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org.openscience.compchem.* (17)org.openscience.jmol.* (4)org.openscience.miniJmol.* (24)
org.openscience.nmrshiftdb.* (258)

Package Samples:

org.openscience.nmrshiftdb.om.map: Torque's OM-Layer for NMRShiftDB.  
org.openscience.nmrshiftdb.modules.actions.portlets: Action handlers for NMRShiftDB.  
org.openscience.nmrshiftdb.util.db.map: Utility classes for NMRShiftDB  
org.openscience.compchem
org.openscience.jmol
org.openscience.miniJmol
org.openscience.nmrshiftdb.daemons
org.openscience.nmrshiftdb
org.openscience.nmrshiftdb.modules.actions.portlets.security
org.openscience.nmrshiftdb.modules.actions
org.openscience.nmrshiftdb.om
org.openscience.nmrshiftdb.portlets
org.openscience.nmrshiftdb.tests
org.openscience.nmrshiftdb.util
org.openscience.nmrshiftdb.util.exception
org.openscience.nmrshiftdb.webservices

Classes:

Gaussian98Reader: A reader for Gaussian98 output. Gaussian 98 is a quantum chemistry program by Gaussian, Inc. (http://www.gaussian.com/). Molecular coordinates, energies, and normal coordinates of vibrations are read. Each set of coordinates is added to the ChemFile in the order they are found. Energies and vibrations are associated with the previously read set of coordinates. This reader was developed from a small set of example output files, and therefore, is not guaranteed to properly read all Gaussian98 output. If you have problems, please contact the author of this code, not the developers of Gaussian98.
BaseAtomType: The basic properties of an atom are represented by the atom type. Each atom type is identified with a unique string label. To ensure that only one atom type exists for each label, atom types can not be created, but only retrieved from a static pool of BaseAtomTypes. If the pool does contain an BaseAtomType for a given label, one will be created upon the first retreival.
PhysicalProperty: A superclass to allow Jmol to talk to the transitory properties of atoms or bonds. For atoms, subclass PhysicalProperty to identify charge, NMR shielding, etc. For bonds, subclass it to identify distances harmonic force constants, etc. For bends, subclass it to identify angles, etc.
XYZReader: XYZ files may contain multiple ChemFrame objects, and may have charges and vector information contained along with atom types and coordinates. XYZ files must have a number of atoms at the beginning of each line then another line (which may be blank) to identify each frame.
WebPagePortletWithURLFromRequest: A class that loads a web page and filters it to have certain features deleted. This class was modified by Stefan Kuhn in order to accept a URL to diplay as Parameter (URL=) Certain URLs are also rewritten to display inside of NMRShiftDB.
Soundex: Find the Soundex of a string. This is an adapted version with it's own soundex rules. This code is taken from jakarta-taglibs who took if from generationjava.com who took it from the codesnippers at sourceforge. The license ? Pff...
PDBReader: PDB files contain a single ChemFrame object. Only the END, ATOM and HETATM command strings are processed for now, and the ATOM and HETATM entries are only used for coordinate information.
AbstractDaemon: An abstract daemon. You should not use this class to implement a daemon. but AbstractDaemonWith(out)ServletConfig. This makes sure that the appropriate run-method is called from DaemonThread.
DBArticlePeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBAtomCountPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBAtomPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBAuthorPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBBondDBAtomPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBBondPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBBookDBPublisherPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBBookPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBChemicalNamePeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBConditionPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBConditionTypePeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBIsotopePeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBJournalPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBJournalVolumePeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBKeywordPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBLiteraturePeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.
DBMoleculeDBKeywordPeer: You should add additional methods to this class to meet the application requirements. This class will only be generated as long as it does not already exist in the output directory.

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