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

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 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 148 of file FingerprintGenerator.h.

Constructor & Destructor Documentation

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

inlinevirtual

Definition at line 203 of file FingerprintGenerator.h.

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