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;
80 :
private boost::noncopyable {
83 const std::vector<std::uint32_t> countBounds,
85 std::uint32_t numBitsPerFeature = 1,
86 bool includeChirality =
false);
117 template <
typename OutputType>
132 const std::vector<std::uint32_t> *atomInvariants,
133 const std::vector<std::uint32_t> *bondInvariants,
135 const bool hashResults =
false,
136 const std::uint64_t fpSize = 0)
const = 0;
138 size_t bitId)
const = 0;
147 template <
typename OutputType>
149 :
private boost::noncopyable {
180 const std::vector<std::uint32_t> *fromAtoms =
nullptr,
181 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
183 const std::vector<std::uint32_t> *atomInvariants =
nullptr,
184 const std::vector<std::uint32_t> *bondInvariants =
nullptr,
185 const bool hashResults =
false)
const = 0;
211 :
private boost::noncopyable {
222 const ROMol &mol)
const = 0;
241 :
private boost::noncopyable {
252 const ROMol &mol)
const = 0;
281 const std::vector<std::uint32_t> *fromAtoms_arg,
282 const std::vector<std::uint32_t> *ignoreAtoms_arg,
int confId_arg,
284 const std::vector<std::uint32_t> *customAtomInvariants_arg,
285 const std::vector<std::uint32_t> *customBondInvariants_arg)
299 template <
typename OutputType>
301 :
private boost::noncopyable {
306 const bool df_ownsAtomInvGenerator;
307 const bool df_ownsBondInvGenerator;
309 std::unique_ptr<SparseIntVect<OutputType>> getFingerprintHelper(
311 const std::uint64_t fpSize = 0)
const;
319 bool ownsAtomInvGenerator =
false,
bool ownsBondInvGenerator =
false);
325 return dp_fingerprintArguments;
341 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
342 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
int confId = -1,
344 const std::vector<std::uint32_t> *customAtomInvariants =
nullptr,
345 const std::vector<std::uint32_t> *customBondInvariants =
nullptr)
const {
347 additionalOutput, customAtomInvariants,
348 customBondInvariants);
349 return getSparseCountFingerprint(mol, ffa).release();
353 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
354 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
int confId = -1,
356 const std::vector<std::uint32_t> *customAtomInvariants =
nullptr,
357 const std::vector<std::uint32_t> *customBondInvariants =
nullptr)
const {
359 additionalOutput, customAtomInvariants,
360 customBondInvariants);
361 return getSparseFingerprint(mol, ffa).release();
365 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
366 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
int confId = -1,
368 const std::vector<std::uint32_t> *customAtomInvariants =
nullptr,
369 const std::vector<std::uint32_t> *customBondInvariants =
nullptr)
const {
371 additionalOutput, customAtomInvariants,
372 customBondInvariants);
373 return getCountFingerprint(mol, ffa).release();
377 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
378 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
int confId = -1,
380 const std::vector<std::uint32_t> *customAtomInvariants =
nullptr,
381 const std::vector<std::uint32_t> *customBondInvariants =
nullptr)
const {
383 additionalOutput, customAtomInvariants,
384 customBondInvariants);
393 const ROMol &,
const std::vector<std::uint32_t> *,
395 const std::vector<std::uint32_t> *,
396 const std::vector<std::uint32_t> *)
const;
399 const ROMol &,
const std::vector<std::uint32_t> *,
401 const std::vector<std::uint32_t> *,
402 const std::vector<std::uint32_t> *)
const;
405 const ROMol &,
const std::vector<std::uint32_t> *,
407 const std::vector<std::uint32_t> *,
408 const std::vector<std::uint32_t> *)
const;
411 const ROMol &,
const std::vector<std::uint32_t> *,
413 const std::vector<std::uint32_t> *,
414 const std::vector<std::uint32_t> *)
const;
417 const ROMol &,
const std::vector<std::uint32_t> *,
419 const std::vector<std::uint32_t> *,
420 const std::vector<std::uint32_t> *)
const;
423 const ROMol &,
const std::vector<std::uint32_t> *,
425 const std::vector<std::uint32_t> *,
426 const std::vector<std::uint32_t> *)
const;
429 const ROMol &,
const std::vector<std::uint32_t> *,
431 const std::vector<std::uint32_t> *,
432 const std::vector<std::uint32_t> *)
const;
435 const ROMol &,
const std::vector<std::uint32_t> *,
437 const std::vector<std::uint32_t> *,
438 const std::vector<std::uint32_t> *)
const;
445 :
public std::exception {
452 const char *
what() const noexcept
override {
return _msg.c_str(); }
477 const std::vector<const
ROMol *> molVector,
FPType fPType);
483 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()
const FingerprintArguments * dp_fingerprintArguments
virtual std::string infoString() const =0
method that returns information about this /c AtomEnvironmentGenerator and its arguments if any
virtual OutputType getResultSize() const =0
Returns the size of the fingerprint based on arguments.
