Uses of Class
org.helm.notation2.Attachment

Packages that use Attachment

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

Uses of Attachment in org.helm.notation2

Methods in org.helm.notation2 that return Attachment

Modifier and Type	Method and Description
static Attachment	DeepCopy.copy(Attachment attachment)
Attachment	Monomer.getAttachment(String label) get a specific attachment by passing in a label

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

Modifier and Type	Method and Description
Map<String,Attachment>	MonomerFactory.getAttachmentDB()
Map<String,Attachment>	MonomerCache.getAttachmentDB()
List<Attachment>	Monomer.getAttachmentList()
static Map<String,Attachment>	AttachmentLoader.loadAttachments(InputStream in) reads the attachments from the given inputstream and returns the attachment db

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

Modifier and Type	Method and Description
boolean	Monomer.addAttachment(Attachment attachment) Try to add a new attachment to this monomer
static Attachment	DeepCopy.copy(Attachment attachment)
static boolean	AttachmentLoader.validateAttachment(Attachment currentAttachment) validates the current attachment

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

Modifier and Type	Method and Description
void	MonomerCache.setAttachmentDB(Map<String,Attachment> attachmentDB)
void	Monomer.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 and Description
static Attachment	MonomerParser.getAttachment(org.jdom2.Element attachment) Convert ATTACHMENT element to Attachment object

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

Modifier and Type	Method and Description
static void	MonomerParser.fillAttachmentInfo(Attachment att)
static org.jdom2.Element	MonomerParser.getAttachementElement(Attachment att) This method converts Attachment to ATTACHMENT XML element
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

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

Modifier and Type	Method and Description
String	WebService.convertMolFileSMILESWithAtomMapping(String molfile, List<Attachment> attachments) method to generate a smiles with atom mapping for a given molfile with the given attachments
static String	SMILES.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 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.