org.openscience.nmrshiftdb.om
Class DBMolecule

java.lang.Object
  org.apache.torque.om.BaseObject
      org.openscience.nmrshiftdb.om.BaseDBMolecule
          org.openscience.nmrshiftdb.om.DBMolecule

All Implemented Interfaces:

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

public class DBMolecule
extends BaseDBMolecule
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) org.openscience.cdk.interfaces.IRingSet	allrings
(package private) java.lang.String	autonomeName
(package private) org.openscience.cdk.interfaces.IMolecule	cdkMolecule
(package private) org.openscience.cdk.interfaces.IMolecule	cdkMoleculeWithoutHs
(package private) org.openscience.cdk.interfaces.IMolecule	cdkMoleculeWithoutHsAndCount
(package private) DBAtom[]	dbatoms
(package private) java.lang.String	filename
(package private) long[]	fppro
(package private) java.util.List	keywordsVector
double	maxsimilarity Description of the Field
(package private) int	setid

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

collDBAtoms, collDBBookmarks, collDBCanonicalNames, collDBChemicalNames, collDBMoleculeDBKeywords, collDBMoleculeHyperlinks, collDBSamples, collDBSpectrums, collDBWishlists

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

NEW_ID

Constructor Summary

DBMolecule()
Constructor for the DBMolecule object

DBMolecule(org.openscience.cdk.interfaces.IMolecule mol, org.openscience.cdk.interfaces.IMolecule molWithH, java.util.Date now, java.lang.String casNumber, int userKey, java.lang.String smilesNonChiral, java.lang.String smilesChiral, boolean isChiral, int numberOfAtomsInMdl, org.openscience.cdk.tools.MFAnalyser mfa, org.openscience.cdk.interfaces.IRingSet allrings, int sssr)
Constructor for the DBMolecule object

