Index (helm2-notationtoolkit 1.3.11 API)

A B C D E F G H I L M N O P R S T U V W X
All Classes|All Packages

A

addAnnotation(AnnotationNotation, int, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to add an annotation at a specific position of the HELM2Notation
addAnnotationToConnection(int, String, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to add an annotation to a connection of the HELM2Notation
addAnnotationToMonomerNotation(PolymerNotation, int, String) - Static method in class org.helm.notation2.tools.ChangeObjects: method to add an annotation to a MonomerNotation
addAnnotationToPolymer(PolymerNotation, String) - Static method in class org.helm.notation2.tools.ChangeObjects: method to add an annotation to a PolymerNotation
addAttachment(Attachment) - Method in class org.helm.notation2.Monomer: Try to add a new attachment to this monomer
addConnection(String, String) - Method in class org.helm.notation2.InterConnections
addConnection(ConnectionNotation, int, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to add a new connection at the position of the HELM2Notation
addCountToMonomerNotation(PolymerNotation, int, String) - Static method in class org.helm.notation2.tools.ChangeObjects: method to set the count of a MonomerNotation
addGroup(GroupingNotation, int, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to add a group to the grouping section of the HELM2Notation
addLastP(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to add a phosphate to the last polymer's nucleotide
addMonomer(Monomer) - Method in class org.helm.notation2.MonomerStore: Adds a monomer to the store
addMonomer(Monomer, boolean) - Method in class org.helm.notation2.MonomerStore: Adds a monomer to the store and optionally sets the dbChanged flag
addMonomerNotation(int, PolymerNotation, MonomerNotation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to add a new MonomerNotation to a PolymerNotation
addNewMonomer(Monomer) - Method in class org.helm.notation2.MonomerFactory: To add new monomer into monomerCache
addNewMonomer(Monomer) - Method in class org.helm.notation2.MonomerStore: Adds a monomer to the store and makes it a temporary new monomer
addPolymerNotation(int, PolymerNotation, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to add a PolymerNotation at a specific position of the HELM2Notation
AminoAcidParser - Class in org.helm.notation2.tools: AminoAcidParser
AminoAcidParser() - Constructor for class org.helm.notation2.tools.AminoAcidParser
AnalogSequenceException - Exception in org.helm.notation2.exception: AnalogSequenceException
AnalogSequenceException(String) - Constructor for exception org.helm.notation2.exception.AnalogSequenceException
areAntiparallel(PolymerNotation, PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to check if two given polymers are complement to each other
ATTACHEMENT_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
ATTACHEMENT_ID_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
ATTACHEMENT_LABEL_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
ATTACHEMENTS_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
ATTACHEMENTS_LIST_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
Attachment - Class in org.helm.notation2: This is a data model for Attachment point on monomer
Attachment() - Constructor for class org.helm.notation2.Attachment
Attachment(String, String) - Constructor for class org.helm.notation2.Attachment
ATTACHMENT_LIST_DELIMITER - Static variable in class org.helm.notation2.Monomer
ATTACHMENT_LIST_ELEMENT - Static variable in class org.helm.notation2.MonomerFactory
attachmentContains(Monomer) - Method in class org.helm.notation2.Monomer
attachmentEquals(Monomer) - Method in class org.helm.notation2.Monomer
AttachmentException - Exception in org.helm.notation2.exception: AttachmentException
AttachmentException(String) - Constructor for exception org.helm.notation2.exception.AttachmentException
AttachmentLoader - Class in org.helm.notation2: loads attachments from a given input stream
ATTACHMENTS_RESOURCE - Static variable in class org.helm.notation2.MonomerFactory

B

BACKBONE_MOMONER_TYPE - Static variable in class org.helm.notation2.Monomer
BACKBONE_MONOMER_BRANCH_ATTACHEMENT - Static variable in class org.helm.notation2.Attachment
BACKBONE_MONOMER_LEFT_ATTACHEMENT - Static variable in class org.helm.notation2.Attachment
BACKBONE_MONOMER_RIGHT_ATTACHEMENT - Static variable in class org.helm.notation2.Attachment
Base64 - Class in org.helm.notation2.tools: A very fast and memory efficient class to encode and decode to and from BASE64 in full accordance with RFC 2045. On Windows XP sp1 with 1.4.2_04 and later ;), this encoder and decoder is about 10 times faster on small arrays (10 - 1000 bytes) and 2-3 times as fast on larger arrays (10000 - 1000000 bytes) compared to <code>sun.misc.Encoder()/Decoder()</code>. On byte arrays the encoder is about 20% faster than Jakarta Commons Base64 Codec for encode and about 50% faster for decoding large arrays. This implementation is about twice as fast on very small arrays (&lt 30 bytes). If source/destination is a <code>String</code> this version is about three times as fast due to the fact that the Commons Codec result has to be recoded to a <code>String</code> from <code>byte[]</code>, which is very expensive. This encode/decode algorithm doesn't create any temporary arrays as many other codecs do, it only allocates the resulting array. This produces less garbage and it is possible to handle arrays twice as large as algorithms that create a temporary array. (E.g. Jakarta Commons Codec). It is unknown whether Sun's <code>sun.misc.Encoder()/Decoder()</code> produce temporary arrays but since performance is quite low it probably does. The encoder produces the same output as the Sun one except that the Sun's encoder appends a trailing line separator if the last character isn't a pad. Unclear why but it only adds to the length and is probably a side effect. Both are in conformance with RFC 2045 though. Commons codec seem to always att a trailing line separator. Note! The encode/decode method pairs (types) come in three versions with the exact same algorithm and thus a lot of code redundancy. This is to not create any temporary arrays for transcoding to/from different format types. The methods not used can simply be commented out. There is also a "fast" version of all decode methods that works the same way as the normal ones, but har a few demands on the decoded input. Normally though, these fast verions should be used if the source if the input is known and it hasn't bee tampered with. If you find the code useful or you find a bug, please send me a note at base64 @ miginfocom . com. Licence (BSD): ============== Copyright (c) 2004, Mikael Grev, MiG InfoCom AB. (base64 @ miginfocom . com) All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of the MiG InfoCom AB nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Base64() - Constructor for class org.helm.notation2.tools.Base64
BRANCH_END_SYMBOL - Static variable in class org.helm.notation2.tools.NucleotideParser
BRANCH_MOMONER_TYPE - Static variable in class org.helm.notation2.Monomer
BRANCH_MONOMER_ATTACHEMENT - Static variable in class org.helm.notation2.Attachment
BRANCH_START_SYMBOL - Static variable in class org.helm.notation2.tools.NucleotideParser
BuilderMolecule - Class in org.helm.notation2.tools: class to build molecules for the HELMNotation
BuilderMoleculeException - Exception in org.helm.notation2.exception: BuilderMoleculeException
BuilderMoleculeException(String) - Constructor for exception org.helm.notation2.exception.BuilderMoleculeException
buildMoleculefromPolymers(List<PolymerNotation>, List<ConnectionNotation>) - Static method in class org.helm.notation2.tools.BuilderMolecule: method to build molecules for the whole HELMNotation
buildMoleculefromSinglePolymer(PolymerNotation) - Static method in class org.helm.notation2.tools.BuilderMolecule: method to build a molecule for a single polymer
buildMonomerCacheFromXML(String) - Method in class org.helm.notation2.MonomerFactory: Build an MonomerCache object with monomerDBXML String
buildNucleotideTemplatesFromXML(String) - Method in class org.helm.notation2.NucleotideFactory

