toxTree.query
Class FunctionalGroups

java.lang.Object
  extended by toxTree.query.FunctionalGroups
Direct Known Subclasses:
FunctionalGroups

public class FunctionalGroups
extends java.lang.Object

This class provides static methods for various functional groups In addition there are several static methods to manipulate searching

Author:
Nina Jeliazkova
Modified 2005-8-8

Field Summary
static java.lang.String ACETAL
           
static java.lang.String ACETYLENIC
           
static java.lang.String ALCOHOL
           
static java.lang.String ALDEHYDE
           
static java.lang.String ALLOCATED
          The intention is to use this property to mark if an atom/bond was already associated with a functional group.
static java.lang.String ANHYDRIDE
           
static java.lang.String AROMATIC_AMINE
           
static java.lang.String AROMATIC_N_OXIDE
           
static java.lang.String C
           
static java.lang.String CARBONATE
           
static java.lang.String CARBONYL
           
static java.lang.String CARBONYL_ABUNSATURATED
           
static java.lang.String CARBOXYLIC_ACID
           
static java.lang.String CARBOXYLIC_ACID_SALT
           
static java.lang.String CH
           
static java.lang.String CH2
           
static java.lang.String CH3
          These constants are used in Atom.setProperty(CH3,true) fashion in order to mark which atoms/bonds belong to the corresponding group Used by markMaps(IAtomContainer, IAtomContainer, List) method
static java.lang.String CYANO
           
static java.lang.String CYCLIC_DIESTER
           
static java.lang.String DIAZO
           
static java.lang.String DONTMARK
          Use DONTMARK constant when building a query QueryAtom atom; atom.setProperty(DONTMARK,query.getID()); This is used as a flag that the atom belongs not to the group but to the neighboring radicals It is also essential for the detachGroup(IAtomContainer, QueryAtomContainer) procedure to work, as the bond to break is the one with one atom having the property set, while the other has the property unset
static java.lang.String ESTER
           
static java.lang.String ETHER
           
protected static org.openscience.cdk.tools.CDKHydrogenAdder h
           
static java.lang.String HYDROCARBON
           
static java.lang.String HYDROCHLORIDE_OF_AMINE
           
static java.lang.String HYDROXY
           
static java.lang.String HYDROXY1
           
static java.lang.String HYDROXYESTERSUBSTITED
           
static java.lang.String ISOPRENE
           
static java.lang.String KETONE
           
static java.lang.String KETONE_SIDECHAIN
           
static java.lang.String LACTONE
           
static TTLogger logger
           
static java.lang.String MERCAPTAN
           
static java.lang.String METHOXY
           
static java.lang.String METHYLETHER
           
static java.lang.String MSG_HASGROUP
          Messages
static java.lang.String MSG_MOLECULEIS
           
static java.lang.String NITRO
           
static java.lang.String NNITROSO
           
static java.lang.String PHOSPHATE
           
static java.lang.String POLYOXYETHYLENE
           
static java.lang.String PRIMARY_AMINE
           
static java.lang.String QUATERNARY_NITROGEN
           
static java.lang.String QUATERNARY_NITROGEN_EXCEPTION
           
static java.lang.String RING_NUMBERING
           
static java.lang.String SECONDARY_AMINE
           
static java.lang.String SECONDARY_AMINE_ALIPHATIC
           
static java.lang.String SULPHAMATE
           
static java.lang.String SULPHATE
           
static java.lang.String SULPHATE_OF_AMINE
           
static java.lang.String SULPHIDE
           
static java.lang.String SULPHONATE
           
static java.lang.String TERTIARY_AMINE
           
static java.lang.String THIOESTER
           
static java.lang.String TRIAZENO
           
 
Constructor Summary
protected FunctionalGroups()
           
