Uses of Class
org.helm.notation2.Attachment
| Package | Description |
|---|---|
| org.helm.notation2 | |
| org.helm.notation2.tools | |
| org.helm.notation2.wsadapter |
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Uses of Attachment in org.helm.notation2
Methods in org.helm.notation2 that return Attachment Modifier and Type Method Description static AttachmentDeepCopy. copy(Attachment attachment)AttachmentMonomer. getAttachment(String label)get a specific attachment by passing in a labelMethods in org.helm.notation2 that return types with arguments of type Attachment Modifier and Type Method Description Map<String,Attachment>MonomerCache. getAttachmentDB()Map<String,Attachment>MonomerFactory. getAttachmentDB()List<Attachment>Monomer. getAttachmentList()static Map<String,Attachment>AttachmentLoader. loadAttachments(InputStream in)reads the attachments from the given inputstream and returns the attachment dbMethods in org.helm.notation2 with parameters of type Attachment Modifier and Type Method Description booleanMonomer. addAttachment(Attachment attachment)Try to add a new attachment to this monomerstatic AttachmentDeepCopy. copy(Attachment attachment)static booleanAttachmentLoader. validateAttachment(Attachment currentAttachment)validates the current attachmentMethod parameters in org.helm.notation2 with type arguments of type Attachment Modifier and Type Method Description voidMonomerCache. setAttachmentDB(Map<String,Attachment> attachmentDB)voidMonomer. setAttachmentList(List<Attachment> attachmentList) -
Uses of Attachment in org.helm.notation2.tools
Methods in org.helm.notation2.tools that return Attachment Modifier and Type Method Description static AttachmentMonomerParser. getAttachment(org.jdom2.Element attachment)Convert ATTACHMENT element to Attachment objectMethods in org.helm.notation2.tools with parameters of type Attachment Modifier and Type Method Description static voidMonomerParser. fillAttachmentInfo(Attachment att)static org.jdom2.ElementMonomerParser. getAttachementElement(Attachment att)This method converts Attachment to ATTACHMENT XML elementstatic booleanMonomerParser. 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 labelMethod parameters in org.helm.notation2.tools with type arguments of type Attachment Modifier and Type Method Description StringWebService. convertMolFileSMILESWithAtomMapping(String molfile, List<Attachment> attachments)method to generate a smiles with atom mapping for a given molfile with the given attachmentsstatic StringSMILES. convertMolToSMILESWithAtomMapping(String molfile, List<Attachment> attachments)Converts molfile with the given attachments in smiles with atom mapping -
Uses of Attachment in org.helm.notation2.wsadapter
Method parameters in org.helm.notation2.wsadapter with type arguments of type Attachment 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.