Uses of Class
org.helm.notation2.exception.MonomerLoadingException

Packages that use MonomerLoadingException

Package	Description
org.helm.notation2
org.helm.notation2.tools

Uses of MonomerLoadingException in org.helm.notation2

Methods in org.helm.notation2 that throw MonomerLoadingException

Modifier and Type	Method and Description
static MonomerFactory	MonomerFactory.getInstance() Initialize MonomerCache and returns the singleton Factory class
static void	MonomerFactory.refreshMonomerCache()

Uses of MonomerLoadingException in org.helm.notation2.tools

Methods in org.helm.notation2.tools that throw MonomerLoadingException

Modifier and Type	Method and Description
Float	WebService.calculateExtinctionCoefficient(String notation) method to calculate from a non-ambiguous HELM string the extinction coefficient
Double	WebService.calculateMolecularWeight(String notation) method to calculate from a non-ambiguous HELM input the molecular weight
String	WebService.convertIntoStandardHELM(String notation) method to convert the input HELM into a standard HELM
static void	Converter.convertMonomerStore()
String	WebService.convertStandardHELMToCanonicalHELM(String notation) method to convert the input HELM into canonical HELM
String	WebService.generateCanSMILESForHELM2(String notation) method to generate a SMILES representation for a whole HELM2 input
String	WebService.generateFasta(String notation) method to generate FASTA-Formats for all rna and peptide sequences from an HELM input
String	WebService.generateHELMFromFastaNucleotide(String notation) method to generate HELM from a FASTA containing rna/dna sequences
String	WebService.generateHELMFromFastaPeptide(String notation) method to generate HELM from a FASTA containing peptide sequence(s)
String	WebService.generateJSON(String helm) method to generate JSON-Output for the HELM
String	WebService.generateNaturalAnalogSequencePeptide(String notation) method to generate the natural analogue sequence for all peptide-sequences from an HELM input
String	WebService.generateNaturalAnalogSequenceRNA(String notation) method to generate the natural analogue sequence for all rna-sequences from an HELM input
String	WebService.generateSMILESForHELM2(String notation) method to generate a SMILES representation for a whole HELM2 input
static Monomer	MethodsMonomerUtils.generateTemporaryMonomer(String id, String polymerType, String naturalAnalog)
static List<Monomer>	Validation.getAllMonomers(org.helm.notation2.parser.notation.polymer.MonomerNotation not, int position) method to get for one MonomerNotation all valid contained monomers
static List<Monomer>	Validation.getAllMonomersOnlyBase(org.helm.notation2.parser.notation.polymer.MonomerNotation not) method to get for one MonomerNotation all valid contained monomers.
static List<String>	AminoAcidParser.getAminoAcidList(String peptideSequence) This method converts peptide sequence into a List of amino acid
static List<String>	AminoAcidParser.getAminoAcidList(String peptideSequence, String delimiter) This method converts peptide sequence into a List of amino acid with optional delimiter
static List<Monomer>	MethodsMonomerUtils.getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) method to get all monomers for all MonomerNotations
String	WebService.getMolecularFormula(String notation) method to calculate from a non-ambiguous HELM input the molecular formula
List<String>	WebService.getMolecularProperties(String notation) method to calculate froma non-ambiguous HELM input the molecular properties: molecular formula, molecular weight, exact mass, extinction coefficient
static String	HELM1Utils.getStandard(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to reproduce a standard HELM in HELM1 - Format
static org.helm.notation2.parser.notation.polymer.MonomerNotation	ChangeObjects.replaceMonomerNotation(org.helm.notation2.parser.notation.polymer.MonomerNotation monomerNotation, String existingMonomerID, String newMonomerID) method to replace the MonomerNotation having the MonomerID with the new MonomerID
static org.helm.notation2.parser.notation.polymer.MonomerNotationList	ChangeObjects.replaceMonomerNotationList(org.helm.notation2.parser.notation.polymer.MonomerNotationList object, String existingMonomerID, String newMonomerID) method to replace the MonomerNotationList having the MonomerID with the new MonomerID
static void	ChangeObjects.replaceSMILESWithTemporaryIds(org.helm.notation2.parser.notation.HELM2Notation helm2notation) This function replaces smiles in complex notation with temporary ids
void	WebService.validateHELM(String helm) method to validate the input HELM-String
protected static boolean	Validation.validateMonomers(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> mon) method to validate a list of MonomerNotation objects
static void	Validation.validateNotationObjects(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to check if the generated notation objects by the parser are correct the polymer ids have to be unique; all monomers have to be valid; all used polymer ids in the grouping section have to be there; all connections have to be valid