virtual std::vector< AtomEnvironment< OutputType > * > getEnvironments(const ROMol &mol, FingerprintArguments *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
abstract base class that holds atom-environments that will be hashed to generate the fingerprint
virtual ~AtomEnvironment()
virtual void updateAdditionalOutput(AdditionalOutput *AdditionalOutput, size_t bitId) const =0
virtual OutputType getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, 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...
virtual ~FingerprintArguments()
virtual std::string infoString() const =0
method that returns information string about the fingerprint specific argument set and the arguments ...
FingerprintArguments(bool countSimulation, const std::vector< std::uint32_t > countBounds, std::uint32_t fpSize, std::uint32_t numBitsPerFeature=1, bool includeChirality=false)
std::uint32_t d_numBitsPerFeature
std::string commonArgumentsString() const
method that returns information string about common fingerprinting arguments' values
std::vector< std::uint32_t > d_countBounds
class that generates same fingerprint style for different output formats
FingerprintGenerator(AtomEnvironmentGenerator< OutputType > *atomEnvironmentGenerator, FingerprintArguments *fingerprintArguments, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, bool ownsAtomInvGenerator=false, bool ownsBondInvGenerator=false)
std::string infoString() const
std::unique_ptr< ExplicitBitVect > getFingerprint(const ROMol &mol, FingerprintFuncArguments &args) const
std::unique_ptr< SparseIntVect< std::uint32_t > > getCountFingerprint(const ROMol &mol, FingerprintFuncArguments &args) 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, int confId=-1, 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, int confId=-1, AdditionalOutput *additionalOutput=nullptr, const std::vector< std::uint32_t > *customAtomInvariants=nullptr, const std::vector< std::uint32_t > *customBondInvariants=nullptr) const
const FingerprintArguments * getOptions() const
FingerprintArguments * getOptions()
std::unique_ptr< SparseBitVect > getSparseFingerprint(const ROMol &mol, FingerprintFuncArguments &args) const
std::unique_ptr< SparseIntVect< OutputType > > getSparseCountFingerprint(const ROMol &mol, FingerprintFuncArguments &args) const
ExplicitBitVect * getFingerprint(const ROMol &mol, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, int confId=-1, AdditionalOutput *additionalOutput=nullptr, const std::vector< std::uint32_t > *customAtomInvariants=nullptr, const std::vector< std::uint32_t > *customBondInvariants=nullptr) const
SparseIntVect< OutputType > * getSparseCountFingerprint(const ROMol &mol, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, int confId=-1, 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
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 SparseIntVect< std::uint32_t > * getFingerprint(const ROMol &mol, unsigned int radius, std::vector< boost::uint32_t > *invariants=nullptr, const std::vector< boost::uint32_t > *fromAtoms=nullptr, bool useChirality=false, bool useBondTypes=true, bool useCounts=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=nullptr, bool includeRedundantEnvironments=false)
returns the Morgan fingerprint for a molecule
RDKIT_FINGERPRINTS_EXPORT std::vector< ExplicitBitVect * > * getFPBulk(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 std::vector< SparseIntVect< std::uint32_t > * > * getCountFPBulk(const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT SparseBitVect * getSparseFP(const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * getFP(const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint64_t > * getSparseCountFP(const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseBitVect * > * getSparseFPBulk(const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint32_t > * getCountFP(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
struct that makes calling the fingerprint generation functions easier
const std::vector< std::uint32_t > * customAtomInvariants
AdditionalOutput * additionalOutput
const std::vector< std::uint32_t > * customBondInvariants
const std::vector< std::uint32_t > * fromAtoms
const std::vector< std::uint32_t > * ignoreAtoms
FingerprintFuncArguments(const std::vector< std::uint32_t > *fromAtoms_arg, const std::vector< std::uint32_t > *ignoreAtoms_arg, int confId_arg, AdditionalOutput *additionalOutput_arg, const std::vector< std::uint32_t > *customAtomInvariants_arg, const std::vector< std::uint32_t > *customBondInvariants_arg)
FingerprintFuncArguments()=default