Package org.helm.notation2.tools

Class Summary

Class	Description
AminoAcidParser	AminoAcidParser
Base64	{@code A very fast and memory efficient class to encode and decode to and from BASE64 in full accordance with RFC 2045.
BuilderMolecule	class to build molecules for the HELMNotation
ChangeObjects	ChangeObjects, class to provide simple methods to change the HELM2Notation objects
Converter	Converter class allowing to convert extended smiles into smiles with atom mapping
FastaFormat	FastaFormat, class to convert FastaFiles to HELMNotation and vice versa
HELM1Utils	HELM1 class to transform a HELM2 into HELM1; this is only possible in the case of no HELM2 features
HELM2NotationUtils	HELM2NotationUtils
Images	Image class to generate image generation of monomers and of the helm molecule
MDLUtils	MDLUtils, class to generate MDL for a HELM molecule.
MethodsMonomerUtils	MethodsMonomerUtils
MolfileEncoder
MonomerParser	MonomerParser
NucleotideParser	NucleotideParser
PeptideUtils	PeptideUtils, class to provide peptide utils
PermutationAndExpansion
PolymerUtils	PolymerUtils, class to provide methods for polymer
RNAUtils	RNAUtils, class to provide methods for rna polymer
SequenceConverter	SequenceConverter class to convert sequence into the HELM2Notation object and vice versa
SiRNANotation	SiRNANotation, class to generate SirnaNotation
SMILES	SMILES class to generate SMILES
Validation	Validation class to validate the whole HELM string
WebService	WebService class containing all required methods for the web-service
xHelmNotationExporter	xHELMNotationExporter
xHelmNotationParser	Class to parse the XHELM XML format