Method Summary

org.openscience.cdk.interfaces.IMolecule	addCdkCoords(java.sql.Connection conn, org.openscience.cdk.interfaces.IMolecule mol, int[] atoms) Adds 3d coords from cdk modelbuilder3d to this molecule.
private java.lang.String	addSymbolToFormula(java.util.SortedMap sm, java.lang.String symbol, java.lang.String formula, boolean withFormat) Adds an element to a chemical formual string
void	addValuesToSubmittingData(SubmittingData subData, DBSpectrum spectrum, boolean no3d) Adds values of an existing molecule to a SubmittingData object.
java.util.List	containsDoubleBondsSpecified() Tells if any double bond is specified in this molecule
void	delete(java.sql.Connection dbconn) Deletes this molecule plus all associated rows (including spectra, independent of review flag).
org.openscience.cdk.interfaces.IMolecule	getAsCDKMolecule(int setid) Gets this molecule as a CDK Molecule object, with all Hs.
static org.openscience.cdk.interfaces.IMolecule	getAsCDKMolecule(int molid, int coordinateSetId) Gets a molecule with a certain ID a CDK Molecule object, with all Hs.
org.openscience.cdk.interfaces.IMolecule	getAsCDKMoleculeAsEntered(int setid, boolean setImplicitHydrogens) Gets this molecule as a cdk molecule with explicit hs as painted by user.
static org.openscience.cdk.interfaces.IMolecule	getAsCDKMoleculeFromId(int molid) Gets a molecule as a cdk molecule with the user input coordinates, with all Hs.
org.openscience.cdk.interfaces.IMolecule	getAsCDKMoleculeWithAny3d() Gets this molecule as a CDK Molecule object, with 3d coordinates, if any, or null.
org.openscience.cdk.interfaces.IMolecule	getAsCDKMoleculeWithoutH() Gets this molecule as a CDK Molecule object without the Hs
org.openscience.cdk.interfaces.IMolecule	getAsCDKMoleculeWithoutHAndCount() Gets this molecule as a CDK Molecule object without the Hs and h counts.
DBAtom	getAtomAt(int i) Gets the atom with mdl number i.
DBAtom	getAtomByHoseCode(java.lang.String hc) Gets an atom of this molecule with a HOSE code starting with hc.
DBAtom[]	getAtomsAsArrayInMdlOrder() Gets the atoms of this molecule as Array In Order of mdl numbers.
static DBAtom[]	getAtomsAsArrayInMdlOrder(int molid, java.util.HashMap map) Gets the atoms of a molecule as Array In Order of mdl numbers.
DBAtom[]	getAtomsAsArrayInMdlOrderWithoutHs() Gets the atoms of this molecule as Array In Order of mdl numbers without Hs.
static DBAtom[]	getAtomsAsArrayInMdlOrderWithoutHs(int molid, java.util.HashMap map) Gets the atoms of a molecule as Array In Order of mdl numbers without the Hs.
java.lang.String	getAutonomeName() Gets the autonomeName attribute of the DBMolecule object
java.util.List	getBonds() Gets all DBBond objects connected with this DBMolecule
java.lang.String	getCanonicalName() Gets the canonicalName of the DBMolecule object as a string, the names shortened and with a link to complete name.
java.lang.String	getCanonicalNameNormal() Gets the canonicalName of the DBMolecule object as a string
java.lang.String	getChemicalNamesAsOneString(boolean escapeForHtml) Gets the chemical names of the DBMolecule object as one string with ; seperation
java.lang.String	getChemicalNamesAsOneString(boolean escapeForHtml, boolean cr) Gets the chemical names of the DBMolecule object as one string with either ; or \n\r seperation.
java.lang.String	getChemicalNamesAsOneStringWithCR(boolean escapeForHtml) Gets the chemical names of the DBMolecule object as one string mit /n/r seperation
java.lang.String	getChemicalNamesAsOneStringWithFallback() Gets the chemical names of the DBMolecule object as one string with either ; seperation and fallback to canonicalname/smiles.
java.lang.String	getChemicalNamesMaxChars() Gets the chemicalNamesMaxChars attribute of the DBMolecule object
java.lang.String	getChemicalNamesOrId() Gets the chemicalNames or, if empty, the id attribute of the DBMolecule object.
nu.xom.Element	getCML(int setid) Gets this molecule as CML, with Hs as entered.
nu.xom.Element	getCML(int setid, boolean withh) Gets this molecule as CML.
java.lang.String	getCMLString(int setid) Gets this molecule as CML as a string.
java.lang.String	getCommentAsOneString() Gets the comments of all spectra of this molecule as one string with ; seperation
java.lang.String	getCondition(java.lang.String conditionName) Gets the conditions of a certain type of the spectra of this molecule.
java.util.List	getCoordinateSetNames() Gets the coordinateSetNames attribute of the DBMolecule object
DBWishlist	getDBWishlist(int pk)
java.lang.String	getEasylink(javax.servlet.http.HttpServletRequest req) Gets a link for imediate display of this molecule.
java.lang.String	getFilename() Gets the filename attribute of the DBMolecule object
int	getIdOfUnreviewedSpectrum(NmrshiftdbUser user) Gets the id of an unreviewed spectrum of this molecule assigned to a certain user.
java.lang.String	getInchi() Gets the inchi (from db, not generatad) for this molecule.
java.lang.String	getIsomerLinks(java.lang.String lastaction, java.lang.String molnumber, java.lang.String startmolecule, javax.servlet.http.HttpSession session) Builds a link to isomers of this molecule.
java.lang.String	getKeywords() Gets the keywords of the DBMolecule object as one string with ; seperation
java.lang.String	getKeywords(boolean separatedByNewline) Gets the keywords of the DBMolecule object as one string with ; or \n\r seperation.
java.util.List	getLinks() Gets the links of the DBMolecule object
java.lang.String	getLinksAsString() Gets the links+their descriptoin of the DBMolecule object as one string with one links+description in one line
java.lang.String	getLiteratureAsOneString() Gets the literature attributes of all spectra of the DBMolecule object as one string with ; seperation
java.lang.String	getMolecularFormula(boolean withFormat) Gets the molecular formula of the DBMolecule object.
float	getMolecularWeightFloat() Get the MolecularWeight
java.lang.String	getMoleculeKeywordsAsOneString() Gets the keywords of the DBMolecule object as one string with ; seperation
java.lang.String	getMoleculeKeywordsAsOneString(java.lang.String separator) Gets the keywords of the DBMolecule object as one string with a given seperation
java.lang.String	getMoleculeLinksAsOneString() Gets the description of the links of the DBMolecule object as one string with ; seperation
java.lang.String	getMySpectraInscription(org.apache.turbine.om.security.User user) Gets the inscription of the result field if a user wants to see his spectra
java.util.List<java.util.List<java.lang.Integer>>	getNewMoleculeIdsOfOldSpectra() Gets the current moleculeIds of all spectra, which were once assigned to this molecule and have been edited and are now assigned to another spectrum.
int	getNumberOfNonHAtoms() Gets the number of non-H atoms of the DBMolecule object
java.lang.String	getSmilesStringChiralStr() Gets the smilesStringChiral attribute of the DBMolecule object as a string.
java.lang.String	getSmilesStringStr() Gets the smilesString attribute of the DBMolecule object as a string.
java.lang.String	getSpectrumIds() Gets a string with the ids of all valid spectra of this molecule
java.lang.String	getSpectrumKeywordsAsOneString() Gets the keywords of all spectra of the DBMolecule object as one string with ; seperation
java.lang.String	getSpectrumLinksAsOneString() Gets the links of all spectra of the DBMolecule object as one string with ; seperation
java.lang.String	getStructureFile(int setid, boolean fallback) Gets this molecule as an MDL mol file, with Hs entered by user as explicit Hs, with no sdfields.
java.lang.String	getStructureFile(int setid, java.util.Map map, boolean fallback) Gets this molecule as an MDL mol file, with Hs entered by user as explicit Hs.
void	handleFingerprints1() Sets fingerprints to 0 and saves old values.
void	handleFingerprints2(java.sql.Connection dbconn) Inserts fingerprint values from handleFingerprints1 via a prepared statement.
boolean	hasAny3d()
boolean	hasCoordinates(int setid) Tells if a coordinateset with setid exists.
boolean	isChiral() Tells if this molecule contains any valid chirality (i.
void	save() A save which handles fingerprints via prepared statements, avoiding sql problems.
void	save(java.sql.Connection dbconn) A save which handles fingerprints via prepared statements, avoiding sql problems.
java.util.List	selectNonHAtoms() Gets the non-H atoms of the DBMolecule
java.util.List	selectSpectra() Gets the DBSpectra associated with this DBMolecule (reviewed as true)
java.util.List	selectSpectra(int editSpectrum) Gets the DBSpectra associated with this DBMolecule (reviewed as true) except one given by editSpectrum.
java.util.Vector	selectSpectra(long fingerprint) Gets the DBSpectra associated with this DBMolecule and matching a fingerprint
java.util.List	selectSpectraByUser(org.apache.jetspeed.om.security.turbine.TurbineUser turbineUser, boolean trueOnly) Gets the DBSpectra of a certain user associated with this DBMolecule (reviewed as true, false, rejected)
void	setFingerprint() Sets the fingerprint values of the DBMolecule object, taking the molecule from db.
void	setFingerprint(org.openscience.cdk.interfaces.IMolecule mol) Sets the fingerprint values of the DBMolecule object.

