| Package | Description |
|---|---|
| org.helm.notation2 | |
| org.helm.notation2.tools |
| 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
|
MonomerCache |
MonomerFactory.buildMonomerCacheFromXML(String monomerDBXML)
Build an MonomerCache object with monomerDBXML String
|
static Attachment |
DeepCopy.copy(Attachment attachment) |
static Monomer |
DeepCopy.copy(Monomer monomer) |
Map<Monomer,Monomer> |
MonomerFactory.getConflictedMonomerMap(MonomerCache remoteMonomerCache) |
void |
MonomerFactory.merge(MonomerCache remoteMonomerCache)
merge remote monomerCache with local monomerCache, will throw exception if
conflicts found.
|
void |
MonomerFactory.saveMonomerCache()
save monomerCache to disk file
|
void |
MonomerFactory.setMonomerCache(MonomerCache remoteMonomerCache)
replace local cache with remote one completely, may cause loss of data
|
| Modifier and Type | Method and Description |
|---|---|
static Nucleotide |
NucleotideParser.convertToNucleotide(String id,
boolean last)
method to convert an string to an nucleotide
|
static void |
MonomerParser.fillAttachmentInfo(Attachment att) |
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<String> |
AminoAcidParser.getAminoAcidList(String peptideSequence)
This method converts peptide sequence into a List of amino acid
|
static List<String> |
AminoAcidParser.getAminoAcidList(String peptideSequence,
String delimiter)
This method converts peptide sequence into a List of amino acid with
optional delimiter
|
static List<Monomer> |
MethodsMonomerUtils.getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations)
method to get all monomers for all MonomerNotations
|
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!
|
static org.jdom2.Element |
MonomerParser.getMonomerElement(Monomer monomer)
This method converts Monomer to MONOMER XML element
|
static List<Monomer> |
MonomerParser.getMonomerList(String monomerXMLString) |
static MonomerStore |
xHelmNotationParser.getMonomerStore(org.jdom2.Element rootElement)
Generates the monomer store from a given XHELM document
|
static String |
xHelmNotationExporter.getXHELM(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
method to get xhelm for the helm notation, only if it was possible to
convert the helm in the old format
|
static String |
xHelmNotationExporter.getXHELM2(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
method to get xhelm for the helm2 notation with the new functionality
|
static void |
ChangeObjects.replaceMonomer(org.helm.notation2.parser.notation.HELM2Notation helm2notation,
String polymerType,
String existingMonomerID,
String newMonomerID)
method to replace the MonomerID with the new MonomerID for a given
polymer type
|
static boolean |
MonomerParser.validateAttachement(Attachment attachment)
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
|
static void |
MonomerParser.validateAttachmentLabel(String label)
This method checks if attachment label is in the format of R#, where # is a
number
|
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
|
static void |
Validation.validateNotationObjects(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
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
|
void |
WebService.validateSyntaxHELM(String helm) |
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