org.openscience.nmrshiftdb.om
Class DBAtom

java.lang.Object
  org.apache.torque.om.BaseObject
      org.openscience.nmrshiftdb.om.BaseDBAtom
          org.openscience.nmrshiftdb.om.DBAtom

All Implemented Interfaces:

java.io.Serializable, org.apache.torque.om.Persistent

public class DBAtom
extends BaseDBAtom
implements org.apache.torque.om.Persistent

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.

Author:

shk3

See Also:

Serialized Form

Field Summary

(package private) DBCoordinateSet2d	coords2
(package private) DBCoordinateSet3d	coords3
private java.util.Vector	couplings
boolean	force3d

Fields inherited from class org.openscience.nmrshiftdb.om.BaseDBAtom

collDBBondDBAtoms, collDBCoordinateSet2ds, collDBCoordinateSet3ds, collDBCouplingsRelatedByAtomId1, collDBCouplingsRelatedByAtomId2, collDBIdentifiers, collDBSignalDBAtoms

Fields inherited from class org.apache.torque.om.BaseObject

NEW_ID

Constructor Summary

DBAtom()
Constructor for the DBAtom object

DBAtom(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainer ac, int dbmol, java.lang.String hoseCode, java.lang.String hoseCodeWithRings, boolean visible)
Constructor for the DBAtom object.

Method Summary

void	delete(java.sql.Connection conn) Deletes this atom.
DBSignal	getAnySignal(int spectrumId) Gets the DBSignal associated with this atom in a certain spectrum.
org.openscience.cdk.interfaces.IAtom	getAsCdkAtom() Gets the asCdkAtom attribute of the DBAtom object
org.openscience.cdk.interfaces.IAtom	getAsCdkAtom(SubmittingData subData) Gets the cdk atom corresponding with this atom int molWithH of a submittingData.
static java.util.List	getAtoms(int molid) Gets the atoms of a certain molecules.
static java.util.List	getAtomsWithoutHs(int molid) Gets the atoms of a certain molecules withouth the Hs.
java.util.Vector	getBonds() Gets the bonds of the DBAtom object
java.util.Vector	getConnectedAtoms() Gets the atoms connected with this atom
java.util.Vector	getConnectedAtoms(org.openscience.cdk.interfaces.IMolecule mol, DBAtom[] dbatoms) Gets the atoms connected with this atom
double[]	getCoordinates(int coordinateSetId) Gets the coordinates of this atom in a coordinate set with a certain coordinate set id.
java.util.Vector	getCouplings(DBSpectrum spectrum) Gets the couplings of this atom in a certain spectrum.
java.lang.String	getCouplingsString(DBSpectrum spectrum) Gets the couplings of this atom in a certain spectrum.as a string
java.util.List	getDBSignals() Gets the dBSignals attribute of the DBAtom object
java.util.List	getDBSignals(char type) Gets the dBSignals attribute of the DBAtom object.
java.util.List	getDBSignals(DBSpectrum spectrum) Gets the dBSignals attribute of the DBAtom object
java.util.List	getDBSignalsBySpectrumType(java.lang.String typname)
int	getHydrogenCount() Gets the nubmer of hydrogens connected to the DBAtom
int	getHydrogenCount(DBAtom[] atoms, org.openscience.cdk.interfaces.IMolecule cdkmol)
java.lang.String	getIdentifier(DBSpectrum spectrum) Gets the identifier attribute of the DBAtom object in a certain spectrum.
java.lang.String	getIdentifier(int spectrum)
int	getIntegralStuff()
int	getIntegralStuff(DBAtom[] atoms, org.openscience.cdk.interfaces.IMolecule cdkmol)
int	getMdlNumber() Gets the mdl number of the Atom.
int	getMdlNumberPlus1() Gets the mdlNumber value + 1
int	getMdlNumberPlus1Heavy() Gets the mdlNumber value + 1, if atom is a heavy atom of the atom itself, if a hydrogen, of the heavy atom it is attached to.
java.lang.String	getMultiplicity(DBSpectrum spectrum) Gets a string giving the multiplicity and coupling constants of the signal of this atom in a certain spectrum.
boolean	hasCouplings(DBSpectrum spectrum) Gets the couplings of this atom in a certain spectrum.as a string
boolean	isCoordinate3d(int coordinateSetId)
void	save(java.sql.Connection dbCon) Saves this object incl.