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

addDBAtom, addDBBookmark, addDBCanonicalName, addDBChemicalName, addDBMoleculeDBKeyword, addDBMoleculeHyperlink, addDBSample, addDBSpectrum, addDBWishlist, copy, copyInto, getByName, getByPeerName, getByPosition, getCasNumber, getComment, getDate, getDBAtoms, getDBAtoms, getDBAtoms, getDBAtoms, getDBAtomsJoinDBMolecule, getDBBookmarks, getDBBookmarks, getDBBookmarks, getDBBookmarks, getDBBookmarksJoinDBMolecule, getDBBookmarksJoinNmrshiftdbUser, getDBCanonicalNames, getDBCanonicalNames, getDBCanonicalNames, getDBCanonicalNames, getDBCanonicalNamesJoinDBCanonicalNameType, getDBCanonicalNamesJoinDBMolecule, getDBChemicalNames, getDBChemicalNames, getDBChemicalNames, getDBChemicalNames, getDBChemicalNamesJoinDBMolecule, getDbe, getDBMoleculeDBKeywords, getDBMoleculeDBKeywords, getDBMoleculeDBKeywords, getDBMoleculeDBKeywords, getDBMoleculeDBKeywordsJoinDBKeyword, getDBMoleculeDBKeywordsJoinDBMolecule, getDBMoleculeHyperlinks, getDBMoleculeHyperlinks, getDBMoleculeHyperlinks, getDBMoleculeHyperlinks, getDBMoleculeHyperlinksJoinDBMolecule, getDBSamples, getDBSamples, getDBSamples, getDBSamples, getDBSamplesJoinDBCondition, getDBSamplesJoinDBMachine, getDBSamplesJoinDBMolecule, getDBSamplesJoinNmrshiftdbUser, getDBSpectrums, getDBSpectrums, getDBSpectrums, getDBSpectrums, getDBSpectrumsJoinDBMolecule, getDBSpectrumsJoinDBSpectrumType, getDBSpectrumsJoinNmrshiftdbUser, getDBWishlists, getDBWishlists, getDBWishlists, getDBWishlists, getDBWishlistsJoinDBMolecule, getDBWishlistsJoinDBSpectrumType, getDBWishlistsJoinNmrshiftdbUser, getFieldNames, getFp0, getFp1, getFp10, getFp11, getFp12, getFp13, getFp14, getFp15, getFp2, getFp3, getFp4, getFp5, getFp6, getFp7, getFp8, getFp9, getMolecularWeight, getMoleculeId, getNmrshiftdbUser, getPeer, getPrimaryKey, getSar, getSmilesString, getSmilesStringChiral, getSssr, getUserId, initDBAtoms, initDBBookmarks, initDBCanonicalNames, initDBChemicalNames, initDBMoleculeDBKeywords, initDBMoleculeHyperlinks, initDBSamples, initDBSpectrums, initDBWishlists, save, setCasNumber, setComment, setDate, setDbe, setFp0, setFp1, setFp10, setFp11, setFp12, setFp13, setFp14, setFp15, setFp2, setFp3, setFp4, setFp5, setFp6, setFp7, setFp8, setFp9, setMolecularWeight, setMoleculeId, setNmrshiftdbUser, setNmrshiftdbUserKey, setPrimaryKey, setPrimaryKey, setSar, setSmilesString, setSmilesStringChiral, setSssr, setUserId, 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, setModified, setNew, setPrimaryKey, setPrimaryKey

Field Detail

maxsimilarity

public double maxsimilarity

Description of the Field

cdkMolecule

org.openscience.cdk.interfaces.IMolecule cdkMolecule

setid

int setid

cdkMoleculeWithoutHs

org.openscience.cdk.interfaces.IMolecule cdkMoleculeWithoutHs

cdkMoleculeWithoutHsAndCount

org.openscience.cdk.interfaces.IMolecule cdkMoleculeWithoutHsAndCount

filename

java.lang.String filename

dbatoms

DBAtom[] dbatoms

fppro

long[] fppro

keywordsVector

java.util.List keywordsVector

autonomeName

java.lang.String autonomeName

allrings

org.openscience.cdk.interfaces.IRingSet allrings

Constructor Detail

DBMolecule

public DBMolecule()

Constructor for the DBMolecule object

DBMolecule

public DBMolecule(org.openscience.cdk.interfaces.IMolecule mol,
                  org.openscience.cdk.interfaces.IMolecule molWithH,
                  java.util.Date now,
                  java.lang.String casNumber,
                  int userKey,
                  java.lang.String smilesNonChiral,
                  java.lang.String smilesChiral,
                  boolean isChiral,
                  int numberOfAtomsInMdl,
                  org.openscience.cdk.tools.MFAnalyser mfa,
                  org.openscience.cdk.interfaces.IRingSet allrings,
                  int sssr)
           throws java.lang.Exception

Constructor for the DBMolecule object

Parameters:

mol - The molecule without Hs.

molWithH - The molecule with Hs.

now - Save time.

casNumber - cas number.

nmrshiftdbnr - nmrshiftdb number.

userKey - UserId of submitting user.

smilesNonChiral - The non chiral smiles.

smilesChiral - The chiral smiles.

isChiral - Is the molecule chiral.

numberOfAtomsInMdl - atom count of molecule.

mfa - an mfa of this molecule.

