| Package | Description |
|---|---|
| org.helm.notation2.tools |
| Modifier and Type | Method and Description |
|---|---|
static void |
RNAUtils.addLastP(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
method to add a phosphate to the last polymer's nucleotide
|
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 RgroupStructure |
BuilderMolecule.buildMoleculefromSinglePolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymernotation)
method to build a molecule for a single polymer
|
static boolean |
SMILES.containsGenericStructurePolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)
method if the any of the given PolymerNotation contains generic
structures
|
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 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 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 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
|
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 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 |
RNAUtils.getSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation one)
method to get the rna sequence of the given PolymerNotation
|
static String |
PeptideUtils.getSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
method to produce for a peptide PolymerNotation the sequence
|
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 |
RNAUtils.getTrimmedNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
method to get the trimmed nucleotide sequence
|
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 void |
RNAUtils.removeLastP(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
method to remove the phosphate of the last nucleotide
|
static void |
ChangeObjects.replaceSMILESWithTemporaryIds(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
This function replaces smiles in complex notation with temporary ids
|
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