verhaar.query
Class FunctionalGroups

java.lang.Object
  extended by toxTree.query.FunctionalGroups
      extended by 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
static java.lang.String ANILINE
           
static java.lang.String AZARIDINE
           
static java.lang.String BENZYLALCOHOL
           
static java.lang.String CYCLICESTER
           
static java.lang.String EPOXIDE
           
static java.lang.String HALOGEN
           
static java.lang.String HALOGEN_ALPHA_FROM_UNSATURATION
           
static java.lang.String HALOGEN_BETA_FROM_UNSATURATION
           
static java.lang.String IONICGROUP
           
static java.lang.String KETONE_A_B_UNSATURATED
           
static java.lang.String n
           
static java.lang.String PEROXIDE
           
static java.lang.String PHENOL
           
static java.lang.String PYRIDINE
           
static java.lang.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
protected FunctionalGroups()
           
 
Method Summary
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(java.lang.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(java.lang.String[] halogens)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer halogenAtAlphaFromUnsaturation(java.lang.String[] halogens)
          Halogen at alpha position from unsaturation.
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer halogenAtBetaFromUnsaturation(java.lang.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.IMolecule 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(java.lang.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 java.lang.String IONICGROUP
See Also:
Constant Field Values

RINGSUBSTITUTED

public static final java.lang.String RINGSUBSTITUTED
See Also:
Constant Field Values

HALOGEN_BETA_FROM_UNSATURATION

public static final java.lang.String HALOGEN_BETA_FROM_UNSATURATION
See Also:
Constant Field Values

HALOGEN_ALPHA_FROM_UNSATURATION

public static final java.lang.String HALOGEN_ALPHA_FROM_UNSATURATION
See Also:
Constant Field Values

HALOGEN

public static final java.lang.String HALOGEN
See Also:
Constant Field Values

EPOXIDE

public static final java.lang.String EPOXIDE
See Also:
Constant Field Values

AZARIDINE

public static final java.lang.String AZARIDINE
See Also:
Constant Field Values

PEROXIDE

public static final java.lang.String PEROXIDE
See Also:
Constant Field Values

PHENOL

public static final java.lang.String PHENOL
See Also:
Constant Field Values

ANILINE

public static final java.lang.String ANILINE
See Also:
Constant Field Values

PYRIDINE

public static final java.lang.String PYRIDINE
See Also:
Constant Field Values

BENZYLALCOHOL

public static final java.lang.String BENZYLALCOHOL
See Also:
Constant Field Values

KETONE_A_B_UNSATURATED

public static final java.lang.String KETONE_A_B_UNSATURATED
See Also:
Constant Field Values

CYCLICESTER

public static final java.lang.String CYCLICESTER
See Also:
Constant Field Values

n

public static final java.lang.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(java.lang.String substituent)

halogenAtAlphaFromUnsaturation

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer halogenAtAlphaFromUnsaturation(java.lang.String[] halogens)
Halogen at alpha position from unsaturation. "X=X[Hal]"

Returns:

halogenAtBetaFromUnsaturation

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

epoxide

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

azaridine

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

peroxide

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

phenol

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

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()

ketone_a_b_unsaturated

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

makeNitroPhenol

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

createAutoQueryContainer

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createAutoQueryContainer(java.lang.String smiles)

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()


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