Throws:

java.lang.Exception - Description of Exception.

Method Detail

getAsCDKMoleculeFromId

public static org.openscience.cdk.interfaces.IMolecule getAsCDKMoleculeFromId(int molid)
                                                                       throws java.lang.Exception

Gets a molecule as a cdk molecule with the user input coordinates, with all Hs.

Parameters:

molid - The id of the molecule to return.

Returns:

The CDK Molecule.

Throws:

java.lang.Exception - Database problems.

getAsCDKMolecule

public static org.openscience.cdk.interfaces.IMolecule getAsCDKMolecule(int molid,
                                                                        int coordinateSetId)
                                                                 throws org.apache.torque.TorqueException,
                                                                        java.io.OptionalDataException,
                                                                        java.io.IOException,
                                                                        com.workingdogs.village.DataSetException

Gets a molecule with a certain ID a CDK Molecule object, with all Hs.

Parameters:

molid - The id of the molecule to be build.

coordinateSetId - The coordinate set type id of the coordinate to include.

Returns:

The CDK Molecule.

Throws:

org.apache.torque.TorqueException - Database problems.

java.io.IOException

java.io.OptionalDataException

com.workingdogs.village.DataSetException

getAtomsAsArrayInMdlOrder

public static DBAtom[] getAtomsAsArrayInMdlOrder(int molid,
                                                 java.util.HashMap map)
                                          throws org.apache.torque.TorqueException

Gets the atoms of a molecule as Array In Order of mdl numbers.

Parameters:

molid - The molecule of which the atoms are wished.

map - This map gets filled with (atomId, mdl number) pairs if !=null.

Returns:

The atomsAsArrayInMdlOrder value.

Throws:

org.apache.torque.TorqueException - Database problems.

getAtomsAsArrayInMdlOrderWithoutHs

public static DBAtom[] getAtomsAsArrayInMdlOrderWithoutHs(int molid,
                                                          java.util.HashMap map)
                                                   throws java.lang.Exception

Gets the atoms of a molecule as Array In Order of mdl numbers without the Hs.

Parameters:

molid - The molecule of which the atoms are wished.

map - This map gets filled with (atomId, mdl number) pairs if !=null.

Returns:

The atomsAsArrayInMdlOrder value.

Throws:

java.lang.Exception - Database problems.

getAtomAt

public DBAtom getAtomAt(int i)
                 throws java.lang.Exception

Gets the atom with mdl number i.

Parameters:

i - atom number to find

Returns:

The atom at i.

Throws:

java.lang.Exception

setFingerprint

public void setFingerprint()
                    throws org.apache.torque.TorqueException,
                           org.openscience.cdk.exception.CDKException

Sets the fingerprint values of the DBMolecule object, taking the molecule from db.

Throws:

java.lang.Exception - Description of Exception,

org.apache.torque.TorqueException

org.openscience.cdk.exception.CDKException

setFingerprint

public void setFingerprint(org.openscience.cdk.interfaces.IMolecule mol)
                    throws org.apache.torque.TorqueException

Sets the fingerprint values of the DBMolecule object.

Parameters:

mol - The cdk molecule of this molecule

Throws:

java.lang.Exception - Description of Exception.

org.apache.torque.TorqueException

getAutonomeName

public java.lang.String getAutonomeName()
                                 throws java.lang.Exception

Gets the autonomeName attribute of the DBMolecule object

Returns:

The autonomeName value

Throws:

java.lang.Exception - Description of Exception

getNumberOfNonHAtoms

public int getNumberOfNonHAtoms()
                         throws java.lang.Exception

Gets the number of non-H atoms of the DBMolecule object

Returns:

The numberOfNonHAtoms value

Throws:

java.lang.Exception - Something wrong with reading database

getLinks

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

Gets the links of the DBMolecule object

Returns:

The links

Throws:

java.lang.Exception - Database problems

getChemicalNamesAsOneString

public java.lang.String getChemicalNamesAsOneString(boolean escapeForHtml)
                                             throws java.lang.Exception

Gets the chemical names of the DBMolecule object as one string with ; seperation

Parameters:

escapeForHtml - true=make html code of ' and ", false=esacpe them with \

Returns:

The chemical names

Throws:

java.lang.Exception - Something wrong with reading database

getChemicalNamesAsOneString

public java.lang.String getChemicalNamesAsOneString(boolean escapeForHtml,
                                                    boolean cr)
                                             throws org.apache.torque.TorqueException

Gets the chemical names of the DBMolecule object as one string with either ; or \n\r seperation.

