| Package | Description |
|---|---|
| org.helm.notation2 | |
| org.helm.notation2.tools |
| Modifier and Type | Method and Description |
|---|---|
static Nucleotide |
DeepCopy.copy(Nucleotide nucleotide) |
static Serializable |
DeepCopy.copy(Serializable input) |
| Modifier and Type | Method and Description |
|---|---|
static Nucleotide |
NucleotideParser.convertToNucleotide(String id,
boolean last)
method to convert an string to an nucleotide
|
String |
WebService.generateCanSMILESForHELM2(String notation)
method to generate a SMILES representation for a whole HELM2 input
|
static String |
MDLUtils.generateMDL(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
method to generate MDL for a HELM molecule
|
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 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 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.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 Monomer |
MethodsMonomerUtils.getMonomer(String type,
String id,
String info)
method to get the monomer from the database!
|
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 org.helm.notation2.parser.notation.HELM2Notation |
SiRNANotation.getSiRNANotation(String senseSeq,
String antiSenseSeq)
this method converts nucleotide sequences into HELM2Notation
|
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 String |
SMILES.getSMILESforPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
method to generate smiles for one single PolymerNotation
|
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 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 boolean |
Validation.validateConnections(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
method to valid all existent connections in the Notation 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
|
Copyright © 2017. All rights reserved.