299 const std::vector<std::uint32_t> *customAtomInvariants =
nullptr,
300 const std::vector<std::uint32_t> *customBondInvariants =
nullptr)
const;
303 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
304 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
306 const std::vector<std::uint32_t> *customAtomInvariants =
nullptr,
307 const std::vector<std::uint32_t> *customBondInvariants =
nullptr)
const;
310 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
311 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
313 const std::vector<std::uint32_t> *customAtomInvariants =
nullptr,
314 const std::vector<std::uint32_t> *customBondInvariants =
nullptr)
const;
317 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
318 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
320 const std::vector<std::uint32_t> *customAtomInvariants =
nullptr,
321 const std::vector<std::uint32_t> *customBondInvariants =
nullptr)
const;
330 :
public std::exception {
337 const char *
what() const noexcept
override {
return _msg.c_str(); }
362 const std::vector<const
ROMol *> molVector,
FPType fPType);
368 const std::vector<const
ROMol *> molVector,
FPType fPType);
a class for bit vectors that are densely occupied
abstract base class that generates atom-environments from a molecule
virtual ~AtomEnvironmentGenerator()
virtual std::vector< AtomEnvironment< OutputType > * > getEnvironments(const ROMol &mol, FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const int confId=-1, const AdditionalOutput *additionalOutput=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *bondInvariants=nullptr, const bool hashResults=false) const =0
generate and return all atom-envorinments from a molecule
virtual std::string infoString() const =0
method that returns information about this /c AtomEnvironmentGenerator and its arguments if any
abstract base class that holds atom-environments that will be hashed to generate the fingerprint
virtual ~AtomEnvironment()
virtual OutputType getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const =0
calculates and returns the bit id to be set for this atom-environment
abstract base class for atom invariants generators
virtual ~AtomInvariantsGenerator()
virtual std::string infoString() const =0
method that returns information about this /c AtomInvariantsGenerator and its arguments
virtual AtomInvariantsGenerator * clone() const =0
virtual std::vector< std::uint32_t > * getAtomInvariants(const ROMol &mol) const =0
get atom invariants from a molecule
abstract base class for bond invariants generators
virtual std::string infoString() const =0
method that returns information about this /c BondInvariantsGenerator and its arguments
virtual ~BondInvariantsGenerator()
virtual BondInvariantsGenerator * clone() const =0
virtual std::vector< std::uint32_t > * getBondInvariants(const ROMol &mol) const =0
get bond invariants from a molecule
Abstract base class that holds molecule independent arguments that are common amongst all fingerprint...
const std::uint32_t d_fpSize
virtual std::string infoString() const =0
method that returns information string about the fingerprint specific argument set and the arguments ...
virtual OutputType getResultSize() const =0
Returns the size of the fingerprint based on arguments.
const std::vector< std::uint32_t > d_countBounds
FingerprintArguments(bool countSimulation, const std::vector< std::uint32_t > countBounds, std::uint32_t fpSize, std::uint32_t numBitsPerFeature=1)
virtual ~FingerprintArguments()
const bool d_countSimulation
std::string commonArgumentsString() const
method that returns information string about common fingerprinting arguments' values
const std::uint32_t d_numBitsPerFeature
class that generates same fingerprint style for different output formats
SparseIntVect< OutputType > * getSparseCountFingerprint(const ROMol &mol, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const int confId=-1, const AdditionalOutput *additionalOutput=nullptr, const std::vector< std::uint32_t > *customAtomInvariants=nullptr, const std::vector< std::uint32_t > *customBondInvariants=nullptr) const
std::string infoString() const
SparseIntVect< std::uint32_t > * getCountFingerprint(const ROMol &mol, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const int confId=-1, const AdditionalOutput *additionalOutput=nullptr, const std::vector< std::uint32_t > *customAtomInvariants=nullptr, const std::vector< std::uint32_t > *customBondInvariants=nullptr) const
SparseBitVect * getSparseFingerprint(const ROMol &mol, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const int confId=-1, const AdditionalOutput *additionalOutput=nullptr, const std::vector< std::uint32_t > *customAtomInvariants=nullptr, const std::vector< std::uint32_t > *customBondInvariants=nullptr) const
FingerprintGenerator(AtomEnvironmentGenerator< OutputType > *atomEnvironmentGenerator, FingerprintArguments< OutputType > *fingerprintArguments, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, bool ownsAtomInvGenerator=false, bool ownsBondInvGenerator=false)
ExplicitBitVect * getFingerprint(const ROMol &mol, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const int confId=-1, const AdditionalOutput *additionalOutput=nullptr, const std::vector< std::uint32_t > *customAtomInvariants=nullptr, const std::vector< std::uint32_t > *customBondInvariants=nullptr) const
a class for efficiently storing sparse vectors of ints
used to indicate errors for unimplemented fp types in convenience functions
UnimplementedFPException(const char *msg)
construct with an error message
~UnimplementedFPException() noexcept override=default
UnimplementedFPException(std::string msg)
construct with an error message
const char * what() const noexcept override
get the error message
a class for bit vectors that are sparsely occupied.
#define RDKIT_FINGERPRINTS_EXPORT
RDKIT_FINGERPRINTS_EXPORT SparseBitVect * getSparseFP(const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseBitVect * > * getSparseFPBulk(const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT std::vector< ExplicitBitVect * > * getFPBulk(const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint64_t > * getSparseCountFP(const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint32_t > * > * getCountFPBulk(const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint64_t > * > * getSparseCountFPBulk(const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint32_t > * getCountFP(const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * getFP(const ROMol &mol, FPType fPType)
void allocateAtomCounts()
std::vector< std::vector< std::uint64_t > > atomToBitsType
std::vector< unsigned int > atomCountsType
void allocateBitInfoMap()
void allocateAtomToBits()
std::map< std::uint64_t, std::vector< std::vector< int > > > bitPathsType
std::map< std::uint64_t, std::vector< std::pair< std::uint32_t, std::uint32_t > > > bitInfoMapType