Parameters:

escapeForHtml - true=make html code of ' and ", false=esacpe them with \.

cr - true=use \n\r, false=use ;.

Returns:

The chemical names.

Throws:

org.apache.torque.TorqueException - Something wrong with reading database.

getChemicalNamesAsOneStringWithFallback

public java.lang.String getChemicalNamesAsOneStringWithFallback()
                                                         throws org.apache.torque.TorqueException

Gets the chemical names of the DBMolecule object as one string with either ; seperation and fallback to canonicalname/smiles.

Returns:

The chemicalNamesAsOneStringWithFallback value

Throws:

org.apache.torque.TorqueException - Something wrong with reading database

getChemicalNamesMaxChars

public java.lang.String getChemicalNamesMaxChars()
                                          throws java.lang.Exception

Gets the chemicalNamesMaxChars attribute of the DBMolecule object

Returns:

The chemicalNamesMaxChars value

Throws:

java.lang.Exception - Description of Exception

getMoleculeLinksAsOneString

public java.lang.String getMoleculeLinksAsOneString()
                                             throws java.lang.Exception

Gets the description of the links of the DBMolecule object as one string with ; seperation

Returns:

The moleculeLinksAsOneString value

Throws:

java.lang.Exception - Something wrong with reading database

getMoleculeKeywordsAsOneString

public java.lang.String getMoleculeKeywordsAsOneString()
                                                throws java.lang.Exception

Gets the keywords of the DBMolecule object as one string with ; seperation

Returns:

The moleculeKeywordsAsOneString value

Throws:

java.lang.Exception - Something wrong with reading database

getMoleculeKeywordsAsOneString

public java.lang.String getMoleculeKeywordsAsOneString(java.lang.String separator)
                                                throws java.lang.Exception

Gets the keywords of the DBMolecule object as one string with a given seperation

Parameters:

separator - The separation character

Returns:

The moleculeKeywordsAsOneString value

Throws:

java.lang.Exception - Something wrong with reading database

getSpectrumKeywordsAsOneString

public java.lang.String getSpectrumKeywordsAsOneString()
                                                throws java.lang.Exception

Gets the keywords of all spectra of the DBMolecule object as one string with ; seperation

Returns:

The spectrumKeywordsAsOneString value

Throws:

java.lang.Exception - Something wrong with reading database

getLiteratureAsOneString

public java.lang.String getLiteratureAsOneString()
                                          throws java.lang.Exception

Gets the literature attributes of all spectra of the DBMolecule object as one string with ; seperation

Returns:

The literatureAsOneString value

Throws:

java.lang.Exception - Something wrong with reading database

getCommentAsOneString

public java.lang.String getCommentAsOneString()
                                       throws java.lang.Exception

Gets the comments of all spectra of this molecule as one string with ; seperation

Returns:

The commentAsOneString value

Throws:

java.lang.Exception - Something wrong with reading database

getSpectrumLinksAsOneString

public java.lang.String getSpectrumLinksAsOneString()
                                             throws java.lang.Exception

Gets the links of all spectra of the DBMolecule object as one string with ; seperation

Returns:

The spectrumLinksAsOneString value

Throws:

java.lang.Exception - Something wrong with reading database

getChemicalNamesAsOneStringWithCR

public java.lang.String getChemicalNamesAsOneStringWithCR(boolean escapeForHtml)
                                                   throws java.lang.Exception

Gets the chemical names of the DBMolecule object as one string mit /n/r seperation

Parameters:

escapeForHtml - true=make html code of ' and ", false=esacpe them with \

Returns:

The chemical names

Throws:

java.lang.Exception - Something wrong with reading database

getLinksAsString

public java.lang.String getLinksAsString()
                                  throws java.lang.Exception

Gets the links+their descriptoin of the DBMolecule object as one string with one links+description in one line

Returns:

The links value

Throws:

java.lang.Exception - Something wrong with reading database

getKeywords

public java.lang.String getKeywords()
                             throws java.lang.Exception

Gets the keywords of the DBMolecule object as one string with ; seperation

Returns:

The keywords value

Throws:

java.lang.Exception - Something wrong with reading database

getKeywords

public java.lang.String getKeywords(boolean separatedByNewline)
                             throws java.lang.Exception

Gets the keywords of the DBMolecule object as one string with ; or \n\r seperation. or

Parameters:

separatedByNewline - true=use \n\r, false=use ;.

Returns:

The keywords value.

Throws:

java.lang.Exception - Something wrong with reading database.

getCanonicalNameNormal

public java.lang.String getCanonicalNameNormal()
                                        throws org.apache.torque.TorqueException

Gets the canonicalName of the DBMolecule object as a string

Returns:

The canonicalName value

Throws:

org.apache.torque.TorqueException - Description of Exception

getCanonicalName

public java.lang.String getCanonicalName()
                                  throws java.lang.Exception

Gets the canonicalName of the DBMolecule object as a string, the names shortened and with a link to complete name.