C

calculate(HELM2Notation) - Method in class org.helm.notation2.calculation.ExtinctionCoefficient: method to calculate the extinction coefficient for the whole HELM molecule
calculate(HELM2Notation, int) - Method in class org.helm.notation2.calculation.ExtinctionCoefficient: method to calculate the extinction coefficient for the whole HELM molecule
calculateExtinctionCoefficient(String) - Method in class org.helm.notation2.tools.WebService: method to calculate from a non-ambiguous HELM string the extinction coefficient
calculateMolecularWeight(String) - Method in class org.helm.notation2.tools.WebService: method to calculate from a non-ambiguous HELM input the molecular weight
CalculationException - Exception in org.helm.notation2.exception: This is the exception thrown for Invalid Structures
CalculationException() - Constructor for exception org.helm.notation2.exception.CalculationException: Creates a new instance of StructureException without detail message.
CalculationException(String) - Constructor for exception org.helm.notation2.exception.CalculationException: Constructs an instance of StructureException with the specified detail message.
CAP_GROUP_H - Static variable in class org.helm.notation2.Attachment
CAP_GROUP_NAME_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
CAP_GROUP_OH - Static variable in class org.helm.notation2.Attachment
CAP_GROUP_SMILES_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
CategorizedMonomer - Class in org.helm.notation2.wsadapter: CategorizedMonomer used as wrapper class for monomer categorization in the HELMEditor.
CategorizedMonomer() - Constructor for class org.helm.notation2.wsadapter.CategorizedMonomer: Default constructor.
CategorizedMonomer(String, String, String, String, String, String, String, String, String) - Constructor for class org.helm.notation2.wsadapter.CategorizedMonomer: Constructor using all possible fields.
changeAnnotation(AnnotationNotation, int, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to change an annotation at the position of the HELM2Notation
changeConnection(int, ConnectionNotation, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to change a connection at the position of the HELM2Notation
changeGroup(GroupingNotation, int, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to change a group of the HELM2Notation
changeMonomerNotation(int, PolymerNotation, MonomerNotation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to change the MonomerNotation on the specific position
ChangeObjects - Class in org.helm.notation2.tools: ChangeObjects, class to provide simple methods to change the HELM2Notation objects
ChangeObjects() - Constructor for class org.helm.notation2.tools.ChangeObjects
changePolymerNotation(int, PolymerNotation, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to change the PolymerNotation at a specific position of the HELM2Notation
characters - Variable in class org.helm.notation2.SimpleNotationGroupIterator
CHEMICAL_POLYMER_TYPE - Static variable in class org.helm.notation2.Monomer
chemistry - Static variable in class org.helm.notation2.Chemistry
Chemistry - Class in org.helm.notation2: Chemistry, singleton class to define which Chemistry-Plugin is used
ChemistryException - Exception in org.helm.notation2.exception: ChemistryException TODO comment me
ChemistryException(String) - Constructor for exception org.helm.notation2.exception.ChemistryException
cleanup(String) - Static method in class org.helm.notation2.tools.AminoAcidParser: remove white space, and convert all lower case to upper case
clearMonomers() - Method in class org.helm.notation2.MonomerStore: Clears the MonomerStore
combineHELM2notation(HELM2Notation, HELM2Notation) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to add a new HELMNotation to another HELM2Notation, the new HELM2Notation will be merged to the first HELM2Notation
complementMap - Static variable in class org.helm.notation2.tools.NucleotideParser
complementMap - Static variable in class org.helm.notation2.tools.SiRNANotation
ConnectionNotationException - Exception in org.helm.notation2.exception: ConnectionNotationException
ConnectionNotationException(String) - Constructor for exception org.helm.notation2.exception.ConnectionNotationException
containAnyAtom() - Method in class org.helm.notation2.Monomer
containsGenericStructurePolymer(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.SMILES: method if the any of the given PolymerNotation contains generic structures
Converter - Class in org.helm.notation2.tools: Converter class allowing to convert extended smiles into smiles with atom mapping
convertIntoAnalogSequence(HELM2Notation) - Static method in class org.helm.notation2.tools.FastaFormat: method to convert all Peptides and RNAs into the natural analogue sequence and generates HELM2Notation
convertIntoStandardHELM(String) - Method in class org.helm.notation2.tools.WebService: method to convert the input HELM into a standard HELM
convertMolFileSMILESWithAtomMapping(String, List<Attachment>) - Method in class org.helm.notation2.tools.WebService: method to generate a smiles with atom mapping for a given molfile with the given attachments
convertMolToSMILESWithAtomMapping(String, List<Attachment>) - Static method in class org.helm.notation2.tools.SMILES: Converts molfile with the given attachments in smiles with atom mapping
convertMonomer(Monomer) - Static method in class org.helm.notation2.tools.Converter
convertMonomerStore() - Static method in class org.helm.notation2.tools.Converter
convertStandardHELMToCanonicalHELM(String) - Method in class org.helm.notation2.tools.WebService: method to convert the input HELM into canonical HELM
convertToNucleotide(String, boolean) - Static method in class org.helm.notation2.tools.NucleotideParser: method to convert an string to an nucleotide
copy(Serializable) - Static method in class org.helm.notation2.DeepCopy
copy(ArrayList) - Static method in class org.helm.notation2.DeepCopy
copy(List) - Static method in class org.helm.notation2.DeepCopy
copy(Attachment) - Static method in class org.helm.notation2.DeepCopy
copy(Monomer) - Static method in class org.helm.notation2.DeepCopy
copy(Nucleotide) - Static method in class org.helm.notation2.DeepCopy

D

decode(byte[]) - Static method in class org.helm.notation2.tools.Base64: Decodes a BASE64 encoded byte array.
decode(char[]) - Static method in class org.helm.notation2.tools.Base64: Decodes a BASE64 encoded char array.
decode(String) - Static method in class org.helm.notation2.tools.Base64: Decodes a BASE64 encoded String.
decode(String) - Static method in class org.helm.notation2.tools.MolfileEncoder
decodeFast(byte[]) - Static method in class org.helm.notation2.tools.Base64: Decodes a BASE64 encoded byte array that is known to be resonably well formatted.
decodeFast(char[]) - Static method in class org.helm.notation2.tools.Base64: Decodes a BASE64 encoded char array that is known to be resonably well formatted.
decodeFast(String) - Static method in class org.helm.notation2.tools.Base64: Decodes a BASE64 encoded string that is known to be resonably well formatted.
decompose(HELM2Notation) - Method in class org.helm.notation2.tools.HELM2NotationUtils: decompose the HELM2 into smaller HELM2 objects
DeepCopy - Class in org.helm.notation2
DeepCopy() - Constructor for class org.helm.notation2.DeepCopy
DEFAULT_BASE_PAIR_CHAR - Static variable in class org.helm.notation2.tools.HELM2NotationUtils
DEFAULT_NAME_SPACE - Static variable in class org.helm.notation2.MonomerFactory
DEFAULT_NAME_SPACE - Static variable in class org.helm.notation2.NucleotideFactory
DEFAULT_NOTATION_SOURCE - Static variable in class org.helm.notation2.tools.NucleotideParser: Deprecated.
DEFAULT_PADDING_CHAR - Static variable in class org.helm.notation2.tools.HELM2NotationUtils
deleteAllAnnotations(HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to delete all annotations of the HELM2Notation
deleteAllConnections(HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to delete all connections of the HELM2Notation
deleteAllGroups(HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to delete all groups of the HELM2Notation
deleteAnnotation(int, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to delete the annotation at the specific position of the HELM2Notation
deleteAnnotationFromMonomerNotation(PolymerNotation, int) - Static method in class org.helm.notation2.tools.ChangeObjects: method to delete the annotation of a MonomerNotation
deleteConnection(int, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to delete the connection at the specific position of the HELM2Notation
deleteConnection(String) - Method in class org.helm.notation2.InterConnections
deleteGroup(int, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to delete a group at a specific position of the HELM2Notation
deleteMonomerNotation(int, PolymerNotation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to delete a MonomerNotation at a specific position of the PolymerNotation
deletePolymerNotation(int, HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to delete the PolymerNotation at a specific position of the HELM2Notation

E

encode(String) - Static method in class org.helm.notation2.tools.MolfileEncoder
EncoderException - Exception in org.helm.notation2.exception: EncoderException TODO comment me
EncoderException(String) - Constructor for exception org.helm.notation2.exception.EncoderException
encodeToByte(byte[], boolean) - Static method in class org.helm.notation2.tools.Base64: Encodes a raw byte array into a BASE64 byte[] representation i accordance with RFC 2045.
encodeToChar(byte[], boolean) - Static method in class org.helm.notation2.tools.Base64: Encodes a raw byte array into a BASE64 char[] representation i accordance with RFC 2045.
encodeToString(byte[], boolean) - Static method in class org.helm.notation2.tools.Base64: Encodes a raw byte array into a BASE64 String representation i accordance with RFC 2045.
ENDING_POSITION_TYPE - Static variable in class org.helm.notation2.Nucleotide
expand(List<List<String[]>>, List<String[]>) - Static method in class org.helm.notation2.tools.PermutationAndExpansion
EXTERNAL_SCHEMA_LOCATION_KEY - Static variable in class org.helm.notation2.MonomerFactory
EXTERNAL_SCHEMA_LOCATION_KEY - Static variable in class org.helm.notation2.NucleotideFactory
ExtinctionCoefficient - Class in org.helm.notation2.calculation: ExtinctionCoefficient class to calculate the extinction coefficient
ExtinctionCoefficientException - Exception in org.helm.notation2.exception: ExtinctionCoefficientException
ExtinctionCoefficientException(String) - Constructor for exception org.helm.notation2.exception.ExtinctionCoefficientException

