RDKit::AtomEnvironmentGenerator< OutputType > Class Template Reference

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

#include <FingerprintGenerator.h>

Inheritance diagram for RDKit::AtomEnvironmentGenerator< OutputType >:

Public Member Functions
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
virtual std::string	infoString () const =0
	method that returns information about this /c AtomEnvironmentGenerator and its arguments if any
virtual void	toJSON (boost::property_tree::ptree &) const
virtual void	fromJSON (const boost::property_tree::ptree &)
virtual OutputType	getResultSize () const =0
	Returns the size of the fingerprint based on arguments.
virtual	~AtomEnvironmentGenerator ()

Public Attributes
const FingerprintArguments *	dp_fingerprintArguments

Detailed Description

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

abstract base class that generates atom-environments from a molecule

Definition at line 161 of file FingerprintGenerator.h.

Constructor & Destructor Documentation

~AtomEnvironmentGenerator()

template<typename OutputType>

virtual RDKit::AtomEnvironmentGenerator< OutputType >::~AtomEnvironmentGenerator ( )

inlinevirtual

Definition at line 219 of file FingerprintGenerator.h.

Member Function Documentation

fromJSON()

template<typename OutputType>

virtual void RDKit::AtomEnvironmentGenerator< OutputType >::fromJSON ( const boost::property_tree::ptree & )

inlinevirtual

Reimplemented in RDKit::MorganFingerprint::MorganEnvGenerator< OutputType >, RDKit::RDKitFP::RDKitFPEnvGenerator< OutputType >, and RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator< OutputType >.

Definition at line 208 of file FingerprintGenerator.h.

getEnvironments()

template<typename OutputType>

virtual std::vector< AtomEnvironment< OutputType > * > RDKit::AtomEnvironmentGenerator< 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

pure virtual

generate and return all atom-envorinments from a molecule

Parameters

mol	molecule to generate the atom-environments from
arguments	fingerprint type specific molecule independent arguments
fromAtoms	atoms to be used during environment generation, usage of this parameter depends on the implementation of different fingerprint types
ignoreAtoms	atoms to be ignored during environment generation, usage of this parameter depends on the implementation of different fingerprint types
confId	which conformation to use during environment generation, needed for some fingerprint types
additionalOutput	contains pointers for additional outputs of fingerprinting operation, usage depends on implementation of the fingerprint type
atomInvariants	atom 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
bondInvariants	bond invariants to be used during environment generation, same as atomInvariants it might be needed
hashResults	if set results will be ready to be modded

Returns

std::vector<AtomEnvironment *> atom-environments generated from this molecule

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

getResultSize()

template<typename OutputType>

virtual OutputType RDKit::AtomEnvironmentGenerator< OutputType >::getResultSize ( ) const

pure virtual

Returns the size of the fingerprint based on arguments.

Returns

OutputType size of the fingerprint

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

infoString()

template<typename OutputType>

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

pure virtual

method that returns information about this /c AtomEnvironmentGenerator and its arguments if any

Returns

std::string information string

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

toJSON()

template<typename OutputType>

virtual void RDKit::AtomEnvironmentGenerator< OutputType >::toJSON ( boost::property_tree::ptree & ) const

inlinevirtual

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

Definition at line 207 of file FingerprintGenerator.h.

Member Data Documentation

dp_fingerprintArguments

template<typename OutputType>

const FingerprintArguments* RDKit::AtomEnvironmentGenerator< OutputType >::dp_fingerprintArguments

Definition at line 217 of file FingerprintGenerator.h.

---

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

• FingerprintGenerator.h