Returns:

The canonicalName value

Throws:

java.lang.Exception - Description of Exception

getBonds

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

Gets all DBBond objects connected with this DBMolecule

Returns:

The bonds value

Throws:

java.lang.Exception - Something wrong with reading database

getMySpectraInscription

public java.lang.String getMySpectraInscription(org.apache.turbine.om.security.User user)
                                         throws java.lang.Exception

Gets the inscription of the result field if a user wants to see his spectra

Parameters:

user - The user logged in

Returns:

The mySpectraInscription value

Throws:

java.lang.Exception - Database problems

getAsCDKMolecule

public org.openscience.cdk.interfaces.IMolecule getAsCDKMolecule(int setid)
                                                          throws org.apache.torque.TorqueException,
                                                                 java.io.OptionalDataException,
                                                                 java.io.IOException,
                                                                 com.workingdogs.village.DataSetException

Gets this molecule as a CDK Molecule object, with all Hs.

Parameters:

setid - The coordinate set id of coordinate set to use..

Returns:

The CDK Molecule.

Throws:

org.apache.torque.TorqueException - Database problems.

java.io.IOException

java.io.OptionalDataException

com.workingdogs.village.DataSetException

getAsCDKMoleculeWithAny3d

public org.openscience.cdk.interfaces.IMolecule getAsCDKMoleculeWithAny3d()
                                                                   throws org.apache.torque.TorqueException,
                                                                          java.io.OptionalDataException,
                                                                          java.io.IOException,
                                                                          com.workingdogs.village.DataSetException

Gets this molecule as a CDK Molecule object, with 3d coordinates, if any, or null.

Returns:

The CDK Molecule with 3d coords or null.

Throws:

org.apache.torque.TorqueException - Database problems.

com.workingdogs.village.DataSetException

java.io.IOException

java.io.OptionalDataException

getStructureFile

public java.lang.String getStructureFile(int setid,
                                         boolean fallback)
                                  throws org.apache.torque.TorqueException

Gets this molecule as an MDL mol file, with Hs entered by user as explicit Hs, with no sdfields.

Parameters:

setid - The coordinate set id of coordinate set to use.

fallbak - true=use coord set 1 if coord setid do not exist, false=fail.

Returns:

The mol file.

Throws:

java.lang.Exception - Database problems.

org.apache.torque.TorqueException

getStructureFile

public java.lang.String getStructureFile(int setid,
                                         java.util.Map map,
                                         boolean fallback)
                                  throws org.apache.torque.TorqueException

Gets this molecule as an MDL mol file, with Hs entered by user as explicit Hs.

Parameters:

setid - The coordinate set id of coordinate set to use.

map - Data to put in the file as sd fields.

fallbak - true=use coord set 1 if coord setid do not exist, false=fail.

Returns:

The mol file.

Throws:

java.lang.Exception - Database problems.

org.apache.torque.TorqueException

hasCoordinates

public boolean hasCoordinates(int setid)
                       throws org.apache.torque.TorqueException

Tells if a coordinateset with setid exists.

Parameters:

setid - The coordinate set id of coordinate set to look for.

Throws:

java.lang.Exception - Database problems.

org.apache.torque.TorqueException

getCML

public nu.xom.Element getCML(int setid,
                             boolean withh)
                      throws org.xmlcml.cml.base.CMLException,
                             java.lang.Exception

Gets this molecule as CML.

Parameters:

setid - The coordinate set to use

withh - Shall implicit hs be reported?

Returns:

The cml.

Throws:

java.lang.Exception - Database problems.

org.xmlcml.cml.base.CMLException - Description of Exception

getCML

public nu.xom.Element getCML(int setid)
                      throws org.xmlcml.cml.base.CMLException,
                             java.lang.Exception

Gets this molecule as CML, with Hs as entered.

Returns:

The cml.

Throws:

java.lang.Exception - Database problems.

org.xmlcml.cml.base.CMLException - Description of Exception

getCMLString

public java.lang.String getCMLString(int setid)
                              throws javax.xml.transform.TransformerConfigurationException,
                                     javax.xml.transform.TransformerException,
                                     org.xmlcml.cml.base.CMLException,
                                     java.lang.Exception

Gets this molecule as CML as a string.

Returns:

The cml.

Throws:

java.lang.Exception - Database problems.

javax.xml.transform.TransformerConfigurationException - Description of Exception

javax.xml.transform.TransformerException - Description of Exception

org.xmlcml.cml.base.CMLException - Description of Exception

getAsCDKMoleculeWithoutHAndCount

public org.openscience.cdk.interfaces.IMolecule getAsCDKMoleculeWithoutHAndCount()
                                                                          throws java.io.IOException,
                                                                                 java.lang.ClassNotFoundException,
                                                                                 java.lang.Exception

Gets this molecule as a CDK Molecule object without the Hs and h counts.

Returns:

The asCDKMolecule value

Throws:

java.io.IOException - Description of Exception

java.lang.ClassNotFoundException - Description of Exception

java.lang.Exception - Description of Exception

getAsCDKMoleculeWithoutH

public org.openscience.cdk.interfaces.IMolecule getAsCDKMoleculeWithoutH()
                                                                  throws java.io.IOException,
                                                                         java.lang.ClassNotFoundException,
                                                                         java.lang.Exception

Gets this molecule as a CDK Molecule object without the Hs

Returns:

The asCDKMolecule value

Throws:

java.io.IOException - Description of Exception

java.lang.ClassNotFoundException - Description of Exception

java.lang.Exception - Description of Exception

getCondition

public java.lang.String getCondition(java.lang.String conditionName)
                              throws java.lang.Exception

Gets the conditions of a certain type of the spectra of this molecule.