 
Method Summary
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ab_unsaturated_carbonyl()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer acetal()
           
static org.openscience.cdk.interfaces.IAtomContainer acrolein()
           
static org.openscience.cdk.interfaces.IAtomContainer acrylicAcid()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer acyclic_acetal()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer alcohol(boolean aliphatic)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer alcoholSecondaryAttachedToTerminalVinyl()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer aldehyde()
          RC(=O)H An aldehyde is either a functional group consisting of a terminal carbonyl group, or a compound containing a terminal carbonyl group.
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer alkoxy()
           
static org.openscience.cdk.interfaces.IAtomContainer allylAlcohol()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer allylAlcoholAcetal()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer allylAlcoholEsterDerivative()
           
static org.openscience.cdk.interfaces.IAtomContainer allylAmine()
           
static org.openscience.cdk.interfaces.IAtomContainer allylMercaptan()
           
static org.openscience.cdk.interfaces.IAtomContainer allylSulphide()
           
static org.openscience.cdk.interfaces.IAtomContainer allylThioester()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer anhydride()
           
static int associateIonic(org.openscience.cdk.interfaces.IAtomContainer a)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer carbonate()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer carbonyl()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer carboxylicAcid()
           
static void clearMark(org.openscience.cdk.interfaces.IAtomContainer a, java.lang.Object id)
           
static void clearMark(org.openscience.cdk.interfaces.IAtomContainer a, org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
           
static void clearMarks(org.openscience.cdk.interfaces.IAtomContainer a)
           
static org.openscience.cdk.interfaces.IAtomContainer cloneDiscardRingAtomAndBonds(org.openscience.cdk.interfaces.IAtomContainer ac, org.openscience.cdk.interfaces.IRing ring)
           
static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles)
           
static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, boolean addHydrogens)
           
static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, boolean addHydrogens, java.lang.String id)
           
static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, boolean addHydrogens, java.lang.String id, ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
           
static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
           
static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, java.lang.String id)
           
static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, java.lang.String id, ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createQuery(java.lang.String smiles)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createQuery(java.lang.String smiles, java.lang.String id)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer cyano()
          SMARTS: C(#N)([C,#1])
static org.openscience.cdk.interfaces.IMoleculeSet detachGroup(org.openscience.cdk.interfaces.IAtomContainer a, org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
          Identifies the fragment to be detached and breaks the relevant bonds In order to function properly, the group has to be defined with at least one atom marked with setProperty(DONTMARK,dontMark).
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer diAzo()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ester()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer esterOfalcoholSecondaryAttachedToTerminalVinyl()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ether()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ethyl()
           
static QueryAtomContainers getAllGroups()
           
static java.util.List getBondMap(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, boolean isPreprocessed)
           
protected static java.lang.String getKeyFromMap(org.openscience.cdk.isomorphism.mcss.RMap rmap)
           
static int getLongestCarbonChainLength(org.openscience.cdk.interfaces.IAtomContainer mol)
           
static java.util.List getUniqueBondMap(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, boolean isPreprocessed)
           
static boolean hasAllSubstructure(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.ArrayList query, boolean isPreprocessed)
           
static boolean hasAnySubstructure(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.ArrayList query)
           
static boolean hasAnySubstructure(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.ArrayList query, org.openscience.cdk.interfaces.IAtomContainer selected)
           
static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q)
           
static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, boolean preprocess)
           
static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, boolean preprocess, org.openscience.cdk.interfaces.IAtomContainer selected)
           
static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, org.openscience.cdk.interfaces.IAtomContainer selected)
           
static boolean hasGroupMarked(org.openscience.cdk.interfaces.IAtomContainer mol, java.lang.String id)
           
static boolean hasGroupMarked(org.openscience.cdk.interfaces.IAtomContainer mol, java.lang.String id, org.openscience.cdk.interfaces.IAtomContainer selection)
           
static boolean hasManyDifferentFunctionalGroups(org.openscience.cdk.interfaces.IAtomContainer mol, int threshold)
           
static boolean hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.Collection id)
          Has to be preprocessed with getBondMap or getUniqueBondMap and markMaps
static boolean hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.Collection id, org.openscience.cdk.interfaces.IAtomContainer selection, org.openscience.cdk.interfaces.IAtomContainer selectionOther)
           
