Package org.lifstools.jgoslin.domain

package org.lifstools.jgoslin.domain

This package contains the main common domain models for lipids.

Class	Description
AcylAlkylGroup	An acyl alkyl group as a functional group.
Adduct	An adduct, generally, consists of a sum formula part, an adduct string, the charge and the charge sign.
CarbonChain	A linear hydrocarbon chain as a functional group.
ConstraintViolationException	An exception that is thrown to indicate that preconditions have been violated.
Cycle	A cyclic hydrocarbon chain as a functional group.
Dictionary	A dictionary typing for HashMap to align this implementation with the other language implementations.
DoubleBonds	An abstraction for double bond counts and positions.
Element	Enumeration for typical chemical elements in lipids.
Elements	Utility class to look up element names, masses, shortcut names, and ordering.
ElementTable	Accounting table for chemical element frequency.
FattyAcid	A fatty acid with a specific type.
FunctionalGroup	A functional group of a fatty acid, it can contain nested functional groups.
GenericList	A typing for ArrayList of objects to align this implementation with the other language implementations.
Headgroup	This class represents functional head groups of lipids.
HeadgroupDecorator
KnownFunctionalGroups	A lookup class that provides access to known functional groups defined in a file following the format of functional-groups.csv.
LipidAdduct	Base class for lipid names parsed using the different grammars.
LipidCategory	The lipid category nomenclature follows the shorthand notation of
LipidClasses	Lookup class for lipid classes, consisting of LipidClassMeta entries, derived from lipid-list.csv.
LipidClassMeta	Metadata information about a lipid on class level.
LipidCompleteStructure	Complete structure level according to the 2020 update of the Liebisch shorthand nomenclature.
LipidException	Base exception for exceptions that relate to lipid parsing or creation of lipids.
LipidFaBondType	The lipid fatty acyl bond types define how the FA is connected to the head group or which variant of a particular bond type it is.
LipidFullStructure	Full structure level according to the 2020 update of the Liebisch shorthand nomenclature.
LipidLevel	Defines the taxonomy of lipid levels, including UNDEFINED for lipids where the level can not be inferred or does not apply.
LipidMolecularSpecies	Molecular species level according to the 2020 update of the Liebisch shorthand nomenclature.
LipidParsingException	Specific exception that is thrown when errors are encountered in a lipid name.
LipidSnPosition	Sn position level according to the 2020 update of the Liebisch shorthand nomenclature.
LipidSpecies	A lipid species is the factual root of the object hierarchy.
LipidSpeciesInfo	This class summarizes the FA parts of a lipid, independent of its head group.
LipidStructureDefined	Structure defined level according to the 2020 update of the Liebisch shorthand nomenclature.
StringFunctions	Utility methods for strings and grammars.
UnsupportedLipidException	This exception is thrown, if a certain type of lipid is not yet supported by the grammar implementations.