Parameters:

conditionName - The condition type the conditions should be of.

Returns:

A string with all conditions.

Throws:

java.lang.Exception - Database problems.

getChemicalNamesOrId

public java.lang.String getChemicalNamesOrId()
                                      throws java.lang.Exception

Gets the chemicalNames or, if empty, the id attribute of the DBMolecule object.

Returns:

The chemicalNames or id value.

Throws:

java.lang.Exception - Description of Exception

getAtomsAsArrayInMdlOrder

public DBAtom[] getAtomsAsArrayInMdlOrder()
                                   throws org.apache.torque.TorqueException

Gets the atoms of this molecule as Array In Order of mdl numbers.

Returns:

The atomsAsArrayInMdlOrder value.

Throws:

org.apache.torque.TorqueException - Database problems.

getAtomsAsArrayInMdlOrderWithoutHs

public DBAtom[] getAtomsAsArrayInMdlOrderWithoutHs()
                                            throws java.lang.Exception

Gets the atoms of this molecule as Array In Order of mdl numbers without Hs.

Returns:

The atomsAsArrayInMdlOrder value.

Throws:

java.lang.Exception - Database problems.

getMolecularFormula

public java.lang.String getMolecularFormula(boolean withFormat)
                                     throws java.lang.Exception

Gets the molecular formula of the DBMolecule object.

Parameters:

withFormat - true=formula gets formatted with html, false=plain text.

Returns:

The molecular formula value.

Throws:

java.lang.Exception - Description of Exception

getFilename

public java.lang.String getFilename()

Gets the filename attribute of the DBMolecule object

Returns:

The filename value

getIdOfUnreviewedSpectrum

public int getIdOfUnreviewedSpectrum(NmrshiftdbUser user)
                              throws java.lang.Exception

Gets the id of an unreviewed spectrum of this molecule assigned to a certain user.

Parameters:

user - The user the spectrum should be assigned to.

Returns:

The id of an unreviewed spectrum.

Throws:

java.lang.Exception - Database problems.

getIsomerLinks

public java.lang.String getIsomerLinks(java.lang.String lastaction,
                                       java.lang.String molnumber,
                                       java.lang.String startmolecule,
                                       javax.servlet.http.HttpSession session)
                                throws java.lang.Exception

Builds a link to isomers of this molecule.

Parameters:

lastaction - The current action parameter.

molnumber - The current molnumber parameter, used for display of resultsPortlet.

startmolecule - The current startmolecule parameter, used for display of resultsPortlet.

Returns:

The isomerLinks value.

Throws:

java.lang.Exception - Database problems.

getSmilesStringStr

public java.lang.String getSmilesStringStr()

Gets the smilesString attribute of the DBMolecule object as a string.

Returns:

The smilesString value

getSmilesStringChiralStr

public java.lang.String getSmilesStringChiralStr()

Gets the smilesStringChiral attribute of the DBMolecule object as a string.

Returns:

The smilesStringChiral value.

isChiral

public boolean isChiral()

Tells if this molecule contains any valid chirality (i. e. if the chiral smiles is different from normal smiles)

Returns:

true/false

getEasylink

public java.lang.String getEasylink(javax.servlet.http.HttpServletRequest req)

Gets a link for imediate display of this molecule.

Parameters:

req - The current requst.

Returns:

The easylink value.

getAtomByHoseCode

public DBAtom getAtomByHoseCode(java.lang.String hc)
                         throws java.lang.Exception

Gets an atom of this molecule with a HOSE code starting with hc.

Parameters:

hc - The HOSE code start wished.

Returns:

An atom having hc.

Throws:

java.lang.Exception - Description of Exception.

getCoordinateSetNames

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

Gets the coordinateSetNames attribute of the DBMolecule object

Returns:

The coordinateSetNames value

Throws:

java.lang.Exception - Description of Exception

selectSpectra

public java.util.List selectSpectra()
                             throws org.apache.torque.TorqueException

Gets the DBSpectra associated with this DBMolecule (reviewed as true)

Returns:

The spectra

Throws:

java.lang.Exception - Something wrong with reading database

org.apache.torque.TorqueException

selectSpectra

public java.util.List selectSpectra(int editSpectrum)
                             throws org.apache.torque.TorqueException

Gets the DBSpectra associated with this DBMolecule (reviewed as true) except one given by editSpectrum.

Parameters:

editSpectrum - The spectrum to be ignored, null if nothing to ignore.

Returns:

The spectra.

Throws:

java.lang.Exception - Something wrong with reading database.

org.apache.torque.TorqueException

selectSpectraByUser

public java.util.List selectSpectraByUser(org.apache.jetspeed.om.security.turbine.TurbineUser turbineUser,
                                          boolean trueOnly)
                                   throws org.apache.torque.TorqueException

Gets the DBSpectra of a certain user associated with this DBMolecule (reviewed as true, false, rejected)

Parameters:

turbineUser - The user of whom the spectra are to be selected

trueOnly - Select only spectra reviewed as true.

