IWebservicesManager
Contains webservices related methods
downloadPDB
- summary
- Fetches an entry from the EBI databases and saves it to filename
- params
- String pdbid, String filename
ISpectrumManager
Contains Spectrum related methods
create
- summary
- Creates a jubmo spectrum from a spectrum
- params
- ISpectrum m
fromCml
- summary
- Creates a jumbo spectrum from a CML String
- params
- String cml
loadSpectrum
- summary
- Loads a spectrum from file.
- params
- IFile file
pickPeaks
- summary
- Does a peak picking on spectruminput and adds a peak list(existing peaks are conserved
- params
- IJumboSpectrum spectruminput
saveSpectrum
- summary
- Saves a jubmo spectrum to a file
- params
- JumboSpectrum spectrum, IFile target, String filetype
IUserManager
Handles users and accounts in Bioclipse. Can store things like database passwords and usernames in an encrypted file.
accountExists
- summary
- Wether an account with a given account id exists
- params
- String accountId
changePassword
- summary
- Changes the password for the logged in user if the oldPassword is given correctly
- params
- String oldPassword, String newPassword
clearAccounts
- summary
- Removes all accounts for the currently logged in user
createAccount
- summary
- Creates a new account of the given accountType and with the given properties
- params
- String accountID, HashMap properties, AccountType accountType
createUser
- summary
- Creates a new user with the given username and password
- params
- String username, String password
deleteUser
- summary
- deletes the user with the given username
- params
- String username
getAccountType
- summary
- Gives the accounttype for account with given account id
- params
- String accountID
getAvailableAccountTypeNames
- summary
- Gives the names of all available account types
getAvailableAccountTypes
- summary
- Gives all available account types
getLoggedInUser
- summary
- gives the logged in user
getLoggedInUserName
- summary
- Gives the name of the currently logged in user
getLoggedInUsersAccountNames
- summary
- Gives the account names of the logged in user
getProperty
- summary
- Gives the value of the given property for the account with the given account id
- params
- String accountId, String property
getPropertyKeys
- summary
- gives the names of the properties for an account with a given account id
- params
- String accountId
getUserNames
- summary
- Gives a list of all user names
isLoggedIn
- summary
- Returns whether a user is logged in
logIn
- summary
- Logs in the user with the given username given that the given password matches the stored one.
- params
- String username, String password
logOut
- summary
- Logs out the currently logged in user
persist
- summary
- Write all data to file
reloadFromFile
- summary
- Reloads all data from file discarding changes
IServiceManager
Services are different implementations of functionality that can have local or networked implementations.
run
- summary
- Runs the service with the given name provided with the given input.
- params
- String serviceName, Object input
ICDKDebugManager
Contains CDK debug related methods
debug
- summary
- Returns a string representation of the data structures.
- params
- ICDKMolecule mol
depictCDKAtomTypes
- summary
- Returns a list of CDK atom types.
- params
- IMolecule mol
depictSybylAtomTypes
- summary
- Returns a list of Sybyl atom types.
- params
- IMolecule mol
diff
- summary
- Returns the differences between the two molecules
- params
- ICDKMolecule mol, ICDKMolecule mol2
IMoleculeManager
Manages light weight molecules
fromSmiles
- summary
- creates a light weight molecule from smiles
- params
- String smiles
IBibtexManager
Contains Specmol related methods
loadBibliodata
- summary
- Loads a bibtex file using jabref.
- params
- String path
ISpecmolManager
Contains Specmol related methods
create
- summary
- Creates a jubmo spectrum from a spectrum
- params
- ISpectrum m
fromCml
- summary
- Creates a jumbo specmol from a CML String
- params
- String cml
loadSpecmol
- summary
- Loads an assigned spectrum from file.
- params
- IFile file
saveSpecmol
- summary
- Saves a jubmo specmol to a file
- params
- JumboSpecmol spemol, IFile target, String filetype
ISenecaManager
Contains Seneca methods
getJobSpecification
- summary
- Loads a job specification from a file.
- params
- IFile file
IJsConsoleManager
Controls access to the Javascript Console.
clear
- summary
- Clears the console.
eval
- summary
- Evaluates a script.
- params
- String command
executeFile
- summary
- Runs a js script file.
- params
- String filePath
print
- summary
- Prints a message to the console.
- params
- String message
say
- summary
- Prints a message to the console, adding a trailing newline.
