RDKit
Open-source cheminformatics and machine learning.
RDKit::AtomEnvironmentGenerator< OutputType > Class Template Referenceabstract

abstract base class that generates atom-environments from a molecule More...

#include <FingerprintGenerator.h>

Inheritance diagram for RDKit::AtomEnvironmentGenerator< OutputType >:
RDKit::AtomPair::AtomPairEnvGenerator< OutputType > RDKit::MorganFingerprint::MorganEnvGenerator< OutputType > RDKit::RDKitFP::RDKitFPEnvGenerator< OutputType > RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator< OutputType >

Public Member Functions

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 More...
 
virtual std::string infoString () const =0
 method that returns information about this /c AtomEnvironmentGenerator and its arguments if any More...
 
virtual ~AtomEnvironmentGenerator ()
 

Detailed Description

template<typename OutputType>
class RDKit::AtomEnvironmentGenerator< OutputType >

abstract base class that generates atom-environments from a molecule

Definition at line 123 of file FingerprintGenerator.h.

Constructor & Destructor Documentation

◆ ~AtomEnvironmentGenerator()

template<typename OutputType >
virtual RDKit::AtomEnvironmentGenerator< OutputType >::~AtomEnvironmentGenerator ( )
inlinevirtual

Definition at line 170 of file FingerprintGenerator.h.

Member Function Documentation

◆ getEnvironments()

template<typename OutputType >
virtual std::vector<AtomEnvironment<OutputType> *> RDKit::AtomEnvironmentGenerator< 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
pure virtual

generate and return all atom-envorinments from a molecule

Parameters
molmolecule to generate the atom-environments from
argumentsfingerprint type specific molecule independent arguments
fromAtomsatoms to be used during environment generation, usage of this parameter depends on the implementation of different fingerprint types
ignoreAtomsatoms to be ignored during environment generation, usage of this parameter depends on the implementation of different fingerprint types
confIdwhich conformation to use during environment generation, needed for some fingerprint types
additionalOutputcontains pointers for additional outputs of fingerprinting operation, usage depends on implementation of the fingerprint type
atomInvariantsatom invariants to be used during environment generation, in some cases some of the hashing can be done during environment generation so it is also passed here
bondInvariantsbond invariants to be used during environment generation, same as atomInvariants it might be needed
hashResultsif set results will be ready to be modded
Returns
std::vector<AtomEnvironment *> atom-environments generated from this molecule

Implemented in RDKit::RDKitFP::RDKitFPEnvGenerator< OutputType >, RDKit::MorganFingerprint::MorganEnvGenerator< OutputType >, RDKit::AtomPair::AtomPairEnvGenerator< OutputType >, and RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator< OutputType >.

◆ infoString()

template<typename OutputType >
virtual std::string RDKit::AtomEnvironmentGenerator< OutputType >::infoString ( ) const
pure virtual

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