Returns:

The spectra

Throws:

org.apache.torque.TorqueException - Something wrong with reading database

selectSpectra

public java.util.Vector selectSpectra(long fingerprint)
                               throws org.apache.torque.TorqueException

Gets the DBSpectra associated with this DBMolecule and matching a fingerprint

Parameters:

fingerprint - The fingerprint to search by

Returns:

The spectra

Throws:

java.lang.Exception - Something wrong with reading database

org.apache.torque.TorqueException

selectNonHAtoms

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

Gets the non-H atoms of the DBMolecule

Returns:

The atoms

Throws:

java.lang.Exception - Something wrong with reading database

containsDoubleBondsSpecified

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

Tells if any double bond is specified in this molecule

Returns:

True=at least one is specified, false=none is specified

Throws:

java.lang.Exception - Database problems

delete

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

Deletes this molecule plus all associated rows (including spectra, independent of review flag).

Parameters:

dbconn - The connection to use.

Throws:

java.lang.Exception - Database problems.

addValuesToSubmittingData

public void addValuesToSubmittingData(SubmittingData subData,
                                      DBSpectrum spectrum,
                                      boolean no3d)
                               throws java.io.IOException,
                                      java.lang.Exception

Adds values of an existing molecule to a SubmittingData object.

Parameters:

subData - The SubmittingData object.

spectrum - The feature to be added to the ValuesToSubmittingData attribute

no3d - The feature to be added to the ValuesToSubmittingData attribute

Throws:

java.io.IOException - Problems deserializing molecule.

java.lang.Exception - Database problems.

save

public void save()
          throws org.apache.torque.TorqueException

A save which handles fingerprints via prepared statements, avoiding sql problems.

Specified by:

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

Overrides:

save in class BaseDBMolecule

Throws:

java.lang.Exception - Description of Exception

org.apache.torque.TorqueException

save

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

A save which handles fingerprints via prepared statements, avoiding sql problems.

Specified by:

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

Overrides:

save in class BaseDBMolecule

Parameters:

dbconn - Description of Parameter

Throws:

java.lang.Exception - Description of Exception

org.apache.torque.TorqueException

handleFingerprints1

public void handleFingerprints1()

Sets fingerprints to 0 and saves old values.

handleFingerprints2

public void handleFingerprints2(java.sql.Connection dbconn)
                         throws org.apache.torque.TorqueException,
                                java.sql.SQLException

Inserts fingerprint values from handleFingerprints1 via a prepared statement.

Parameters:

dbconn - Description of Parameter

Throws:

java.lang.Exception - Description of Exception

org.apache.torque.TorqueException

java.sql.SQLException

getAsCDKMoleculeAsEntered

public org.openscience.cdk.interfaces.IMolecule getAsCDKMoleculeAsEntered(int setid,
                                                                          boolean setImplicitHydrogens)
                                                                   throws org.apache.torque.TorqueException,
                                                                          java.io.OptionalDataException,
                                                                          java.io.IOException,
                                                                          com.workingdogs.village.DataSetException

Gets this molecule as a cdk molecule with explicit hs as painted by user. Implicit Hs are set to total count (including explicit ones).

Parameters:

setid - The coordinate set type id of coordinate set to use.

Returns:

The molecule.

Throws:

org.apache.torque.TorqueException - Database problems.

java.io.IOException

java.io.OptionalDataException

com.workingdogs.village.DataSetException

addSymbolToFormula

private java.lang.String addSymbolToFormula(java.util.SortedMap sm,
                                            java.lang.String symbol,
                                            java.lang.String formula,
                                            boolean withFormat)

Adds an element to a chemical formual string

Parameters:

sm - The map containing the elements

symbol - The symbol to add

formula - The chemical formula

withFormat - The feature to be added to the SymbolToFormula attribute

Returns:

Description of the Returned Value

getMolecularWeightFloat

public float getMolecularWeightFloat()

Get the MolecularWeight

Returns:

double

addCdkCoords

public org.openscience.cdk.interfaces.IMolecule addCdkCoords(java.sql.Connection conn,
                                                             org.openscience.cdk.interfaces.IMolecule mol,
                                                             int[] atoms)
                                                      throws java.lang.Exception

Adds 3d coords from cdk modelbuilder3d to this molecule.

Parameters:

conn - DBConnection to use.

mol - This molecule as cdk molecule.

atoms - DBAtoms of this molecule.

Returns:

mol with 3d coords added.

Throws:

java.lang.Exception - Database problems.

getDBWishlist

public DBWishlist getDBWishlist(int pk)
                         throws java.lang.Exception

Throws:

java.lang.Exception

hasAny3d

public boolean hasAny3d()
                 throws java.lang.Exception

Throws:

java.lang.Exception

getInchi

public java.lang.String getInchi()
                          throws org.apache.torque.TorqueException

Gets the inchi (from db, not generatad) for this molecule.

Returns:

The inchi.

Throws:

org.apache.torque.TorqueException - Database problems.

getSpectrumIds

public java.lang.String getSpectrumIds()
                                throws org.apache.torque.TorqueException

Gets a string with the ids of all valid spectra of this molecule

Returns:

The string

Throws:

org.apache.torque.TorqueException - Database problems

getNewMoleculeIdsOfOldSpectra

public java.util.List<java.util.List<java.lang.Integer>> getNewMoleculeIdsOfOldSpectra()
                                                                                throws org.apache.torque.TorqueException

Gets the current moleculeIds of all spectra, which were once assigned to this molecule and have been edited and are now assigned to another spectrum.

Returns:

The ids.

Throws:

org.apache.torque.TorqueException - Database problems.