- params
- String message
ICDKManager
Contains CDK related methods
addExplicitHydrogens
- summary
- Adds explicit hydrogens to this molecule
- params
- IMolecule mol
addImplicitHydrogens
- summary
- Adds implicit hydrogens to this molecule
- params
- IMolecule mol
calculateMass
- summary
- Calculate and return the molecular weight for the molecule.
- params
- IMolecule molecule
calculateSMILES
- summary
- Returns the SMILES for a molecule
- params
- IMolecule molecule
create
- summary
- Creates a cdk molecule from a molecule
- params
- IMolecule m
createConformerIterator
- params
- String path
createMoleculeIterator
- summary
- Creates and iterator to the molecules in the file at the path
- params
- String path
determineFormat
- summary
- Determines the file format if the file, if chemical
- params
- String path
fingerPrintMatches
- summary
- Returns true if the fingerprint of the subStructure is a subset of thefingerprint for the molecule
- params
- ICDKMolecule molecule, ICDKMolecule subStructure
fromCml
- summary
- Creates a cdk molecule from a CML String
- params
- String cml
fromSMILES
- summary
- Creates a cdk molecule from SMILES
- params
- String SMILES
generate2dCoordinates
- summary
- Create 2D coordinate for the given molecule
- params
- IMolecule molecule
generate3dCoordinates
- summary
- Create 3D coordinate for the given molecule
- params
- IMolecule molecule
getInfo
- summary
- Returns number of molecules in file.
- params
- String path
getNoMolecules
- summary
- Returns number of molecules in file.
- params
- String path
has2d
- summary
- Returns true if molecule has 2D coordinates, false otherwise.
- params
- IMolecule mol
has3d
- summary
- Returns true if molecule has 3D coordinates, false otherwise.
- params
- IMolecule mol
loadConformers
- summary
- Loads the molecules at the path into a list, and take conformers into account. Currently only reads SDFiles.
- params
- String path
loadMolecule
- summary
- Loads a molecule from file. Returns the first if multiple molecules exists in the file
- params
- String path
loadMolecules
- summary
- Loads molecules from a file at a given path into a list of molecules
- params
- String path
loadSMILESFile
- summary
- Loads molecules from a SMILES file at a given path into a list of molecules
- params
- String path
numberOfEntriesInSDF
- summary
- Counts the number of entries in an SDF file at the given file path. Returns 0 in case of problem.
- params
- String filePath
saveCML
- summary
- Saves a molecule in the Chemical Markup Language format (filename must be a relative to workspace root and folder must exist
- params
- ICDKMolecule molecule, String filename
saveMDLMolfile
- summary
- Saves a molecule in the MDL molfile V2000 format (filename must be a relative to workspace root and folder must exist
- params
- ICDKMolecule molecule, String filename
saveMolecule
- summary
- saves mol to a file (filename must be a relative to workspace root and folder must exist, filetype must be one of the constants given by getPossibleFiletypes
- params
- IMolecule mol, String filename, String filetype
smartsMatches
- summary
- Returns true if the given SMARTS matches the given molecule
- params
- ICDKMolecule molecule, String smarts
structureMatches
- summary
- Returns true if the paramater named molecule1 and the paramater named molecule2 are isomorph. \n(Performs an isomophism test without checking fingerprints
- params
- ICDKMolecule molecule1, ICDKMolecule molecule2
subStructureMatches
- summary
- Returns true if the paramater named subStructure is a substructure of the paramater named molecule. \n(Performs an isomophism test without checking fingerprints
- params
- ICDKMolecule molecule, ICDKMolecule subStructure
IUIManager
Controls access to Bioclipse UI.
open
- summary
- Opens a file in an editor.
- params
- String filePath
remove
- summary
- Deletes a file.
- params
- String filePath
IJChemPaintManager
Manager for the JChemPaintEditor scripting language."
addAtom
- summary
- Adds a new atom bonded to the given atom.
- params
- String element symbol, IAtom atom to attach the new atom too
addBond
- summary
- Create a new bond between the two given atoms.
- params
- IAtom first atom in the bond, IAtom second atom in the bond
cleanup
- summary
- Recalculates 2D coordinates for the complete molecule.
getBondOrder
- summary
- Returns a IBond.Order matching the given order.
- params
- int order
getClosestAtom
- summary
- Returns the IAtom closest to the world coordinate.
- params
- Point2d worldCoordinate
getClosestBond
- summary
- Returns the IBond closest to the world coordinate.