F

FastaFormat - Class in org.helm.notation2.tools: FastaFormat, class to convert FastaFiles to HELMNotation and vice versa
FastaFormatException - Exception in org.helm.notation2.exception: FastaFormatException
FastaFormatException(String) - Constructor for exception org.helm.notation2.exception.FastaFormatException
fillAttachmentInfo(Attachment) - Static method in class org.helm.notation2.tools.MonomerParser
finalizeMonomerCache() - Static method in class org.helm.notation2.MonomerFactory
fromJSON(String) - Static method in class org.helm.notation2.Monomer
fromJSON(String) - Static method in class org.helm.notation2.Nucleotide

G

generateCanSMILESForHELM2(String) - Method in class org.helm.notation2.tools.WebService: method to generate a SMILES representation for a whole HELM2 input
generateElementsforRNA(String, HELMEntity) - Static method in class org.helm.notation2.tools.FastaFormat: method to fill a rna polymer with its elements (MonomerNotationUnits)
generateElementsOfPeptide(String, HELMEntity) - Static method in class org.helm.notation2.tools.FastaFormat: method to fill a peptide polymer with its elements (MonomerNotationUnits)
generateFasta(String) - Method in class org.helm.notation2.tools.WebService: method to generate FASTA-Formats for all rna and peptide sequences from an HELM input
generateFasta(HELM2Notation) - Static method in class org.helm.notation2.tools.FastaFormat: method to generate for the whole HELM2Notation fasta-files, it contains fasta for all rna and peptides
generateFastaFromPeptide(List<Monomer>) - Static method in class org.helm.notation2.tools.FastaFormat: method to generate Fasta for a list of peptide monomers
generateFastaFromPeptidePolymer(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.FastaFormat: method to generate Fasta for peptide polymers
generateFastaFromRNA(List<Monomer>) - Static method in class org.helm.notation2.tools.FastaFormat: method to generate Fasta for a list of rna monomers
generateFastaFromRNAPolymer(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.FastaFormat: method to generate Fasta for rna polymers
generateHELMFromFastaNucleotide(String) - Method in class org.helm.notation2.tools.WebService: method to generate HELM from a FASTA containing rna/dna sequences
generateHELMFromFastaPeptide(String) - Method in class org.helm.notation2.tools.WebService: method to generate HELM from a FASTA containing peptide sequence(s)
generateImageForHELMMolecule(String) - Method in class org.helm.notation2.tools.WebService: method to generate a HELM molecule
generateImageForMonomer(Monomer, boolean) - Method in class org.helm.notation2.tools.WebService: method to generate an image for a monomer
generateImageHELMMolecule(HELM2Notation) - Static method in class org.helm.notation2.tools.Images: method to generate an image of the HELM molecule
generateImageofMonomer(Monomer, boolean) - Static method in class org.helm.notation2.tools.Images: generates an image of the atom/bond representation of monomer
generateJSON(String) - Method in class org.helm.notation2.tools.WebService: method to generate JSON-Output for the HELM
generateMDL(HELM2Notation) - Static method in class org.helm.notation2.tools.MDLUtils: method to generate MDL for a HELM molecule
generateNaturalAnalogSequencePeptide(String) - Method in class org.helm.notation2.tools.WebService: method to generate the natural analogue sequence for all peptide-sequences from an HELM input
generateNaturalAnalogSequenceRNA(String) - Method in class org.helm.notation2.tools.WebService: method to generate the natural analogue sequence for all rna-sequences from an HELM input
generatePeptidePolymersFromFASTAFormatHELM1(String) - Static method in class org.helm.notation2.tools.FastaFormat: method to read the information from a FastaFile-Format + generate peptide polymers, be careful, it produces only polymers in the HELM1 standard, no ambiguity
generateRNAPolymersFromFastaFormatHELM1(String) - Static method in class org.helm.notation2.tools.FastaFormat: method to read the information from a FastaFile-Format + generate RNA Polymers be careful, it produces only polymers in the HELM1 standard, no ambiguity
generateSMILESForHELM2(String) - Method in class org.helm.notation2.tools.WebService: method to generate a SMILES representation for a whole HELM2 input
generateTemporaryMonomer(String, String, String) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils
getAllBasePairConnections(List<ConnectionNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to get all base pair connections of a given list of ConnectionNotation
getAllEdgeConnections(List<ConnectionNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to get all edge connections of a given List of ConnectionNotation
getAllMonomers(MonomerNotation, int) - Static method in class org.helm.notation2.tools.Validation: method to get for one MonomerNotation all valid contained monomers
getAllMonomersList() - Method in class org.helm.notation2.MonomerStore: This method returns all monomers of the store as list sorted by polymer type
getAllMonomersOnlyBase(MonomerNotation) - Static method in class org.helm.notation2.tools.Validation: method to get for one MonomerNotation all valid contained monomers.
getAlternateId() - Method in class org.helm.notation2.Attachment
getAlternateId() - Method in class org.helm.notation2.Monomer
getAminoAcidList(String) - Static method in class org.helm.notation2.tools.AminoAcidParser: This method converts peptide sequence into a List of amino acid
getAminoAcidList(String, String) - Static method in class org.helm.notation2.tools.AminoAcidParser: This method converts peptide sequence into a List of amino acid with optional delimiter
getAntiparallel(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to get the antiparallel polymer for a rna/dna polymer
getAttachementElement(Attachment) - Static method in class org.helm.notation2.tools.MonomerParser: This method converts Attachment to ATTACHMENT XML element
getAttachment(String) - Method in class org.helm.notation2.Monomer: get a specific attachment by passing in a label
getAttachment(Element) - Static method in class org.helm.notation2.tools.MonomerParser: Convert ATTACHMENT element to Attachment object
getAttachmentDB() - Method in class org.helm.notation2.MonomerCache
getAttachmentDB() - Method in class org.helm.notation2.MonomerFactory
getAttachmentLabelIDs() - Method in class org.helm.notation2.MonomerFactory
getAttachmentList() - Method in class org.helm.notation2.Monomer
getAttachmentListString() - Method in class org.helm.notation2.Monomer
getBackgroundColor() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Returns the background color.
getBaseMonomer() - Method in class org.helm.notation2.Nucleotide: get the base monomer, the return value could be null if this nucleotide does not have a base
getBaseMonomer(MonomerStore) - Method in class org.helm.notation2.Nucleotide: get the base monomer, the return value could be null if this nucleotide does not have a base
getBLOBPolymers(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to get all blob polymers given a list of PolymerNotation objects
getCanonical(HELM2Notation) - Static method in class org.helm.notation2.tools.HELM1Utils: method to generate from a helm2notation a valid canonical HELM1
getCanonicalSMILESForAll(HELM2Notation) - Static method in class org.helm.notation2.tools.SMILES: method to generate canonical smiles for the whole HELMNotation
getCanonicalSMILESForPolymer(PolymerNotation) - Static method in class org.helm.notation2.tools.SMILES: method to generate canonical smiles for one single PolymerNotation
getCanSMILES() - Method in class org.helm.notation2.Monomer
getCapGroupName() - Method in class org.helm.notation2.Attachment
getCapGroupSMILES() - Method in class org.helm.notation2.Attachment
getCapMoleculeInfo(String) - Method in class org.helm.notation2.Monomer: This method returns the MoleculeInfo for the input R group label of this monomer
getCategory() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Returns the category.
getChemistry() - Method in class org.helm.notation2.Chemistry
getCHEMPolymers(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to get all chem polymers given a list of PolymerNotation objects
getComplement(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to get the normal complement polymer for a given rna/dna polymer
getComplexNotationString(Element) - Static method in class org.helm.notation2.tools.xHelmNotationParser: Extracts the complex notation string from the root node of the XHELM document
getConflictedMonomerMap(MonomerCache) - Method in class org.helm.notation2.MonomerFactory
getDefaultUnit() - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
getDefaultUnitType() - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
getExactMass() - Method in class org.helm.notation2.MoleculeProperty
getExactMass(HELM2Notation) - Static method in class org.helm.notation2.calculation.MoleculePropertyCalculator: method to get the ExactMass for the whole HELM
getExternalAttachmentsPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
getExternalMonomersPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
getExternalNucleotidesPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
getExtinctionCoefficient() - Method in class org.helm.notation2.MoleculeProperty
getFontColor() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Returns the font color.
getFormatedSirnaSequences(HELM2Notation) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: generate formated siRNA sequence with default padding char " " and base-pair char "|"
getFormatedSirnaSequences(HELM2Notation, String, String) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
getHELMNotationString(Element) - Static method in class org.helm.notation2.tools.xHelmNotationParser: Extracts the HELM string from the root node of the XHELM document
getId() - Method in class org.helm.notation2.Attachment
getId() - Method in class org.helm.notation2.Monomer
getInstance() - Static method in class org.helm.notation2.calculation.ExtinctionCoefficient
getInstance() - Static method in class org.helm.notation2.Chemistry: method to get the singleton instance
getInstance() - Static method in class org.helm.notation2.MonomerFactory: Initialize MonomerCache and returns the singleton Factory class
getInstance() - Static method in class org.helm.notation2.NucleotideFactory
getInstance() - Static method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Creates singleton instance of MonomerStoreConfiguration and returns it.
getInterConnections() - Method in class org.helm.notation2.InterConnections
getInverse(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to get the polymer with the inverse sequence of the current polymer
getLabel() - Method in class org.helm.notation2.Attachment
getLinkerNotation() - Method in class org.helm.notation2.Nucleotide: This method returns the HELM notation for nucleotide linker
getListOfHandledMonomers(List<MonomerNotation>) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils: method to get all HELM1 valid MonomerNotations Only on these monomers required HELM1 functions are performed
getListOfHandledMonomersOnlyBase(List<MonomerNotation>) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils: method to get all HELM1 valid MonomerNotations Only on these monomers required HELM1 functions are performed
getListOfMonomer(List<MonomerNotation>) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils: method to get all monomers for all MonomerNotations
getListOfMonomerNotation(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils: method to get all MonomerNotations for all given polymers
getListOfPolymersSpecificType(String, List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to get all polymers for one specific polymer type
getManipulator() - Method in class org.helm.notation2.Chemistry: method to get the Manipulator
getMatchingBracketPosition(char[], int, char, char) - Static method in class org.helm.notation2.tools.NucleotideParser
getMaxMatchFragment(String, String) - Static method in class org.helm.notation2.tools.RNAUtils: method to get the largest matched fragment between two sequences, replace T with U before Match
getMaxMatchFragment(String, String, int) - Static method in class org.helm.notation2.tools.RNAUtils: This method returns the largest matched fragment between two sequences, replace T with U before match
getModifiedNucleotideSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to get the modifiedNucleotideSequence of the given PolymerNotation
getMolecularFormula() - Method in class org.helm.notation2.MoleculeProperty
getMolecularFormula(String) - Method in class org.helm.notation2.tools.WebService: method to calculate from a non-ambiguous HELM input the molecular formula
getMolecularFormular(HELM2Notation) - Static method in class org.helm.notation2.calculation.MoleculePropertyCalculator: method to get the MolecularFormular for the whole HELM
getMolecularProperties(String) - Method in class org.helm.notation2.tools.WebService: method to calculate froma non-ambiguous HELM input the molecular properties: molecular formula, molecular weight, exact mass, extinction coefficient
getMolecularWeight() - Method in class org.helm.notation2.MoleculeProperty
getMolecularWeight(HELM2Notation) - Static method in class org.helm.notation2.calculation.MoleculePropertyCalculator: method to get the molecular weight for the whole HELM
getMolecule() - Method in class org.helm.notation2.RgroupStructure
getMolecule(String) - Static method in class org.helm.notation2.tools.BuilderMolecule
getMoleculeForMonomer(Monomer) - Static method in class org.helm.notation2.tools.BuilderMolecule: method to build a molecule for a given monomer
getMoleculeProperties(HELM2Notation) - Static method in class org.helm.notation2.calculation.MoleculePropertyCalculator: method to get all molecule properties for one HELM2Notation
getMolfile() - Method in class org.helm.notation2.Monomer
getMonomer(String) - Method in class org.helm.notation2.MonomerStore: Returns the monomer by smiles string
getMonomer(String) - Static method in class org.helm.notation2.tools.MonomerParser
getMonomer(String, String) - Method in class org.helm.notation2.MonomerStore: Returns the monomer specified by polymerType and alternatId
getMonomer(String, String, String) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils: method to get the monomer from the database!
getMonomer(Element) - Static method in class org.helm.notation2.tools.MonomerParser: Convert monomer element to Monomer object
getMonomerCountForRNA(String) - Static method in class org.helm.notation2.tools.NucleotideParser
getMonomerDB() - Method in class org.helm.notation2.MonomerCache
getMonomerDB() - Method in class org.helm.notation2.MonomerFactory: retruns the monomer database
getMonomerDB() - Method in class org.helm.notation2.MonomerStore: returns MonomerDB
getMonomerDB(boolean) - Method in class org.helm.notation2.MonomerFactory: returns the monomer database including monomers that where temporary marked as new, else without those monomers
getMonomerElement(Monomer) - Static method in class org.helm.notation2.tools.MonomerParser: This method converts Monomer to MONOMER XML element
getMonomerID() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Returns the monomer ID.
getMonomerIDListFromNucleotide(String) - Static method in class org.helm.notation2.tools.NucleotideParser
getMonomerList(String) - Static method in class org.helm.notation2.tools.MonomerParser
getMonomerName() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Returns the monomer name.
getMonomers(String) - Method in class org.helm.notation2.MonomerStore: Returns all monomers by polymerType
getMonomerStore() - Method in class org.helm.notation2.MonomerFactory: create a MonomerStore instance based on MonomerFactory's monomerDB and smilesMonomerDB
getMonomerStore(Element) - Static method in class org.helm.notation2.tools.xHelmNotationParser: Generates the monomer store from a given XHELM document
getMonomerType() - Method in class org.helm.notation2.Monomer
getMonomerType() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Returns the monomer type.
getMonomerTypes() - Method in class org.helm.notation2.MonomerFactory
getName() - Method in class org.helm.notation2.Monomer
getNaturalAnalog() - Method in class org.helm.notation2.Monomer: get the natural analog of this monomer.
getNaturalAnalog() - Method in class org.helm.notation2.Nucleotide: return the natural analog of this nucleotide
getNaturalAnalog(MonomerStore) - Method in class org.helm.notation2.Nucleotide: return the natural analog of this nucleotide
getNaturalAnalogon() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Returns the natural analogon.
getNaturalAnalogSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to generate the natural analogue sequence of a rna/dna of a given polymer
getNaturalAnalogueSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.PeptideUtils: method to produce for a peptide PolymerNotation the natural analogue sequence
getNotation() - Method in class org.helm.notation2.Nucleotide
getNucleosideNotation() - Method in class org.helm.notation2.Nucleotide: This method returns the HELM notation for nucleoside
getNucleotide(String) - Static method in class org.helm.notation2.tools.NucleotideParser
getNucleotide(Element) - Static method in class org.helm.notation2.tools.NucleotideParser
getNucleotideList(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to get all nucleotides for one polymer
getNucleotideNaturalAnalogSequenceFromNotation(HELM2Notation) - Static method in class org.helm.notation2.tools.SequenceConverter: method to generate for all rna polymers the natural analogue sequence
getNucleotideSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to get the nucleotide sequence for the polymer
getNucleotideSequenceFromNotation(HELM2Notation) - Static method in class org.helm.notation2.tools.SequenceConverter: method to get for all rna/dnas the nucleotide sequence form an HELM2Notation
getNucleotideTemplates() - Method in class org.helm.notation2.NucleotideFactory
getNucleotideTemplates(Element) - Static method in class org.helm.notation2.tools.NucleotideParser
getNucleotideTemplatesXML(Map<String, Map<String, String>>) - Static method in class org.helm.notation2.tools.NucleotideParser
getPeptideNaturalAnalogSequenceFromNotation(HELM2Notation) - Static method in class org.helm.notation2.tools.SequenceConverter: method to generate for all peptide polymers the natural analogue sequence
getPeptidePolymers(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to get all peptide polymers given a list of PolymerNotation objects
getPeptideSequenceFromNotation(HELM2Notation) - Static method in class org.helm.notation2.tools.SequenceConverter: method to get for all peptides the sequence
getPeptideUnit() - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
getPhosphateMonomer() - Method in class org.helm.notation2.Nucleotide: return the phosphate monomer of this nucleotide
getPhosphateMonomer(MonomerStore) - Method in class org.helm.notation2.Nucleotide: return the phosphate monomer of this nucleotide
getPolymerType() - Method in class org.helm.notation2.Monomer
getPolymerType() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Returns the polymer type.
getPolymerTypes() - Method in class org.helm.notation2.MonomerFactory
getPolymerTypeSet() - Method in class org.helm.notation2.MonomerStore: Returns the polymer type set
getPositionType() - Method in class org.helm.notation2.Nucleotide
getResource(String) - Static method in class org.helm.notation2.wsadapter.WSAdapterUtils: Call a GET routine on given resource URL.
getReverseComplement(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to get the polymer with the reverse complement sequence of the current polymer
getReverseNucleotideTemplateMap() - Method in class org.helm.notation2.NucleotideFactory
getReverseSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to generate the reverse rna/dna sequence of a given polymer
getRgroupMap() - Method in class org.helm.notation2.RgroupStructure
getRNAPolymers(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to get all rna polymers given a List of PolymerNotation objects
getRnaUnit() - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
getSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.PeptideUtils: method to produce for a peptide PolymerNotation the sequence
getSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to get the rna sequence of the given PolymerNotation
getShape() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Returns the shape.
getSirnaNotation(String, String, String) - Static method in class org.helm.notation2.tools.SiRNANotation: this method converts nucleotide sequences into HELM notation based on design pattern
getSiRNANotation(String, String) - Static method in class org.helm.notation2.tools.SiRNANotation: this method converts nucleotide sequences into HELM2Notation
getSMILESForAll(HELM2Notation) - Static method in class org.helm.notation2.tools.SMILES: method to generate smiles for the whole HELMNotation
getSMILESforPolymer(PolymerNotation) - Static method in class org.helm.notation2.tools.SMILES: method to generate smiles for one single PolymerNotation
getSmilesMonomerDB() - Method in class org.helm.notation2.MonomerCache
getSmilesMonomerDB() - Method in class org.helm.notation2.MonomerFactory
getSmilesMonomerDB() - Method in class org.helm.notation2.MonomerStore: returns SmilesMonomerDB
getSmilesMonomerDB(boolean) - Method in class org.helm.notation2.MonomerFactory
getStandard(HELM2Notation) - Static method in class org.helm.notation2.tools.HELM1Utils: method to reproduce a standard HELM in HELM1 - Format
getSugarMonomer() - Method in class org.helm.notation2.Nucleotide: get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugar
getSugarMonomer(MonomerStore) - Method in class org.helm.notation2.Nucleotide: get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugar
getSymbol() - Method in class org.helm.notation2.Nucleotide
getTotalMonomerCount(HELM2Notation) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to get the total number of MonomerNotationUnits in a HELMNotation object
getTotalMonomerCount(PolymerNotation) - Static method in class org.helm.notation2.tools.PolymerUtils: method to get the total monomer count of one PolymerNotation
getTrimmedNucleotideSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to get the trimmed nucleotide sequence
getUniqueExtendedSMILES(String) - Static method in class org.helm.notation2.tools.SMILES
getUnit(int) - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
getWebserviceEditorCategorizationFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns URL and Path to monomer categorization resource combined.
getWebserviceEditorCategorizationPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns path to monomer categorization resource.
getWebserviceEditorCategorizationURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns URL without path to monomer categorization resource.
getWebserviceMonomersFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns URL and Path to monomer resource combined.
getWebserviceMonomersPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns path to monomer resource.
getWebserviceMonomersPutFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns URL and Path to monomer PUT resource combined.
getWebserviceMonomersURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns URL without path to monomer resource.
getWebserviceNucleotidesFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns URL and Path to nucleotide resource combined.
getWebserviceNucleotidesPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns path to nucleotide resource.
getWebserviceNucleotidesPutFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns URL and Path to nucleotide PUT resource combined.
getWebserviceNucleotidesURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns URL without path to nucleotide resource.
getXHELM(HELM2Notation) - Static method in class org.helm.notation2.tools.xHelmNotationExporter: method to get xhelm for the helm notation, only if it was possible to convert the helm in the old format
getXHELM2(HELM2Notation) - Static method in class org.helm.notation2.tools.xHelmNotationExporter: method to get xhelm for the helm2 notation with the new functionality
GroupingNotationException - Exception in org.helm.notation2.exception: GroupingNotationException
GroupingNotationException(String) - Constructor for exception org.helm.notation2.exception.GroupingNotationException

