static void |
RNAUtils.addLastP(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to add a phosphate to the last polymer's nucleotide
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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
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static RgroupStructure |
BuilderMolecule.buildMoleculefromSinglePolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymernotation) |
method to build a molecule for a single polymer
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static boolean |
SMILES.containsGenericStructurePolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) |
method if the any of the given PolymerNotation contains generic
structures
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String |
WebService.generateNaturalAnalogSequencePeptide(String notation) |
method to generate the natural analogue sequence for all
peptide-sequences from an HELM input
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String |
WebService.generateNaturalAnalogSequenceRNA(String notation) |
method to generate the natural analogue sequence for all rna-sequences
from an HELM input
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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 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 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
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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
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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
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static String |
SequenceConverter.getPeptideNaturalAnalogSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2Notation) |
method to generate for all peptide polymers the natural analogue sequence
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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 |
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
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static org.helm.notation2.parser.notation.HELM2Notation |
SiRNANotation.getSiRNANotation(String senseSeq,
String antiSenseSeq) |
this method converts nucleotide sequences into HELM2Notation
|
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
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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
|
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
|