Methods inherited from class org.openscience.nmrshiftdb.om.BaseDBAtom

addDBBondDBAtom, addDBCoordinateSet2d, addDBCoordinateSet3d, addDBCouplingRelatedByAtomId1, addDBCouplingRelatedByAtomId2, addDBIdentifier, addDBSignalDBAtom, copy, copyInto, getAtomicMass, getAtomId, getByName, getByPeerName, getByPosition, getDBBondDBAtoms, getDBBondDBAtoms, getDBBondDBAtoms, getDBBondDBAtoms, getDBBondDBAtomsJoinDBAtom, getDBBondDBAtomsJoinDBBond, getDBCoordinateSet2ds, getDBCoordinateSet2ds, getDBCoordinateSet2ds, getDBCoordinateSet2ds, getDBCoordinateSet2dsJoinDBAtom, getDBCoordinateSet2dsJoinDBCoordinateSetType, getDBCoordinateSet3ds, getDBCoordinateSet3ds, getDBCoordinateSet3ds, getDBCoordinateSet3ds, getDBCoordinateSet3dsJoinDBAtom, getDBCoordinateSet3dsJoinDBCoordinateSetType, getDBCouplingsRelatedByAtomId1, getDBCouplingsRelatedByAtomId1, getDBCouplingsRelatedByAtomId1, getDBCouplingsRelatedByAtomId1, getDBCouplingsRelatedByAtomId1JoinDBAtomRelatedByAtomId2, getDBCouplingsRelatedByAtomId1JoinDBSpectrum, getDBCouplingsRelatedByAtomId2, getDBCouplingsRelatedByAtomId2, getDBCouplingsRelatedByAtomId2, getDBCouplingsRelatedByAtomId2, getDBCouplingsRelatedByAtomId2JoinDBAtomRelatedByAtomId1, getDBCouplingsRelatedByAtomId2JoinDBSpectrum, getDBIdentifiers, getDBIdentifiers, getDBIdentifiers, getDBIdentifiers, getDBIdentifiersJoinDBAtom, getDBIdentifiersJoinDBLiterature, getDBMolecule, getDBSignalDBAtoms, getDBSignalDBAtoms, getDBSignalDBAtoms, getDBSignalDBAtoms, getDBSignalDBAtomsJoinDBAtom, getDBSignalDBAtomsJoinDBSignal, getFieldNames, getFormalCharge, getHetero, getHoseCode, getHoseCodeWithRings, getIsAromatic, getIsVisible, getMoleculeId, getPeer, getPrimaryKey, getSymbol, initDBBondDBAtoms, initDBCoordinateSet2ds, initDBCoordinateSet3ds, initDBCouplingsRelatedByAtomId1, initDBCouplingsRelatedByAtomId2, initDBIdentifiers, initDBSignalDBAtoms, save, save, setAtomicMass, setAtomId, setDBMolecule, setDBMoleculeKey, setFormalCharge, setHetero, setHoseCode, setHoseCodeWithRings, setIsAromatic, setIsVisible, setMoleculeId, setPrimaryKey, setPrimaryKey, setSymbol, toString

Methods inherited from class org.apache.torque.om.BaseObject

equals, equals, getLog, hashCode, isModified, isNew, log, resetModified, setModified, setNew, setPrimaryKey

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.apache.torque.om.Persistent

getPrimaryKey, isModified, isNew, save, save, setModified, setNew, setPrimaryKey, setPrimaryKey

Field Detail

coords3

DBCoordinateSet3d coords3

coords2

DBCoordinateSet2d coords2

force3d

public boolean force3d

couplings

private java.util.Vector couplings

Constructor Detail

DBAtom

public DBAtom()

Constructor for the DBAtom object

DBAtom

public DBAtom(org.openscience.cdk.interfaces.IAtom atom,
              org.openscience.cdk.interfaces.IAtomContainer ac,
              int dbmol,
              java.lang.String hoseCode,
              java.lang.String hoseCodeWithRings,
              boolean visible)
       throws java.lang.Exception

Constructor for the DBAtom object.