H

hasDBChanged() - Static method in class org.helm.notation2.MonomerFactory: Returns whether one of the stored databases has changed, for example by adding or removing monomers.
hasKey(String) - Method in class org.helm.notation2.InterConnections
hasMonomer(String, String) - Method in class org.helm.notation2.MonomerStore: Checks if a specific monomer exists in the store
hasNextGroup() - Method in class org.helm.notation2.SimpleNotationGroupIterator: Checks if there is a next group
hasNucleotideModification(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to check if any of the rna polymers have a modified nucleotide
hasNucleotideModification(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to check if the given PolymerNotation has a nucleotide Modification
HELM_NOTATION_ELEMENT - Static variable in class org.helm.notation2.tools.xHelmNotationExporter
HELM1FormatException - Exception in org.helm.notation2.exception: HELM1FormatException
HELM1FormatException(String) - Constructor for exception org.helm.notation2.exception.HELM1FormatException
HELM1Utils - Class in org.helm.notation2.tools: HELM1 class to transform a HELM2 into HELM1; this is only possible in the case of no HELM2 features
HELM2HandledException - Exception in org.helm.notation2.exception: HELM2HandledException
HELM2HandledException(String) - Constructor for exception org.helm.notation2.exception.HELM2HandledException
HELM2NotationUtils - Class in org.helm.notation2.tools: HELM2NotationUtils
hybridize(HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: 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
hybridize(PolymerNotation, PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to hybridize two given PolymerNotations together
hybridizeAntiparallel(PolymerNotation, PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to hybridize two PolymerNotations together if they are antiparallel

I

ID_A - Static variable in class org.helm.notation2.Monomer
ID_ALA - Static variable in class org.helm.notation2.Monomer
ID_ARG - Static variable in class org.helm.notation2.Monomer
ID_ASN - Static variable in class org.helm.notation2.Monomer
ID_ASP - Static variable in class org.helm.notation2.Monomer
ID_C - Static variable in class org.helm.notation2.Monomer
ID_CHEMICAL_STRUCTURE - Static variable in class org.helm.notation2.Monomer
ID_CYS - Static variable in class org.helm.notation2.Monomer
ID_dR - Static variable in class org.helm.notation2.Monomer
ID_G - Static variable in class org.helm.notation2.Monomer
ID_GLN - Static variable in class org.helm.notation2.Monomer
ID_GLU - Static variable in class org.helm.notation2.Monomer
ID_GLY - Static variable in class org.helm.notation2.Monomer
ID_HIS - Static variable in class org.helm.notation2.Monomer
ID_ILE - Static variable in class org.helm.notation2.Monomer
ID_LEU - Static variable in class org.helm.notation2.Monomer
ID_LYS - Static variable in class org.helm.notation2.Monomer
ID_MET - Static variable in class org.helm.notation2.Monomer
ID_P - Static variable in class org.helm.notation2.Monomer
ID_PHE - Static variable in class org.helm.notation2.Monomer
ID_PRO - Static variable in class org.helm.notation2.Monomer
ID_R - Static variable in class org.helm.notation2.Monomer
ID_SER - Static variable in class org.helm.notation2.Monomer
ID_T - Static variable in class org.helm.notation2.Monomer
ID_THR - Static variable in class org.helm.notation2.Monomer
ID_TRP - Static variable in class org.helm.notation2.Monomer
ID_TYR - Static variable in class org.helm.notation2.Monomer
ID_U - Static variable in class org.helm.notation2.Monomer
ID_VAL - Static variable in class org.helm.notation2.Monomer
ID_X - Static variable in class org.helm.notation2.Monomer
ImageGenerationException - Exception in org.helm.notation2.exception: ImageGenerationException
ImageGenerationException(String) - Constructor for exception org.helm.notation2.exception.ImageGenerationException
Images - Class in org.helm.notation2.tools: Image class to generate image generation of monomers and of the helm molecule
initializeNucleotideTemplatesFromWebService() - Static method in class org.helm.notation2.NucleotideFactory
InterConnections - Class in org.helm.notation2: InterConnections, class to save the interconnections of a HELM
InterConnections() - Constructor for class org.helm.notation2.InterConnections
InterConnections(Map<String, String>) - Constructor for class org.helm.notation2.InterConnections
isAdHocMonomer() - Method in class org.helm.notation2.Monomer
isConnected(String) - Static method in class org.helm.notation2.tools.SMILES: returns if structure is connected
isModified() - Method in class org.helm.notation2.Monomer: Test if this monomer has been modified.
isModified() - Method in class org.helm.notation2.Nucleotide
isMonomerStoreEmpty() - Method in class org.helm.notation2.MonomerStore: Checks for the empty store
isNewMonomer() - Method in class org.helm.notation2.Monomer
isNormalDirection(String) - Static method in class org.helm.notation2.tools.FastaFormat: method to check if the sequence is in normal direction 5' to 3'
isSameType(Monomer) - Method in class org.helm.notation2.Monomer: Compare this momoner with another one, polymerType, monomerType and naturalAnalog (could be derived) must be the same to return true
isUpdateAutomatic() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns whether all webservices should be fetched at all times, or be refreshed manually.
isUseExternalAttachments() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
isUseExternalMonomers() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
isUseExternalNucleotides() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
isUseWebservice() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Returns whether webservice should be used or not.