- params
- Point2d worldCoordinate
getModel
- summary
- Returns the ICDKMolecule of the active JChemPaint editor.
moveTo
- summary
- Moves the center of the bond to the new point.
- params
- IBond bond to move, Point2d point to move the atom to
newPoint2d
- summary
- Creates a new javax.vecmath.Point2d.
- params
- double x coordinate, double y coordinate
removeAtom
- summary
- Removes an IAtom from the data model.
- params
- IAtom atom to remove
setCharge
- summary
- Changes the formal charge of this atom.
- params
- IAtom atom to change, int new formal charge
setMassNumber
- summary
- Changes the mass number of this element.
- params
- IAtom atom to change, int new mass number
setModel
- summary
- Sets the ICDKMolecule of the active JChemPaint editor.
setOrder
- summary
- Changes the order of the bond.
- params
- IBond bond to change, IBond.Order new bond order
setSymbol
- summary
- Changes the element of this atom.
- params
- IAtom atom to change, Symbol new element symbol
setWedgeType
- summary
- Changes the wedge type of the bond.
- params
- IBond bond to change, int new wedge type
updateImplicitHydrogenCounts
- summary
- Updates the implicit hydrogen counts, given the given the current connectivity.
updateView
- summary
- Refreshes the JChemPaint view screen.
zap
- summary
- Deletes all atoms and bonds.
IStructuredbManager
Handles structure databases
addMoleculeFromSDF
- summary
- Saves all molecules in a given sdf file in the database with the given name. The molecules are annotated with file_origin
- params
- String databaseName, String filePath
allAnnotations
- summary
- Fetches all annotations from a database with a given name
- params
- String databaseName
allDatabaseNames
- summary
- Returns a list with the names of all structuredb database instances.
allLabels
- summary
- Returns all labels in a database. That is: all TextAnnotations with the corresponding Property being \
- params
- String databaseName
allMolecules
- summary
- Fetches all molecules from a database with a given name
- params
- String databaseName
allMoleculesByName
- summary
- Fetches all structures by a given name from a database with a given name
- params
- String databaseName, String name
allUsers
- summary
- Fetches all users from a database with a given name
- params
- String databaseName
createChoiceAnnotation
- summary
- Creates a ChoiceAnnotation with the given property (which must be a ChoiceProperty, name and saves it in the database with the given name
- params
- String databaseName, String propertyName, String value
createDatabase
- summary
- Creates a local structure database with the given name if no such database already exists.
- params
- String databaseName
createMolecule
- summary
- Creates a database molecule with the given name from the given cdkmolecule and saves it in the database with the given name
- params
- String databaseName, String moleculeName, ICDKMolecule cdkMolecule
createRealNumberAnnotation
- summary
- Creates a RealNumberAnnotation with the given property (which must be a RealNumberProperty, name and saves it in the database with the given name
- params
- String databaseName, String propertyName, String value
createTextAnnotation
- summary
- Creates a TextAnnotation with the given property (which must be a TextProperty, name and saves it in the database with the given name
- params
- String databaseName, String propertyName, String value
createUser
- summary
- Creates a user with the given username and password and with administrator rights if that variable is true
- params
- String databaseName, String username, String password, boolean administrator
deleteAnnotation
- summary
- Deletes the given annotation from the given database
- params
- String database, Annotation annotation
deleteDatabase
- summary
- Removes a local database with the given name if such exists, otherwise does nothing
- params
- String databaseName
deleteStructure
- summary
- Deletes the given molecule from the given database
- params
- String database, DBMolecule molecule
deleteWithMolecules
- summary
- Deletes the given annotation from the specified database and all molecules annotated with that annotation
- params
- String name, Annotation annotation
save
- summary
- Saves changes on a annotation retrieved from the database back to the database.
- params
- String database, Annotation annotation
smartsQuery
- summary
- Performs a SMARTS query returning a list of hitting molecules in the database
- params
- String database, String smarts
smartsQueryIterator
- summary
- Performs a SMARTS query returning an iterator to the hitting molecules in the database
- params
- String database, String smarts
subStructureSearch
- summary
- Returns a list of all molecules in the given database that contains the given molecule
- params
- String databaseName, IMolecule molecule
subStructureSearchIterator
- summary
- Returns an iterator to all molecules in the given database that contains the given molecule
- params
- String databaseName, IMolecule molecule
userByName
- summary
- Fetches a user with a given username from a database with a given name
- params
- String databaseName, String username