Parameters:

atom - The cdk atom this atom is supposed to represent.

dbmol - The molecule it comes from

hoseCode - The hose code.

visible - Should this atom be visible.

Throws:

java.lang.Exception - Description of Exception.

Method Detail

getAtoms

public static java.util.List getAtoms(int molid)
                               throws org.apache.torque.TorqueException

Gets the atoms of a certain molecules.

Parameters:

molid - The molecule.

Returns:

The atoms.

Throws:

java.lang.Exception - Database problems.

org.apache.torque.TorqueException

getAtomsWithoutHs

public static java.util.List getAtomsWithoutHs(int molid)
                                        throws org.apache.torque.TorqueException

Gets the atoms of a certain molecules withouth the Hs.

Parameters:

molid - The molecule.

Returns:

The atoms.

Throws:

java.lang.Exception - Database problems.

org.apache.torque.TorqueException

getBonds

public java.util.Vector getBonds()
                          throws java.lang.Exception

Gets the bonds of the DBAtom object

Returns:

The bonds

Throws:

java.lang.Exception - Database problems

getConnectedAtoms

public java.util.Vector getConnectedAtoms(org.openscience.cdk.interfaces.IMolecule mol,
                                          DBAtom[] dbatoms)
                                   throws java.lang.Exception

Gets the atoms connected with this atom

Returns:

The connected atoms

Throws:

java.lang.Exception - Database Problems

getConnectedAtoms

public java.util.Vector getConnectedAtoms()
                                   throws java.lang.Exception

Gets the atoms connected with this atom

Returns:

The connected atoms

Throws:

java.lang.Exception - Database Problems

getHydrogenCount

public int getHydrogenCount()
                     throws java.lang.Exception

Gets the nubmer of hydrogens connected to the DBAtom

Returns:

The hydrogenCount value

Throws:

java.lang.Exception - Database problems

getHydrogenCount

public int getHydrogenCount(DBAtom[] atoms,
                            org.openscience.cdk.interfaces.IMolecule cdkmol)
                     throws java.lang.Exception

Throws:

java.lang.Exception

getAnySignal

public DBSignal getAnySignal(int spectrumId)
                      throws java.lang.Exception

Gets the DBSignal associated with this atom in a certain spectrum.

Parameters:

spectrumId - The spectrum of which the signal should be.

Returns:

The DBSignal value.

Throws:

java.lang.Exception - Database problems.

getMdlNumberPlus1Heavy

public int getMdlNumberPlus1Heavy()
                           throws java.lang.Exception

Gets the mdlNumber value + 1, if atom is a heavy atom of the atom itself, if a hydrogen, of the heavy atom it is attached to.

Returns:

The mdlNumberPlus1 value

Throws:

java.lang.Exception - Description of Exception

getIdentifier

public java.lang.String getIdentifier(int spectrum)
                               throws java.lang.Exception

Throws:

java.lang.Exception

getMdlNumberPlus1

public int getMdlNumberPlus1()
                      throws java.lang.Exception

Gets the mdlNumber value + 1

Returns:

The mdlNumberPlus1 value

Throws:

java.lang.Exception - Description of Exception

getMdlNumber

public int getMdlNumber()
                 throws java.lang.Exception

Gets the mdl number of the Atom. The mdl number is the number of the atom in the molecule, in the order as they were in the mdl of the original submit. Starts with 0.

Returns:

The mdlNumber value.

Throws:

java.lang.Exception - Database problems.

getAsCdkAtom

public org.openscience.cdk.interfaces.IAtom getAsCdkAtom()
                                                  throws java.lang.Exception

Gets the asCdkAtom attribute of the DBAtom object

Returns:

The asCdkAtom value

Throws:

java.lang.Exception - Description of Exception

getAsCdkAtom

public org.openscience.cdk.interfaces.IAtom getAsCdkAtom(SubmittingData subData)
                                                  throws java.lang.Exception

Gets the cdk atom corresponding with this atom int molWithH of a submittingData.

Parameters:

subData - The submittingData.

Returns:

The Cdk Atom.