L

linearize(List<List<String[]>>) - Static method in class org.helm.notation2.tools.PermutationAndExpansion
loadAttachments(InputStream) - Static method in class org.helm.notation2.AttachmentLoader: reads the attachments from the given inputstream and returns the attachment db
loadMonomerCategorization() - Static method in class org.helm.notation2.wsadapter.MonomerWSLoader: Loads the monomer categories using the URL configured in MonomerStoreConfiguration.
loadMonomerStore(Map<String, Attachment>) - Method in class org.helm.notation2.wsadapter.MonomerWSLoader: Loads the monomer store using the URL configured in MonomerStoreConfiguration and the polymerType that was given to constructor.
loadNucleotideStore() - Method in class org.helm.notation2.wsadapter.NucleotideWSLoader: Loads the nucleotide store using the URL configured in MonomerStoreConfiguration.
LOCAL_NUCLEOTIDE_TEMPLATE_FILE_NAME - Static variable in class org.helm.notation2.NucleotideFactory
LOCAL_NUCLEOTIDE_TEMPLATE_FILE_PATH - Static variable in class org.helm.notation2.NucleotideFactory

M

MDLUtils - Class in org.helm.notation2.tools: MDLUtils, class to generate MDL for a HELM molecule.
merge(MonomerCache) - Method in class org.helm.notation2.MonomerFactory: merge remote monomerCache with local monomerCache, will throw exception if conflicts found.
mergeRgroups(AbstractMolecule) - Static method in class org.helm.notation2.tools.BuilderMolecule: method to merge all unused rgroups into a molecule
MethodsMonomerUtils - Class in org.helm.notation2.tools: MethodsMonomerUtils
MIDDLE_POSITION_TYPE - Static variable in class org.helm.notation2.Nucleotide
MINUMUM_MATCH_FRAGMENT_LENGTH - Static variable in class org.helm.notation2.tools.NucleotideParser
MINUMUM_MATCH_FRAGMENT_LENGTH - Static variable in class org.helm.notation2.tools.RNAUtils
MODIFICATION_END_SYMBOL - Static variable in class org.helm.notation2.tools.NucleotideParser
MODIFICATION_START_SYMBOL - Static variable in class org.helm.notation2.tools.NucleotideParser
MoleculeProperty - Class in org.helm.notation2: MoleculeInfo
MoleculeProperty() - Constructor for class org.helm.notation2.MoleculeProperty
MoleculePropertyCalculator - Class in org.helm.notation2.calculation: MoleculeInformation, class to
MolfileEncoder - Class in org.helm.notation2.tools
MolfileEncoder() - Constructor for class org.helm.notation2.tools.MolfileEncoder
Monomer - Class in org.helm.notation2: This is a data model for Monomer. alternateId is used in polymer notation.
Monomer() - Constructor for class org.helm.notation2.Monomer: constructor
Monomer(String, String, String, String) - Constructor for class org.helm.notation2.Monomer: Create a new monomer.
MONOMER_CACHE_FILE_NAME - Static variable in class org.helm.notation2.MonomerFactory
MONOMER_CACHE_FILE_PATH - Static variable in class org.helm.notation2.MonomerFactory
MONOMER_COUNT_THRESHOLD - Static variable in interface org.helm.notation2.NotationConstant
MONOMER_DB_FILE_NAME - Static variable in class org.helm.notation2.MonomerFactory
MONOMER_DB_FILE_PATH - Static variable in class org.helm.notation2.MonomerFactory
MONOMER_DB_SCHEMA_RESOURCE - Static variable in class org.helm.notation2.MonomerFactory
MONOMER_DB_XML_RESOURCE - Static variable in class org.helm.notation2.MonomerFactory
MONOMER_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
MONOMER_ELEMENT - Static variable in class org.helm.notation2.tools.xHelmNotationExporter
MONOMER_GROUP_COUNT_INTERVAL - Static variable in interface org.helm.notation2.NotationConstant
MONOMER_ID_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
MONOMER_LIST_ELEMENT - Static variable in class org.helm.notation2.tools.xHelmNotationExporter
MONOMER_MOL_FILE_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
MONOMER_NAME_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
MONOMER_SMILES_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
MONOMER_TYPE_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
MonomerCache - Class in org.helm.notation2
MonomerCache() - Constructor for class org.helm.notation2.MonomerCache
MonomerException - Exception in org.helm.notation2.exception: This is the exception thrown for Invalid Monomers
MonomerException() - Constructor for exception org.helm.notation2.exception.MonomerException: Creates a new instance of MonomerException without detail message.
MonomerException(String) - Constructor for exception org.helm.notation2.exception.MonomerException: Constructs an instance of MonomerException with the specified detail message.
MonomerException(String, Throwable) - Constructor for exception org.helm.notation2.exception.MonomerException
MonomerFactory - Class in org.helm.notation2: This is a factory class to build monomer database from MonomerDBGZEnconded.xml document
MonomerLoadingException - Exception in org.helm.notation2.exception: This is the exception thrown for errors while loading monomers from source to store.
MonomerLoadingException() - Constructor for exception org.helm.notation2.exception.MonomerLoadingException: Creates a new instance of MonomerLoadingException without detail message.
MonomerLoadingException(String) - Constructor for exception org.helm.notation2.exception.MonomerLoadingException: Constructs an instance of MonomerLoadingException with the specified detail message.
MonomerLoadingException(String, Throwable) - Constructor for exception org.helm.notation2.exception.MonomerLoadingException
MonomerParser - Class in org.helm.notation2.tools: MonomerParser
MonomerParser() - Constructor for class org.helm.notation2.tools.MonomerParser
monomerStore - Variable in class org.helm.notation2.MonomerFactory
MonomerStore - Class in org.helm.notation2: This class represents a store for monomers.
MonomerStore() - Constructor for class org.helm.notation2.MonomerStore: Constructs empty MonomerStore
MonomerStore(Map<String, Map<String, Monomer>>, Map<String, Monomer>) - Constructor for class org.helm.notation2.MonomerStore: Constructor with Monomer- and SmilesDB
MonomerStoreConfiguration - Class in org.helm.notation2.wsadapter: Singleton MonomerStoreConfiguration stores the webservice configuration, e.g.
MonomerWSLoader - Class in org.helm.notation2.wsadapter: MonomerWSLoader loads monomers from the webservice configured in MonomerStoreConfiguration.
MonomerWSLoader(String) - Constructor for class org.helm.notation2.wsadapter.MonomerWSLoader: Constructor using polymerType as parameter.
MonomerWSSaver - Class in org.helm.notation2.wsadapter: MonomerWSSaver saves monomers to the webservice configured in MonomerStoreConfiguration.
MonomerWSSaver() - Constructor for class org.helm.notation2.wsadapter.MonomerWSSaver

