static boolean |
RNAUtils.areAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymerOne,
org.helm.notation2.parser.notation.polymer.PolymerNotation polymerTwo) |
method to check if two given polymers are complement to each other
|
static List<org.helm.chemtoolkit.AbstractMolecule> |
BuilderMolecule.buildMoleculefromPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers,
List<org.helm.notation2.parser.notation.connection.ConnectionNotation> connections) |
method to build molecules for the whole HELMNotation
|
static RgroupStructure |
BuilderMolecule.buildMoleculefromSinglePolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymernotation) |
method to build a molecule for a single polymer
|
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
|
static boolean |
SMILES.containsGenericStructurePolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) |
method if the any of the given PolymerNotation contains generic
structures
|
static org.helm.notation2.parser.notation.HELM2Notation |
FastaFormat.convertIntoAnalogSequence(org.helm.notation2.parser.notation.HELM2Notation helm2Notation) |
method to convert all Peptides and RNAs into the natural analogue
sequence and generates HELM2Notation
|
String |
WebService.convertIntoStandardHELM(String notation) |
method to convert the input HELM into a standard HELM
|
String |
WebService.convertMolFileSMILESWithAtomMapping(String molfile,
List<Attachment> attachments) |
method to generate a smiles with atom mapping for a given molfile with the given attachments
|
static String |
SMILES.convertMolToSMILESWithAtomMapping(String molfile,
List<Attachment> attachments) |
Converts molfile with the given attachments in smiles with atom mapping
|
static Monomer |
Converter.convertMonomer(Monomer m) |
|
static void |
Converter.convertMonomerStore() |
|
String |
WebService.convertStandardHELMToCanonicalHELM(String notation) |
method to convert the input HELM into canonical HELM
|
static Nucleotide |
NucleotideParser.convertToNucleotide(String id,
boolean last) |
method to convert an string to an nucleotide
|
static void |
MonomerParser.fillAttachmentInfo(Attachment att) |
|
String |
WebService.generateCanSMILESForHELM2(String notation) |
method to generate a SMILES representation for a whole HELM2 input
|
protected static org.helm.notation2.parser.notation.polymer.PolymerListElements |
FastaFormat.generateElementsforRNA(String sequence,
org.helm.notation2.parser.notation.polymer.HELMEntity entity) |
method to fill a rna polymer with its elements (MonomerNotationUnits)
|
protected static org.helm.notation2.parser.notation.polymer.PolymerListElements |
FastaFormat.generateElementsOfPeptide(String sequence,
org.helm.notation2.parser.notation.polymer.HELMEntity entity) |
method to fill a peptide polymer with its elements (MonomerNotationUnits)
|
static String |
FastaFormat.generateFasta(org.helm.notation2.parser.notation.HELM2Notation helm2Notation2) |
method to generate for the whole HELM2Notation fasta-files, it contains
fasta for all rna and peptides
|
String |
WebService.generateFasta(String notation) |
method to generate FASTA-Formats for all rna and peptide sequences from
an HELM input
|
static String |
FastaFormat.generateFastaFromPeptidePolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) |
method to generate Fasta for peptide polymers
|
static String |
FastaFormat.generateFastaFromRNAPolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) |
method to generate Fasta for rna polymers
|
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)
|
byte[] |
WebService.generateImageForHELMMolecule(String notation) |
method to generate a HELM molecule
|
byte[] |
WebService.generateImageForMonomer(Monomer monomer,
boolean showRgroups) |
method to generate an image for a monomer
|
static byte[] |
Images.generateImageHELMMolecule(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to generate an image of the HELM molecule
|
static byte[] |
Images.generateImageofMonomer(Monomer monomer,
boolean rgroupsInformation) |
generates an image of the atom/bond representation of monomer
|
String |
WebService.generateJSON(String helm) |
method to generate JSON-Output for the HELM
|
static String |
MDLUtils.generateMDL(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to generate MDL for a HELM molecule
|
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
|
static org.helm.notation2.parser.notation.HELM2Notation |
FastaFormat.generatePeptidePolymersFromFASTAFormatHELM1(String fasta) |
method to read the information from a FastaFile-Format + generate peptide
polymers, be careful, it produces only polymers in the HELM1 standard, no
ambiguity
|
static org.helm.notation2.parser.notation.HELM2Notation |
FastaFormat.generateRNAPolymersFromFastaFormatHELM1(String fasta) |
method to read the information from a FastaFile-Format + generate RNA
