static Nucleotide |
NucleotideParser.convertToNucleotide(String id,
boolean last) |
method to convert an string to an nucleotide
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String |
WebService.generateCanSMILESForHELM2(String notation) |
method to generate a SMILES representation for a whole HELM2 input
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static String |
MDLUtils.generateMDL(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to generate MDL for a HELM molecule
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static Monomer |
MethodsMonomerUtils.generateTemporaryMonomer(String id,
String polymerType,
String naturalAnalog) |
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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
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static List<Monomer> |
Validation.getAllMonomersOnlyBase(org.helm.notation2.parser.notation.polymer.MonomerNotation not) |
method to get for one MonomerNotation all valid contained monomers.
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static List<String> |
AminoAcidParser.getAminoAcidList(String peptideSequence) |
This method converts peptide sequence into a List of amino acid
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static List<String> |
AminoAcidParser.getAminoAcidList(String peptideSequence,
String delimiter) |
This method converts peptide sequence into a List of amino acid with
optional delimiter
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static String |
SMILES.getCanonicalSMILESForAll(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to generate canonical smiles for the whole HELMNotation
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static String |
SMILES.getCanonicalSMILESForPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to generate canonical smiles for one single PolymerNotation
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static String[] |
HELM2NotationUtils.getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
generate formated siRNA sequence with default padding char " " and
base-pair char "|"
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static String[] |
HELM2NotationUtils.getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation,
String paddingChar,
String basePairChar) |
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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
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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
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static List<Monomer> |
MethodsMonomerUtils.getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) |
method to get all monomers for all MonomerNotations
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static Monomer |
MethodsMonomerUtils.getMonomer(String type,
String id,
String info) |
method to get the monomer from the database!
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static String |
SequenceConverter.getPeptideSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to get for all peptides the sequence
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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
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static String |
RNAUtils.getReverseSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to generate the reverse rna/dna sequence of a given polymer
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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
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static org.helm.notation2.parser.notation.HELM2Notation |
SiRNANotation.getSiRNANotation(String senseSeq,
String antiSenseSeq) |
this method converts nucleotide sequences into HELM2Notation
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static String |
SMILES.getSMILESforPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to generate smiles for one single PolymerNotation
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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
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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
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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
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static boolean |
Validation.validateConnections(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
method to valid all existent connections in the Notation objects
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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
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