N

NATURAL_ANALOG_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
nextGroup() - Method in class org.helm.notation2.SimpleNotationGroupIterator: Returns the next group
NOTATION_DIRECTORY - Static variable in class org.helm.notation2.MonomerFactory
NOTATION_DIRECTORY - Static variable in interface org.helm.notation2.NotationConstant
NOTATION_DIRECTORY - Static variable in class org.helm.notation2.NucleotideFactory
NOTATION_SOURCE - Static variable in interface org.helm.notation2.NotationConstant
NotationConstant - Interface in org.helm.notation2
NotationException - Exception in org.helm.notation2.exception: This is the exception thrown for Invalid Notations
NotationException() - Constructor for exception org.helm.notation2.exception.NotationException: Creates a new instance of NotationException without detail message.
NotationException(String) - Constructor for exception org.helm.notation2.exception.NotationException: Constructs an instance of NotationException with the specified detail message.
NotationException(String, Throwable) - Constructor for exception org.helm.notation2.exception.NotationException
notationString - Variable in class org.helm.notation2.SimpleNotationGroupIterator
Nucleotide - Class in org.helm.notation2: This is a data model class for nucleotide
Nucleotide() - Constructor for class org.helm.notation2.Nucleotide
Nucleotide(String, int) - Constructor for class org.helm.notation2.Nucleotide
Nucleotide(String, String) - Constructor for class org.helm.notation2.Nucleotide
Nucleotide(String, String, int) - Constructor for class org.helm.notation2.Nucleotide
NUCLEOTIDE_TEMPLATE_SCHEMA_RESOURCE - Static variable in class org.helm.notation2.NucleotideFactory
NUCLEOTIDE_TEMPLATE_XML_RESOURCE - Static variable in class org.helm.notation2.NucleotideFactory
NucleotideFactory - Class in org.helm.notation2: This is a factory class to build nucleotide templates
NucleotideLoadingException - Exception in org.helm.notation2.exception: This is the exception thrown for errors while loading nucleotides from source to store.
NucleotideLoadingException() - Constructor for exception org.helm.notation2.exception.NucleotideLoadingException: Creates a new instance of NucleotideLoadingException without detail message.
NucleotideLoadingException(String) - Constructor for exception org.helm.notation2.exception.NucleotideLoadingException: Constructs an instance of NucleotideLoadingException with the specified detail message.
NucleotideLoadingException(String, Throwable) - Constructor for exception org.helm.notation2.exception.NucleotideLoadingException
NucleotideParser - Class in org.helm.notation2.tools: NucleotideParser
NucleotideParser() - Constructor for class org.helm.notation2.tools.NucleotideParser
NucleotideWSLoader - Class in org.helm.notation2.wsadapter: NucleotideWSLoader loads nucleotides from the webservice configured in MonomerStoreConfiguration.
NucleotideWSLoader() - Constructor for class org.helm.notation2.wsadapter.NucleotideWSLoader: Default constructor.
NucleotideWSSaver - Class in org.helm.notation2.wsadapter: NucleotideWSSaver saves nucleotides to the webservice configured in MonomerStoreConfiguration.
NucleotideWSSaver() - Constructor for class org.helm.notation2.wsadapter.NucleotideWSSaver
NUCLIEC_ACID_POLYMER_TYPE - Static variable in class org.helm.notation2.Monomer

O

org.helm.notation2 - package org.helm.notation2
org.helm.notation2.calculation - package org.helm.notation2.calculation
org.helm.notation2.exception - package org.helm.notation2.exception
org.helm.notation2.tools - package org.helm.notation2.tools
org.helm.notation2.wsadapter - package org.helm.notation2.wsadapter

P

PAIR_ATTACHMENT - Static variable in class org.helm.notation2.Attachment
ParserException - Exception in org.helm.notation2.exception: ParserException
ParserException(String) - Constructor for exception org.helm.notation2.exception.ParserException
PEPTIDE_POLYMER_TYPE - Static variable in class org.helm.notation2.Monomer
PEPTIDE_UNIT_TYPE - Static variable in class org.helm.notation2.calculation.ExtinctionCoefficient
PeptideUtils - Class in org.helm.notation2.tools: PeptideUtils, class to provide peptide utils
PeptideUtilsException - Exception in org.helm.notation2.exception: PeptideUtilsException
PeptideUtilsException(String) - Constructor for exception org.helm.notation2.exception.PeptideUtilsException
permutate(List<String[]>, String[], int) - Static method in class org.helm.notation2.tools.PermutationAndExpansion
permutate(List<String[]>, List<String>) - Static method in class org.helm.notation2.tools.PermutationAndExpansion
PermutationAndExpansion - Class in org.helm.notation2.tools
PermutationAndExpansion() - Constructor for class org.helm.notation2.tools.PermutationAndExpansion
POLYMER_ELEMENT - Static variable in class org.helm.notation2.MonomerFactory
POLYMER_LIST_ELEMENT - Static variable in class org.helm.notation2.MonomerFactory
POLYMER_TYPE_ATTRIBUTE - Static variable in class org.helm.notation2.MonomerFactory
POLYMER_TYPE_ELEMENT - Static variable in class org.helm.notation2.tools.MonomerParser
PolymerIDsException - Exception in org.helm.notation2.exception: PolymerIDsException
PolymerIDsException(String) - Constructor for exception org.helm.notation2.exception.PolymerIDsException
PolymerUtils - Class in org.helm.notation2.tools: PolymerUtils, class to provide methods for polymer
PolymerUtils() - Constructor for class org.helm.notation2.tools.PolymerUtils
position - Variable in class org.helm.notation2.SimpleNotationGroupIterator
produceMonomerNotationUnitWithOtherID(MonomerNotation, String) - Static method in class org.helm.notation2.tools.ChangeObjects: method to replace the MonomerNotationUnit having the MonomerID with the new MonomerID
putResource(String, String) - Static method in class org.helm.notation2.wsadapter.WSAdapterUtils: Calls a PUT routine with given JSON on given resource URL.

R

readNotation(String) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
readPeptide(String) - Static method in class org.helm.notation2.tools.SequenceConverter: method to read a peptide sequence and generate a HELM2Notation object of it
readPeptide(String) - Method in class org.helm.notation2.tools.WebService: method to read a single peptide sequence and generates HELM
readRNA(String) - Static method in class org.helm.notation2.tools.SequenceConverter: method to read a rna/dna sequence and generate a HELM2Notation object of it
readRNA(String) - Method in class org.helm.notation2.tools.WebService: method to read a single rna sequence and generates HELM
refresh() - Method in class org.helm.notation2.Chemistry
refresh() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Refreshes the configuration using the local properties file.
refreshMonomerCache() - Static method in class org.helm.notation2.MonomerFactory
refreshMonomerCache() - Method in class org.helm.notation2.tools.WebService: method to refresh the monomer cache of the MonomerFactory
removeAnnotationOfPolmyer(PolymerNotation) - Static method in class org.helm.notation2.tools.ChangeObjects: method to remove a current annotation of a PolymerNotation
removeLastP(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils: method to remove the phosphate of the last nucleotide
replaceMonomer(HELM2Notation, String, String, String) - Static method in class org.helm.notation2.tools.ChangeObjects: method to replace the MonomerID with the new MonomerID for a given polymer type
replaceMonomerNotation(MonomerNotation, String, String) - Static method in class org.helm.notation2.tools.ChangeObjects: method to replace the MonomerNotation having the MonomerID with the new MonomerID
replaceMonomerNotationGroup(MonomerNotationGroup, String, String) - Static method in class org.helm.notation2.tools.ChangeObjects: method to replace the MonomerNotationGroup having the MonomerID with the new MonomerID
replaceMonomerNotationList(MonomerNotationList, String, String) - Static method in class org.helm.notation2.tools.ChangeObjects: method to replace the MonomerNotationList having the MonomerID with the new MonomerID
replaceSMILESWithTemporaryIds(HELM2Notation) - Static method in class org.helm.notation2.tools.ChangeObjects: This function replaces smiles in complex notation with temporary ids
resetDBChanged() - Static method in class org.helm.notation2.MonomerFactory
RgroupStructure - Class in org.helm.notation2: RgroupStructure
RgroupStructure() - Constructor for class org.helm.notation2.RgroupStructure
RNA_DESIGN_DICER_27_L - Static variable in class org.helm.notation2.tools.NucleotideParser
RNA_DESIGN_DICER_27_R - Static variable in class org.helm.notation2.tools.NucleotideParser
RNA_DESIGN_NONE - Static variable in class org.helm.notation2.tools.NucleotideParser
RNA_DESIGN_TUSCHL_19_PLUS_2 - Static variable in class org.helm.notation2.tools.NucleotideParser
RNA_UNIT_TYPE - Static variable in class org.helm.notation2.calculation.ExtinctionCoefficient
RNAUtils - Class in org.helm.notation2.tools: RNAUtils, class to provide methods for rna polymer
RNAUtilsException - Exception in org.helm.notation2.exception: RNAUtilsException
RNAUtilsException(String) - Constructor for exception org.helm.notation2.exception.RNAUtilsException