Polymers be careful, it produces only polymers in the HELM1 standard, no
ambiguity
|
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 org.helm.notation2.parser.notation.polymer.PolymerNotation |
RNAUtils.getAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the antiparallel polymer for a rna/dna polymer
|
static String |
HELM1Utils.getCanonical(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to generate from a helm2notation a valid canonical HELM1
|
static String |
SMILES.getCanonicalSMILESForAll(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to generate canonical smiles for the whole HELMNotation
|
static String |
SMILES.getCanonicalSMILESForPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to generate canonical smiles for one single PolymerNotation
|
static org.helm.notation2.parser.notation.polymer.PolymerNotation |
RNAUtils.getComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the normal complement polymer for a given rna/dna polymer
|
static String[] |
HELM2NotationUtils.getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
generate formated siRNA sequence with default padding char " " and
base-pair char "|"
|
static String[] |
HELM2NotationUtils.getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation,
String paddingChar,
String basePairChar) |
|
static org.helm.notation2.parser.notation.polymer.PolymerNotation |
RNAUtils.getInverse(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the polymer with the inverse sequence of the current
polymer
|
static List<Monomer> |
MethodsMonomerUtils.getListOfHandledMonomers(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) |
method to get all HELM1 valid MonomerNotations Only on these monomers
required HELM1 functions are performed
|
static List<Monomer> |
MethodsMonomerUtils.getListOfHandledMonomersOnlyBase(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) |
method to get all HELM1 valid MonomerNotations Only on these monomers
required HELM1 functions are performed
|
static List<Monomer> |
MethodsMonomerUtils.getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) |
method to get all monomers for all MonomerNotations
|
static String |
RNAUtils.getModifiedNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the modifiedNucleotideSequence of the given PolymerNotation
|
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 org.helm.chemtoolkit.AbstractMolecule |
BuilderMolecule.getMolecule(String smiles) |
|
static org.helm.chemtoolkit.AbstractMolecule |
BuilderMolecule.getMoleculeForMonomer(Monomer monomer) |
method to build a molecule for a given monomer
|
static Monomer |
MethodsMonomerUtils.getMonomer(String type,
String id,
String info) |
method to get the monomer from the database!
|
static List<Monomer> |
MonomerParser.getMonomerList(String monomerXMLString) |
|
static String |
RNAUtils.getNaturalAnalogSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to generate the natural analogue sequence of a rna/dna of a given
polymer
|
static String |
PeptideUtils.getNaturalAnalogueSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to produce for a peptide PolymerNotation the natural analogue
sequence
|
static List<Nucleotide> |
RNAUtils.getNucleotideList(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get all nucleotides for one polymer
|
static String |
SequenceConverter.getNucleotideNaturalAnalogSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2Notation) |
method to generate for all rna polymers the natural analogue sequence
|
static String |
RNAUtils.getNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the nucleotide sequence for the polymer
|
static String |
SequenceConverter.getNucleotideSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to get for all rna/dnas the nucleotide sequence form an
HELM2Notation
|
static String |
SequenceConverter.getPeptideNaturalAnalogSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2Notation) |
method to generate for all peptide polymers the natural analogue sequence
|
static String |
SequenceConverter.getPeptideSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to get for all peptides the sequence
|
static org.helm.notation2.parser.notation.polymer.PolymerNotation |
RNAUtils.getReverseComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the polymer with the reverse complement sequence of the
current polymer
|
static String |
RNAUtils.getReverseSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to generate the reverse rna/dna sequence of a given polymer
|
static String |
PeptideUtils.getSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to produce for a peptide PolymerNotation the sequence
|
static String |
RNAUtils.getSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation one) |
method to get the rna sequence of the given PolymerNotation
|
static org.helm.notation2.parser.notation.HELM2Notation |
