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
|
void |
WebService.refreshMonomerCache() |
method to refresh the monomer cache of the MonomerFactory
|
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
|