verhaar.query

Class FunctionalGroups

java.lang.Object

toxTree.query.FunctionalGroups

verhaar.query.FunctionalGroups

public class FunctionalGroups
extends FunctionalGroups

A singleton class providing static methods for various functional groups in VerhaarScheme. In future could be modified to use a different approach rather than static methods.

Author:

Nina Jeliazkova Modified 2005-10-30

Field Summary

Fields

Modifier and Type	Field and Description
static String	ANILINE
static String	AZARIDINE
static String	BENZYLALCOHOL
static String	CYCLICESTER
static String	EPOXIDE
static String	HALOGEN
static String	HALOGEN_ALPHA_FROM_UNSATURATION
static String	HALOGEN_BETA_FROM_UNSATURATION
static String	IONICGROUP
static String	KETONE_A_B_UNSATURATED
static String	n
static String	PEROXIDE
static String	PHENOL
static String	PYRIDINE
static String	RINGSUBSTITUTED

Fields inherited from class toxTree.query.FunctionalGroups

ACETAL, ACETYLENIC, ALCOHOL, ALDEHYDE, ALLOCATED, ANHYDRIDE, AROMATIC_AMINE, AROMATIC_N_OXIDE, C, CARBONATE, CARBONYL, CARBONYL_ABUNSATURATED, CARBOXYLIC_ACID, CARBOXYLIC_ACID_SALT, CH, CH2, CH3, CYANO, CYCLIC_DIESTER, DIAZO, DONTMARK, ESTER, ETHER, h, HYDROCARBON, HYDROCHLORIDE_OF_AMINE, HYDROXY, HYDROXY1, HYDROXYESTERSUBSTITED, ISOPRENE, KETONE, KETONE_SIDECHAIN, LACTONE, logger, MERCAPTAN, METHOXY, METHYLETHER, MSG_HASGROUP, MSG_MOLECULEIS, NITRO, NNITROSO, PHOSPHATE, POLYOXYETHYLENE, PRIMARY_AMINE, QUATERNARY_NITROGEN, QUATERNARY_NITROGEN_EXCEPTION, RING_NUMBERING, SECONDARY_AMINE, SECONDARY_AMINE_ALIPHATIC, SULPHAMATE, SULPHATE, SULPHATE_OF_AMINE, SULPHIDE, SULPHONATE, TERTIARY_AMINE, THIOESTER, TRIAZENO

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	FunctionalGroups()

Method Summary

Modifier and Type	Method and Description
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	aniline()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	azaridine()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	benzylAlcohol()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	createAutoQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	createAutoQueryContainer(String smiles)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	cyclicEster()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	epoxide()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	halogen()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	halogen(String[] halogens)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	halogenAtAlphaFromUnsaturation(String[] halogens) Halogen at alpha position from unsaturation.
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	halogenAtBetaFromUnsaturation(String[] halogens) Halogen at beta position from unsaturation.
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	ionicGroup()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	ketone_a_b_unsaturated()
static org.openscience.cdk.interfaces.IAtomContainer	makeNitroPhenol()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	peroxide()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	phenol()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	pyridine_character()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	pyridine()
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	ringSubstituted(String substituent)