SiRNANotation.getSirnaNotation(String senseSeq,
String antiSenseSeq,
String rnaDesignType) |
this method converts nucleotide sequences into HELM notation based on
design pattern
|
static org.helm.notation2.parser.notation.HELM2Notation |
SiRNANotation.getSiRNANotation(String senseSeq,
String antiSenseSeq) |
this method converts nucleotide sequences into HELM2Notation
|
static String |
SMILES.getSMILESForAll(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to generate smiles for the whole HELMNotation
|
static String |
SMILES.getSMILESforPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to generate smiles for one single PolymerNotation
|
static String |
HELM1Utils.getStandard(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to reproduce a standard HELM in HELM1 - Format
|
static String |
RNAUtils.getTrimmedNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the trimmed nucleotide sequence
|
static String |
xHelmNotationExporter.getXHELM(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to get xhelm for the helm notation, only if it was possible to
convert the helm in the old format
|
static String |
xHelmNotationExporter.getXHELM2(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to get xhelm for the helm2 notation with the new functionality
|
static void |
ChangeObjects.hybridize(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
this method will automatically add base pair info into notation only if
it contains two RNA polymer notations and there is no base pairing info
|
static List<org.helm.notation2.parser.notation.connection.ConnectionNotation> |
RNAUtils.hybridize(org.helm.notation2.parser.notation.polymer.PolymerNotation one,
org.helm.notation2.parser.notation.polymer.PolymerNotation two) |
method to hybridize two given PolymerNotations together
|
static List<org.helm.notation2.parser.notation.connection.ConnectionNotation> |
RNAUtils.hybridizeAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation one,
org.helm.notation2.parser.notation.polymer.PolymerNotation two) |
method to hybridize two PolymerNotations together if they are
antiparallel
|
static boolean |
SMILES.isConnected(String molfile) |
returns if structure is connected
|
static org.helm.chemtoolkit.AbstractMolecule |
BuilderMolecule.mergeRgroups(org.helm.chemtoolkit.AbstractMolecule molecule) |
method to merge all unused rgroups into a molecule
|
static org.helm.notation2.parser.notation.HELM2Notation |
SequenceConverter.readPeptide(String notation) |
method to read a peptide sequence and generate a HELM2Notation object of
it
|
String |
WebService.readPeptide(String peptide) |
method to read a single peptide sequence and generates HELM
|
static org.helm.notation2.parser.notation.HELM2Notation |
SequenceConverter.readRNA(String notation) |
method to read a rna/dna sequence and generate a HELM2Notation object of
it
|
String |
WebService.readRNA(String rna) |
method to read a single rna sequence and generates HELM
|
void |
WebService.refreshMonomerCache() |
method to refresh the monomer cache of the MonomerFactory
|
static void |
ChangeObjects.replaceMonomer(org.helm.notation2.parser.notation.HELM2Notation helm2notation,
String polymerType,
String existingMonomerID,
String newMonomerID) |
method to replace the MonomerID with the new MonomerID for a given
polymer type
|
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
|
static boolean |
MonomerParser.validateAttachement(Attachment attachment) |
This method validates Attachment by the following rules
Attachment must have unique ID
cap group SMILES must be valid
cap group SMILES must contain one R group
R group in SMILES must match R group label
|
static boolean |
Validation.validateConnections(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to valid all existent connections in the Notation objects
|
void |
WebService.validateHELM(String helm) |
method to validate the input HELM-String
|
static boolean |
MonomerParser.validateMonomer(Monomer monomer) |
This methods checks the validity of the monomer based on the following
rules
monomer cannot be null
polymer type cannot be null
and must be one of the defined polymer type
monomer type cannot be null and must be one of the defined monomer type for a given polymer
type
Monomer ID cannot be null
structure cannot be null for non-chemical type monomer
structure SMILES must be valid
attachment labels on monomer must be unique
Attachment number on SMILES must match attachment List size
Each attachment in attachment list must be valid (call validateAttachment())
Attachment labels on monomer must match atachment label on attachment
list
For non-chemical type monomers, modified monomer (ID length
greater than 1) must have natural analog
All monomers must have at least one attachment
|
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
|
void |
WebService.validateSyntaxHELM(String helm) |
|