Throws:

java.lang.Exception - Description of Exception

getIdentifier

public java.lang.String getIdentifier(DBSpectrum spectrum)
                               throws java.lang.Exception

Gets the identifier attribute of the DBAtom object in a certain spectrum.

Parameters:

spectrum - The spectrum the identifier should be in.

Returns:

The identifier value.

Throws:

java.lang.Exception - Database problems.

getMultiplicity

public java.lang.String getMultiplicity(DBSpectrum spectrum)
                                 throws java.lang.Exception

Gets a string giving the multiplicity and coupling constants of the signal of this atom in a certain spectrum.

Parameters:

spectrum - Spectrum in which the signal should be.

Returns:

The multiplicity value.

Throws:

java.lang.Exception - Database problems.

hasCouplings

public boolean hasCouplings(DBSpectrum spectrum)
                     throws java.lang.Exception

Gets the couplings of this atom in a certain spectrum.as a string

Parameters:

spectrum - The spectrum.

Returns:

The couplings.

Throws:

java.lang.Exception - Database problems.

getCouplingsString

public java.lang.String getCouplingsString(DBSpectrum spectrum)
                                    throws java.lang.Exception

Gets the couplings of this atom in a certain spectrum.as a string

Parameters:

spectrum - The spectrum.

Returns:

The couplings.

Throws:

java.lang.Exception - Database problems.

getCouplings

public java.util.Vector getCouplings(DBSpectrum spectrum)
                              throws java.lang.Exception

Gets the couplings of this atom in a certain spectrum.

Parameters:

spectrum - The spectrum.

Returns:

The couplings.

Throws:

java.lang.Exception - Database problems.

getCoordinates

public double[] getCoordinates(int coordinateSetId)
                        throws java.lang.Exception

Gets the coordinates of this atom in a coordinate set with a certain coordinate set id.

Parameters:

coordinateSetId - The coordinate set id

Returns:

The coordinates value [0]=x,[1]=y,[2]=z only with 3d coordinates.

Throws:

java.lang.Exception - Description of Exception

isCoordinate3d

public boolean isCoordinate3d(int coordinateSetId)
                       throws java.lang.Exception

Throws:

java.lang.Exception

getDBSignals

public java.util.List getDBSignals()
                            throws java.lang.Exception

Gets the dBSignals attribute of the DBAtom object

Returns:

The dBSignals value

Throws:

java.lang.Exception - Description of Exception

getDBSignals

public java.util.List getDBSignals(char type)
                            throws org.apache.torque.TorqueException

Gets the dBSignals attribute of the DBAtom object.

Parameters:

type - m=only measured signals,c=only calculated signals included

Returns:

The dBSignals value

Throws:

java.lang.Exception - Description of Exception

org.apache.torque.TorqueException

getDBSignals

public java.util.List getDBSignals(DBSpectrum spectrum)
                            throws org.apache.torque.TorqueException

Gets the dBSignals attribute of the DBAtom object

Parameters:

spectrum - The spectrum the signal should come from

Returns:

The dBSignals value

Throws:

java.lang.Exception - Description of Exception

org.apache.torque.TorqueException

save

public void save(java.sql.Connection dbCon)
          throws org.apache.torque.TorqueException

Saves this object incl. coordinates.

Specified by:

save in interface org.apache.torque.om.Persistent

Overrides:

save in class BaseDBAtom

Parameters:

dbCon - A database connection.

Throws:

java.lang.Exception - Description of Exception

org.apache.torque.TorqueException

delete

public void delete(java.sql.Connection conn)
            throws java.lang.Exception

Deletes this atom.

Parameters:

conn - The description to use.

Throws:

java.lang.Exception - Database problems.

getDBSignalsBySpectrumType

public java.util.List getDBSignalsBySpectrumType(java.lang.String typname)
                                          throws java.lang.Exception

Throws:

java.lang.Exception

getIntegralStuff

public int getIntegralStuff(DBAtom[] atoms,
                            org.openscience.cdk.interfaces.IMolecule cdkmol)
                     throws java.lang.Exception

Throws:

java.lang.Exception

getIntegralStuff

public int getIntegralStuff()
                     throws java.lang.Exception

Throws:

java.lang.Exception