S

saveMonomerCache() - Method in class org.helm.notation2.MonomerFactory: save monomerCache to disk file
saveMonomerToStore(Monomer) - Method in class org.helm.notation2.wsadapter.MonomerWSSaver: Adds or updates a single monomer to the monomer store using the URL configured in MonomerStoreConfiguration .
saveNucleotideTemplates() - Method in class org.helm.notation2.NucleotideFactory: save Nucleotide Templates to disk file
saveNucleotideToStore(Nucleotide) - Method in class org.helm.notation2.wsadapter.NucleotideWSSaver: Adds or updates a single nucleotide to the nucleotide store using the URL configured in MonomerStoreConfiguration.
SEQUENCE_DELIMETERS - Static variable in class org.helm.notation2.tools.AminoAcidParser
SequenceConverter - Class in org.helm.notation2.tools: SequenceConverter class to convert sequence into the HELM2Notation object and vice versa
setAdHocMonomer(boolean) - Method in class org.helm.notation2.Monomer
setAlternateId(String) - Method in class org.helm.notation2.Attachment
setAlternateId(String) - Method in class org.helm.notation2.Monomer
setAttachmentDB(Map<String, Attachment>) - Method in class org.helm.notation2.MonomerCache
setAttachmentList(List<Attachment>) - Method in class org.helm.notation2.Monomer
setBackgroundColor(String) - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Sets the background color.
setCanSMILES(String) - Method in class org.helm.notation2.Monomer
setCapGroupName(String) - Method in class org.helm.notation2.Attachment
setCapGroupSMILES(String) - Method in class org.helm.notation2.Attachment
setCategory(String) - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Sets the category.
setCountToDefault(PolymerNotation, int) - Static method in class org.helm.notation2.tools.ChangeObjects: method to set the count of a MonomerNotation to default (=1)
setDBChanged(boolean) - Static method in class org.helm.notation2.MonomerFactory
setExactMass(double) - Method in class org.helm.notation2.MoleculeProperty
setExternalAttachmentsPath(String) - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
setExtinctionCoefficient(float) - Method in class org.helm.notation2.MoleculeProperty
setFontColor(String) - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Sets the font color.
setId(int) - Method in class org.helm.notation2.Attachment
setId(int) - Method in class org.helm.notation2.Monomer
setLabel(String) - Method in class org.helm.notation2.Attachment
setModified(boolean) - Method in class org.helm.notation2.Nucleotide: Deprecated.
setMolecularFormula(String) - Method in class org.helm.notation2.MoleculeProperty
setMolecularWeight(double) - Method in class org.helm.notation2.MoleculeProperty
setMolecule(AbstractMolecule) - Method in class org.helm.notation2.RgroupStructure
setMolfile(String) - Method in class org.helm.notation2.Monomer
setMonomerCache(MonomerCache) - Method in class org.helm.notation2.MonomerFactory: replace local cache with remote one completely, may cause loss of data
setMonomerDB(Map<String, Map<String, Monomer>>) - Method in class org.helm.notation2.MonomerCache
setMonomerID(String) - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Sets the monomer ID.
setMonomerName(String) - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Sets the monomer name.
setMonomerType(String) - Method in class org.helm.notation2.Monomer
setMonomerType(String) - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Sets the monomer type.
setName(String) - Method in class org.helm.notation2.Monomer
setNaturalAnalog(String) - Method in class org.helm.notation2.Monomer
setNaturalAnalog(String) - Method in class org.helm.notation2.Nucleotide: Deprecated.
setNaturalAnalogon(String) - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Sets the natural analogon.
setNewMonomer(boolean) - Method in class org.helm.notation2.Monomer
setNotation(String) - Method in class org.helm.notation2.Nucleotide
setNucleotideTemplates(Map<String, Map<String, String>>) - Method in class org.helm.notation2.NucleotideFactory
setPolymerType(String) - Method in class org.helm.notation2.Monomer
setPolymerType(String) - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Sets the polymerType.
setPositionType(int) - Method in class org.helm.notation2.Nucleotide
setRgroupMap(Map<String, IAtomBase>) - Method in class org.helm.notation2.RgroupStructure
setShape(String) - Method in class org.helm.notation2.wsadapter.CategorizedMonomer: Sets the shape.
setSmilesMonomerDB(Map<String, Monomer>) - Method in class org.helm.notation2.MonomerCache
setSymbol(String) - Method in class org.helm.notation2.Nucleotide
setupBuilder() - Static method in class org.helm.notation2.MonomerFactory
setUpdateAutomatic(boolean) - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration: Sets whether all webservices should be fetched at all times, or be refreshed manually.
setUseExternalAttachments(boolean) - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
SimpleNotationGroupIterator - Class in org.helm.notation2: Iterator class for groups within a simple notation string
SimpleNotationGroupIterator(String) - Constructor for class org.helm.notation2.SimpleNotationGroupIterator: Constructs a group iterator for a notation string
SiRNANotation - Class in org.helm.notation2.tools: SiRNANotation, class to generate SirnaNotation
SiRNANotation() - Constructor for class org.helm.notation2.tools.SiRNANotation
SMILES - Class in org.helm.notation2.tools: SMILES class to generate SMILES
SMILES() - Constructor for class org.helm.notation2.tools.SMILES
SMILES_EXTENSION_SEPARATOR_REGEX - Static variable in class org.helm.notation2.tools.MonomerParser
STARTING_MONOMER_ATTACHEMENT - Static variable in class org.helm.notation2.Attachment
STARTING_NAME - Static variable in class org.helm.notation2.Monomer
STARTING_POSITION_TYPE - Static variable in class org.helm.notation2.Nucleotide
SUPPORTED_DESIGN_LIST - Static variable in class org.helm.notation2.tools.NucleotideParser
SUPPORTED_POLYMER_TYPES - Static variable in class org.helm.notation2.Monomer

T

toJSON() - Method in class org.helm.notation2.Monomer
toJSON() - Method in class org.helm.notation2.Nucleotide
toJSON(HELM2Notation) - Static method in class org.helm.notation2.tools.HELM2NotationUtils: method to generate a JSON-Object from the given HELM2Notation
toString() - Method in class org.helm.notation2.Attachment
toString() - Method in class org.helm.notation2.MonomerStore
toString() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration

U

UNDEFINED_MOMONER_TYPE - Static variable in class org.helm.notation2.Monomer
unmodifiedWithoutPhosphate() - Method in class org.helm.notation2.Nucleotide: Returns true if the nucleotide is unmodified except for a missing phosphate group.

V

validateAttachement(Attachment) - Static method in class org.helm.notation2.tools.MonomerParser: 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
validateAttachment(Attachment) - Static method in class org.helm.notation2.AttachmentLoader: validates the current attachment
validateAttachmentLabel(String) - Static method in class org.helm.notation2.tools.MonomerParser: This method checks if attachment label is in the format of R#, where # is a number
validateConnections(HELM2Notation) - Static method in class org.helm.notation2.tools.Validation: method to valid all existent connections in the Notation objects
validateGrouping(HELM2Notation) - Static method in class org.helm.notation2.tools.Validation: method to validate every GroupNotation of the Notation objects
validateHELM(String) - Method in class org.helm.notation2.tools.WebService: method to validate the input HELM-String
validateMonomer(Monomer) - Static method in class org.helm.notation2.tools.MonomerParser: 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
validateMonomers(List<MonomerNotation>) - Static method in class org.helm.notation2.tools.Validation: method to validate a list of MonomerNotation objects
validateNotationObjects(HELM2Notation) - Static method in class org.helm.notation2.tools.Validation: 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
validateSimpleNotationForRNA(String) - Static method in class org.helm.notation2.tools.NucleotideParser: validate RNA simple notation
validateSyntaxHELM(String) - Method in class org.helm.notation2.tools.WebService
validateUniquePolymerIDs(HELM2Notation) - Static method in class org.helm.notation2.tools.Validation: method to check if all existent polymer ids are unique
Validation - Class in org.helm.notation2.tools: Validation class to validate the whole HELM string
ValidationException - Exception in org.helm.notation2.exception: ValidationException
ValidationException(String) - Constructor for exception org.helm.notation2.exception.ValidationException

W

WebService - Class in org.helm.notation2.tools: WebService class containing all required methods for the web-service
WebService() - Constructor for class org.helm.notation2.tools.WebService
WSAdapterUtils - Class in org.helm.notation2.wsadapter: WSAdapterUtils is used to generalize webservice calls.

X

XHELM_ELEMENT - Static variable in class org.helm.notation2.tools.xHelmNotationExporter
xHelmNotationExporter - Class in org.helm.notation2.tools: xHELMNotationExporter
xHelmNotationParser - Class in org.helm.notation2.tools: Class to parse the XHELM XML format
xHelmNotationParser() - Constructor for class org.helm.notation2.tools.xHelmNotationParser
XML_SCHEMA_VALIDATION_FEATURE - Static variable in class org.helm.notation2.MonomerFactory
XML_SCHEMA_VALIDATION_FEATURE - Static variable in class org.helm.notation2.NucleotideFactory

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