Uses of Class
org.helm.notation2.Monomer

Packages that use Monomer

Package	Description
org.helm.notation2
org.helm.notation2.tools
org.helm.notation2.wsadapter

Uses of Monomer in org.helm.notation2

Methods in org.helm.notation2 that return Monomer

Modifier and Type	Method and Description
static Monomer	DeepCopy.copy(Monomer monomer)
static Monomer	Monomer.fromJSON(String json)
Monomer	Nucleotide.getBaseMonomer() get the base monomer, the return value could be null if this nucleotide does not have a base
Monomer	Nucleotide.getBaseMonomer(MonomerStore monomerStore) get the base monomer, the return value could be null if this nucleotide does not have a base
Monomer	MonomerStore.getMonomer(String smiles) Returns the monomer by smiles string
Monomer	MonomerStore.getMonomer(String polymerType, String alternateId) Returns the monomer specified by polymerType and alternatId
Monomer	Nucleotide.getPhosphateMonomer() return the phosphate monomer of this nucleotide
Monomer	Nucleotide.getPhosphateMonomer(MonomerStore monomerStore) return the phosphate monomer of this nucleotide
Monomer	Nucleotide.getSugarMonomer() get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugar
Monomer	Nucleotide.getSugarMonomer(MonomerStore monomerStore) get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugar

Methods in org.helm.notation2 that return types with arguments of type Monomer

Modifier and Type	Method and Description
List<Monomer>	MonomerStore.getAllMonomersList() This method returns all monomers of the store as list sorted by polymer type
Map<Monomer,Monomer>	MonomerFactory.getConflictedMonomerMap(MonomerCache remoteMonomerCache)
Map<Monomer,Monomer>	MonomerFactory.getConflictedMonomerMap(MonomerCache remoteMonomerCache)
Map<String,Map<String,Monomer>>	MonomerStore.getMonomerDB() returns MonomerDB
Map<String,Map<String,Monomer>>	MonomerFactory.getMonomerDB() retruns the monomer database
Map<String,Map<String,Monomer>>	MonomerCache.getMonomerDB()
Map<String,Map<String,Monomer>>	MonomerFactory.getMonomerDB(boolean includeNewMonomers) returns the monomer database including monomers that where temporary marked as new, else without those monomers
Map<String,Monomer>	MonomerStore.getMonomers(String polymerType) Returns all monomers by polymerType
Map<String,Monomer>	MonomerStore.getSmilesMonomerDB() returns SmilesMonomerDB
Map<String,Monomer>	MonomerFactory.getSmilesMonomerDB()
Map<String,Monomer>	MonomerCache.getSmilesMonomerDB()
Map<String,Monomer>	MonomerFactory.getSmilesMonomerDB(boolean includeNewMonomers)

Methods in org.helm.notation2 with parameters of type Monomer

Modifier and Type	Method and Description
void	MonomerStore.addMonomer(Monomer monomer) Adds a monomer to the store
void	MonomerStore.addMonomer(Monomer monomer, boolean dbChanged) Adds a monomer to the store and optionally sets the dbChanged flag
void	MonomerStore.addNewMonomer(Monomer monomer) Adds a monomer to the store and makes it a temporary new monomer
void	MonomerFactory.addNewMonomer(Monomer monomer) To add new monomer into monomerCache
boolean	Monomer.attachmentContains(Monomer monomer)
boolean	Monomer.attachmentEquals(Monomer monomer)
static Monomer	DeepCopy.copy(Monomer monomer)
boolean	Monomer.isSameType(Monomer m) Compare this momoner with another one, polymerType, monomerType and naturalAnalog (could be derived) must be the same to return true

Method parameters in org.helm.notation2 with type arguments of type Monomer

Modifier and Type	Method and Description
void	MonomerCache.setMonomerDB(Map<String,Map<String,Monomer>> monomerDB)
void	MonomerCache.setSmilesMonomerDB(Map<String,Monomer> smilesMonomerDB)

Constructor parameters in org.helm.notation2 with type arguments of type Monomer

Constructor and Description
MonomerStore(Map<String,Map<String,Monomer>> monomerDB, Map<String,Monomer> smilesMonomerDB) Constructor with Monomer- and SmilesDB
MonomerStore(Map<String,Map<String,Monomer>> monomerDB, Map<String,Monomer> smilesMonomerDB) Constructor with Monomer- and SmilesDB

Uses of Monomer in org.helm.notation2.tools

Methods in org.helm.notation2.tools that return Monomer

Modifier and Type	Method and Description
static Monomer	Converter.convertMonomer(Monomer m)
static Monomer	MethodsMonomerUtils.generateTemporaryMonomer(String id, String polymerType, String naturalAnalog)
static Monomer	MonomerParser.getMonomer(org.jdom2.Element monomer) Convert monomer element to Monomer object
static Monomer	MonomerParser.getMonomer(String monomerXMLString)
static Monomer	MethodsMonomerUtils.getMonomer(String type, String id, String info) method to get the monomer from the database!

Methods in org.helm.notation2.tools that return types with arguments of type Monomer

Modifier and Type	Method and 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 monomers
static List<Monomer>	Validation.getAllMonomersOnlyBase(org.helm.notation2.parser.notation.polymer.MonomerNotation not) method to get for one MonomerNotation all valid contained monomers.
static List<Monomer>	MethodsMonomerUtils.getListOfHandledMonomers(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) method to get all HELM1 valid MonomerNotations Only on these monomers required HELM1 functions are performed
static List<Monomer>	MethodsMonomerUtils.getListOfHandledMonomersOnlyBase(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) method to get all HELM1 valid MonomerNotations Only on these monomers required HELM1 functions are performed
static List<Monomer>	MethodsMonomerUtils.getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) method to get all monomers for all MonomerNotations
static List<Monomer>	MonomerParser.getMonomerList(String monomerXMLString)

Methods in org.helm.notation2.tools with parameters of type Monomer

Modifier and Type	Method and Description
static Monomer	Converter.convertMonomer(Monomer m)
byte[]	WebService.generateImageForMonomer(Monomer monomer, boolean showRgroups) method to generate an image for a monomer
static byte[]	Images.generateImageofMonomer(Monomer monomer, boolean rgroupsInformation) generates an image of the atom/bond representation of monomer
static org.helm.chemtoolkit.AbstractMolecule	BuilderMolecule.getMoleculeForMonomer(Monomer monomer) method to build a molecule for a given monomer
static org.jdom2.Element	MonomerParser.getMonomerElement(Monomer monomer) This method converts Monomer to MONOMER XML element
static boolean	MonomerParser.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 attachment

Method parameters in org.helm.notation2.tools with type arguments of type Monomer

Modifier and Type	Method and Description
protected static String	FastaFormat.generateFastaFromPeptide(List<Monomer> monomers) method to generate Fasta for a list of peptide monomers
protected static String	FastaFormat.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 and Description
Map<String,Monomer>	MonomerWSLoader.loadMonomerStore(Map<String,Attachment> attachmentDB) Loads the monomer store using the URL configured in MonomerStoreConfiguration and the polymerType that was given to constructor.

Methods in org.helm.notation2.wsadapter with parameters of type Monomer

Modifier and Type	Method and Description
String	MonomerWSSaver.saveMonomerToStore(Monomer monomer) Adds or updates a single monomer to the monomer store using the URL configured in MonomerStoreConfiguration .