Methods inherited from class toxTree.query.FunctionalGroups

ab_unsaturated_carbonyl, acetal, acrolein, acrylicAcid, acyclic_acetal, alcohol, alcoholSecondaryAttachedToTerminalVinyl, aldehyde, alkoxy, allylAlcohol, allylAlcoholAcetal, allylAlcoholEsterDerivative, allylAmine, allylMercaptan, allylSulphide, allylThioester, anhydride, associateIonic, carbonate, carbonyl, carboxylicAcid, clearMark, clearMark, clearMarks, cloneDiscardRingAtomAndBonds, createAtomContainer, createAtomContainer, createAtomContainer, createAtomContainer, createAtomContainer, createAtomContainer, createAtomContainer, createQuery, createQuery, cyano, detachGroup, diAzo, ester, esterOfalcoholSecondaryAttachedToTerminalVinyl, ether, ethyl, getAllGroups, getBondMap, getKeyFromMap, getLongestCarbonChainLength, getUniqueBondMap, hasAllSubstructure, hasAnySubstructure, hasAnySubstructure, hasGroup, hasGroup, hasGroup, hasGroup, hasGroupMarked, hasGroupMarked, hasManyDifferentFunctionalGroups, hasMarkedOnlyTheseGroups, hasMarkedOnlyTheseGroups, hasMarkedOnlyTheseGroups, hasOnlyTheseGroups, hasOnlyTheseGroups, hasSubstituents, hydrocarbon, hydrochlorideOfAmine, hydrochlorideOfAmine3, hydrochlorideOfAmineBreakable, hydroxy_ring, hydroxy1, hydroxyEsterSubstituted, isAcetylenic, isCommonTerpene, isCommonTerpene, isCyclicDiester, isopreneUnit, isOverlapped, isSubstance, ketalAttachedToTerminalVinyl, ketone_ring, ketone, ketoneAttachedToTerminalVinyl, lactone, lactoneBreakable, mapHydrocarbon, mapToString, mapToString, mapToString, mark, markAtomsInRing, markCHn, markMaps, markOneMap, markUniqueBondMap, mercaptan, methacrolein, methacroleinAcetal, methacrylicAcid, methoxy_ring, methoxy, methyl, methylether, needsPreprocessing, nitro1double, nitro2double, Nnitroso, noxide_aromatic, phosphate, polyoxyethylene, preProcess, primaryAmine, quarternaryNitrogenException, quaternaryNitrogen1, quaternaryNitrogen2, ring, saltOfCarboxylicAcid, saltOfCarboxylicAcid1, saltOfCarboxylicAcid2, saltOfCarboxylicAcidBreakable, saltOfCarboxylicAcidBreakable1, saltOfCarboxylicAcidBreakable2, secondaryAmine, sidechain_ketone, singleFusedRing, stericallyHindered, sulphamate, sulphate, sulphateOfAmine, sulphateOfAmineBreakable, sulphide, sulphonate, sulphonate, tertiaryAmine, thioester, triAzeno, vicinalDiKetone

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

IONICGROUP

public static final String IONICGROUP

See Also:

Constant Field Values

RINGSUBSTITUTED

public static final String RINGSUBSTITUTED

See Also:

Constant Field Values

HALOGEN_BETA_FROM_UNSATURATION

public static final String HALOGEN_BETA_FROM_UNSATURATION

See Also:

Constant Field Values

HALOGEN_ALPHA_FROM_UNSATURATION

public static final String HALOGEN_ALPHA_FROM_UNSATURATION

See Also:

Constant Field Values

HALOGEN

public static final String HALOGEN

See Also:

Constant Field Values

EPOXIDE

public static final String EPOXIDE

See Also:

Constant Field Values

AZARIDINE

public static final String AZARIDINE

See Also:

Constant Field Values

PEROXIDE

public static final String PEROXIDE

See Also:

Constant Field Values

PHENOL

public static final String PHENOL

See Also:

Constant Field Values

ANILINE

public static final String ANILINE

See Also:

Constant Field Values

PYRIDINE

public static final String PYRIDINE

See Also:

Constant Field Values

BENZYLALCOHOL

public static final String BENZYLALCOHOL

See Also:

Constant Field Values

KETONE_A_B_UNSATURATED

public static final String KETONE_A_B_UNSATURATED

See Also:

Constant Field Values

CYCLICESTER

public static final String CYCLICESTER

See Also:

Constant Field Values

n

public static final String n

See Also:

Constant Field Values

Constructor Detail

FunctionalGroups

protected FunctionalGroups()

Method Detail

ionicGroup

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ionicGroup()

ringSubstituted

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ringSubstituted(String substituent)

halogenAtAlphaFromUnsaturation

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer halogenAtAlphaFromUnsaturation(String[] halogens)

Halogen at alpha position from unsaturation. "X=X[Hal]"

Returns:

halogenAtBetaFromUnsaturation

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer halogenAtBetaFromUnsaturation(String[] halogens)

Halogen at beta position from unsaturation. "X=XX[Hal]"

Returns:

halogen

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer halogen()

halogen

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer halogen(String[] halogens)

epoxide

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer epoxide()
                                                                           throws Exception

Throws:

Exception

azaridine

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer azaridine()
                                                                             throws Exception

Throws:

Exception

peroxide

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer peroxide()
                                                                            throws Exception

Throws:

Exception

phenol

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer phenol()
                                                                          throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

aniline

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer aniline()

pyridine

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer pyridine()

pyridine_character

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer pyridine_character()

benzylAlcohol

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer benzylAlcohol()
                                                                                 throws Exception

Throws:

Exception

ketone_a_b_unsaturated

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ketone_a_b_unsaturated()
                                                                                          throws Exception

Throws:

Exception

makeNitroPhenol

public static org.openscience.cdk.interfaces.IAtomContainer makeNitroPhenol()

createAutoQueryContainer

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createAutoQueryContainer(String smiles)
                                                                                            throws Exception

Throws:

Exception

createAutoQueryContainer

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createAutoQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)

cyclicEster

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer cyclicEster()