bibtex

Contains Specmol related methods

loadBibliodata

summary
Loads a bibtex file using jabref.
params
String path

biojava

Provides bioinformatics services through the BioJava project.

DNAToProtein

summary
Converts a BiojavaDNASequence into a BiojavaAASequence.
params
BiojavaDNASequence sequence

DNAtoRNA

summary
Converts a DNA sequence into RNA (transcription.
params
BiojavaDNASequence sequence

RNAtoDNA

summary
Converts a RNA sequence into DNA (reverse transcription.
params
BiojavaRNASequence rnaSeq

RNAtoProtein

summary
Convert a BiojavaRNASequence into a BiojavaAASequence.
params
BiojavaRNASequence sequence

createSequence

summary
Creates sequence from a name and a plain sequence string (content.
params
String name, String content

createSequenceFromFasta

summary
Creates sequence from a plain sequence string. Will set name to empty.
params
String content

loadSequence

summary
Loads sequence from InputStream.
params
InputStream instream

loadSequences

summary
Loads sequenceCollection from InputStream.
params
String path

renderAs

summary
Converts a BiojavaSequence to a String representation in a given format.
params
SequenceFormat format

saveSequence

summary
Saves a Biojava sequence to a given path using a given format.
params
BiojavaSequence seq, String path, SequenceFormat format

cdk

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

areIsomorphic

summary
Returns true if the paramater named molecule1 and the paramater named molecule2 are isomorph.
(Performs an isomophism test without checking fingerprints
params
ICDKMolecule molecule1, ICDKMolecule molecule2

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

createSDFile

summary
Creates an sd file from a number of molecules
params
String file, IMolecule[] entries

createSDFileIndex

summary
Creates a index file for the SD-file.
params
String filePath

determineFormat

summary
Determines the file format if the file, if chemical
params
String path

extractFromSDFile

summary
Extracts a number of entries from an sd file. Does not read the complete file for this.
params
String file, int startenty, int endentry

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

fromString

summary
Creates a cdk molecule from a String.
params
String input file

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

molecularFormula

summary
Gives the molecularformula as a String
params
ICDKMolecule m

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. If overwrite=true then file will be overwritten if exists.
params
IMolecule mol, String filename, String filetype, boolean overwrite

smartsMatches

summary
Returns true if the given SMARTS matches the given molecule
params
ICDKMolecule molecule, String smarts

subStructureMatches

summary
Returns true if the paramater named subStructure is a substructure of the paramater named molecule.
(Performs an isomophism test without checking fingerprints
params
ICDKMolecule molecule, ICDKMolecule subStructure

cdx

Contains CDK debug related methods

debug

summary
Returns a string representation of the data structures.
params
ICDKMolecule mol

diff

summary
Returns the differences between the two molecules
params
ICDKMolecule mol, ICDKMolecule mol2

perceiveCDKAtomTypes

summary
Returns a list of CDK atom types.
params
IMolecule mol

perceiveSybylAtomTypes

summary
Returns a list of Sybyl atom types.
params
IMolecule mol

inchi

Manager for creating InChI and InChIKeys.

generate

summary
Generates the InChI for the given molecule.
params
IMolecule molecule

generateKey

summary
Generates the InChIKey for the given molecule.
params
IMolecule molecule

jcp

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

addPhenyl

summary
Adds a phenyl ring fused with the given bond.
params
IBond bond to add the phenyl ring to

addRing

summary
Adds a carbon ring of the given size fused with the given bond.
params
IBond bond to add the ring to, int ring size

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

removeBond

summary
Removes a IBond from the data model.
params
IBond bond 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.

js

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

molecule

Manages light weight molecules

fromSmiles

summary
creates a light weight molecule from smiles
params
String smiles

seneca

Contains Seneca methods

getJobSpecification

summary
Loads a job specification from a file.
params
IFile file

services

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

specmol

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

spectrum

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

structuredb

Handles structure databases

addMoleculesFromSDF

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

ui

Controls access to Bioclipse UI.

fileExists

summary
Determines if the given file exists in the workspace
params
String filePath

open

summary
Opens editor of given ID with bioObject
params
IBioObject bioObject, String editorID

remove

summary
Deletes a file.
params
String filePath

save

summary
Save the content of the InputStream to the given path.
params
String filePath, InputStream content

userManager

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<String, String> 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

webservices

Contains webservices related methods

downloadDbEntry

summary
Fetches an entry from the EBI databases
params
String db, String query, String format

downloadDbEntryAsFile

summary
Fetches an entry from the EBI databases and saves it
params
String db, String query, String format

downloadPDBAsFile

summary
Fetches a PDB entry with ID="pdbid' from the EBI databases and saves it under the specified filename
params
String pdbid, String filename