Uses of Class
org.helm.notation2.Monomer
| Package | Description |
|---|---|
| org.helm.notation2 | |
| org.helm.notation2.tools | |
| org.helm.notation2.wsadapter |
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Uses of Monomer in org.helm.notation2
Methods in org.helm.notation2 that return Monomer Modifier and Type Method Description static MonomerDeepCopy. copy(Monomer monomer)static MonomerMonomer. fromJSON(String json)MonomerNucleotide. getBaseMonomer()get the base monomer, the return value could be null if this nucleotide does not have a baseMonomerNucleotide. getBaseMonomer(MonomerStore monomerStore)get the base monomer, the return value could be null if this nucleotide does not have a baseMonomerMonomerStore. getMonomer(String smiles)Returns the monomer by smiles stringMonomerMonomerStore. getMonomer(String polymerType, String alternateId)Returns the monomer specified by polymerType and alternatIdMonomerNucleotide. getPhosphateMonomer()return the phosphate monomer of this nucleotideMonomerNucleotide. getPhosphateMonomer(MonomerStore monomerStore)return the phosphate monomer of this nucleotideMonomerNucleotide. getSugarMonomer()get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugarMonomerNucleotide. getSugarMonomer(MonomerStore monomerStore)get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugarMethods in org.helm.notation2 that return types with arguments of type Monomer Modifier and Type Method Description List<Monomer>MonomerStore. getAllMonomersList()This method returns all monomers of the store as list sorted by polymer typeMap<Monomer,Monomer>MonomerFactory. getConflictedMonomerMap(MonomerCache remoteMonomerCache)Map<Monomer,Monomer>MonomerFactory. getConflictedMonomerMap(MonomerCache remoteMonomerCache)Map<String,Map<String,Monomer>>MonomerCache. getMonomerDB()Map<String,Map<String,Monomer>>MonomerFactory. getMonomerDB()retruns the monomer databaseMap<String,Map<String,Monomer>>MonomerFactory. getMonomerDB(boolean includeNewMonomers)returns the monomer database including monomers that where temporary marked as new, else without those monomersMap<String,Map<String,Monomer>>MonomerStore. getMonomerDB()returns MonomerDBMap<String,Monomer>MonomerStore. getMonomers(String polymerType)Returns all monomers by polymerTypeMap<String,Monomer>MonomerCache. getSmilesMonomerDB()Map<String,Monomer>MonomerFactory. getSmilesMonomerDB()Map<String,Monomer>MonomerFactory. getSmilesMonomerDB(boolean includeNewMonomers)Map<String,Monomer>MonomerStore. getSmilesMonomerDB()returns SmilesMonomerDBMethods in org.helm.notation2 with parameters of type Monomer Modifier and Type Method Description voidMonomerStore. addMonomer(Monomer monomer)Adds a monomer to the storevoidMonomerStore. addMonomer(Monomer monomer, boolean dbChanged)Adds a monomer to the store and optionally sets the dbChanged flagvoidMonomerFactory. addNewMonomer(Monomer monomer)To add new monomer into monomerCachevoidMonomerStore. addNewMonomer(Monomer monomer)Adds a monomer to the store and makes it a temporary new monomerbooleanMonomer. attachmentContains(Monomer monomer)booleanMonomer. attachmentEquals(Monomer monomer)static MonomerDeepCopy. copy(Monomer monomer)booleanMonomer. isSameType(Monomer m)Compare this momoner with another one, polymerType, monomerType and naturalAnalog (could be derived) must be the same to return trueMethod parameters in org.helm.notation2 with type arguments of type Monomer Modifier and Type Method Description voidMonomerCache. setMonomerDB(Map<String,Map<String,Monomer>> monomerDB)voidMonomerCache. setSmilesMonomerDB(Map<String,Monomer> smilesMonomerDB) -
Uses of Monomer in org.helm.notation2.tools
Methods in org.helm.notation2.tools that return Monomer Modifier and Type Method Description static MonomerConverter. convertMonomer(Monomer m)static MonomerMethodsMonomerUtils. generateTemporaryMonomer(String id, String polymerType, String naturalAnalog)static MonomerMethodsMonomerUtils. getMonomer(String type, String id, String info)method to get the monomer from the database!static MonomerMonomerParser. getMonomer(String monomerXMLString)static MonomerMonomerParser. getMonomer(org.jdom2.Element monomer)Convert monomer element to Monomer objectMethods in org.helm.notation2.tools that return types with arguments of type Monomer Modifier and Type Method Description static List<Monomer>Validation. getAllMonomers(org.helm.notation2.parser.notation.polymer.MonomerNotation not, int position)method to get for one MonomerNotation all valid contained monomersstatic List<Monomer>Validation. getAllMonomersOnlyBase(org.helm.notation2.parser.notation.polymer.MonomerNotation not)method to get for one MonomerNotation all valid contained monomers.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 performedstatic 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 performedstatic List<Monomer>MethodsMonomerUtils. getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations)method to get all monomers for all MonomerNotationsstatic List<Monomer>MonomerParser. getMonomerList(String monomerXMLString)Methods in org.helm.notation2.tools with parameters of type Monomer Modifier and Type Method Description static MonomerConverter. convertMonomer(Monomer m)byte[]WebService. generateImageForMonomer(Monomer monomer, boolean showRgroups)method to generate an image for a monomerstatic byte[]Images. generateImageofMonomer(Monomer monomer, boolean rgroupsInformation)generates an image of the atom/bond representation of monomerstatic org.helm.chemtoolkit.AbstractMoleculeBuilderMolecule. getMoleculeForMonomer(Monomer monomer)method to build a molecule for a given monomerstatic org.jdom2.ElementMonomerParser. getMonomerElement(Monomer monomer)This method converts Monomer to MONOMER XML elementstatic booleanMonomerParser. validateMonomer(Monomer monomer)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 attachmentMethod parameters in org.helm.notation2.tools with type arguments of type Monomer Modifier and Type Method Description protected static StringFastaFormat. generateFastaFromPeptide(List<Monomer> monomers)method to generate Fasta for a list of peptide monomersprotected static StringFastaFormat. generateFastaFromRNA(List<Monomer> monomers)method to generate Fasta for a list of rna monomers -
Uses of Monomer in org.helm.notation2.wsadapter
Methods in org.helm.notation2.wsadapter that return types with arguments of type Monomer Modifier and Type Method Description Map<String,Monomer>MonomerWSLoader. loadMonomerStore(Map<String,Attachment> attachmentDB)Loads the monomer store using the URL configured inMonomerStoreConfigurationand the polymerType that was given to constructor.Methods in org.helm.notation2.wsadapter with parameters of type Monomer Modifier and Type Method Description StringMonomerWSSaver. saveMonomerToStore(Monomer monomer)Adds or updates a single monomer to the monomer store using the URL configured inMonomerStoreConfiguration.