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
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 |
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 |
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
FunctionalGroups
protected FunctionalGroups()
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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