static boolean hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, QueryAtomContainers query)
           
static boolean hasOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, QueryAtomContainers query, java.util.Collection ids, boolean isPreprocessed)
           
static boolean hasOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, QueryAtomContainers query, java.util.Collection ids, boolean isPreprocessed, org.openscience.cdk.interfaces.IAtomContainer selected)
           
static boolean hasSubstituents(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IRingSet rings)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrocarbon()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrochlorideOfAmine(int amine)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrochlorideOfAmine3()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrochlorideOfAmineBreakable()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydroxy_ring()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydroxy1()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydroxyEsterSubstituted()
           
static boolean isAcetylenic(org.openscience.cdk.interfaces.IAtomContainer mol)
           
static boolean isCommonTerpene(org.openscience.cdk.interfaces.IAtomContainer mol)
           
static boolean isCommonTerpene(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IRingSet rings)
           
static boolean isCyclicDiester(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IRingSet rings)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer isopreneUnit()
           
protected static boolean isOverlapped(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, java.util.List first)
           
static boolean isSubstance(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ketalAttachedToTerminalVinyl()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ketone_ring()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ketone()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ketoneAttachedToTerminalVinyl()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer lactone(boolean abUnsaturated)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer lactoneBreakable()
           
static void mapHydrocarbon(org.openscience.cdk.interfaces.IMolecule mol)
           
static java.lang.StringBuffer mapToString(org.openscience.cdk.interfaces.IAtomContainer mol)
           
static java.lang.StringBuffer mapToString(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.Collection id)
           
static java.lang.StringBuffer mapToString(org.openscience.cdk.interfaces.IAtomContainer mol, java.lang.String id)
           
static int mark(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.ArrayList elements)
           
static void markAtomsInRing(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
           
static int markCHn(org.openscience.cdk.interfaces.IAtomContainer mol)
           
static void markMaps(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, java.util.List list)
           
static void markOneMap(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, java.util.List first, int j)
           
static boolean markUniqueBondMap(org.openscience.cdk.interfaces.IMolecule mol, java.util.ArrayList query, boolean isPreprocessed)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer mercaptan()
           
static org.openscience.cdk.interfaces.IAtomContainer methacrolein()
           
static org.openscience.cdk.interfaces.IAtomContainer methacroleinAcetal()
           
static org.openscience.cdk.interfaces.IAtomContainer methacrylicAcid()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methoxy_ring()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methoxy()
          Query for methoxy group.
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methyl()
          Query for Methyl group.
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methylether()
           
protected static boolean needsPreprocessing(org.openscience.cdk.interfaces.IAtomContainer query)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer nitro1double()
          SMARTS: [N+](=O)([O-])([!#1])
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer nitro2double()
          SMARTS: N(=O)(=O)([!#1])
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer Nnitroso()
          SMARTS: O=NN([!#1])([!#1])
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer noxide_aromatic()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer phosphate(java.lang.String[] setOfAtoms)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer polyoxyethylene(int n)
           
static void preProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer primaryAmine(boolean aliphatic)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer quarternaryNitrogenException()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer quaternaryNitrogen1(boolean charged)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer quaternaryNitrogen2(boolean charged)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ring(int size)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcid(java.lang.String[] metals)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcid1(java.lang.String[] metals)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcid2(java.lang.String[] metals)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcidBreakable(java.lang.String[] metals)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcidBreakable1(java.lang.String[] metals)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcidBreakable2(java.lang.String[] metals)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer secondaryAmine(boolean aliphatic)
          SMARTS: [C;R0]-;!@[N;R0;H1]-;!@[C;R0]
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sidechain_ketone()
           
static boolean singleFusedRing(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IRingSet rings)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer stericallyHindered()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphamate(java.lang.String[] metals)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphate(java.lang.String[] setOfAtoms)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphateOfAmine(int amine)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphateOfAmineBreakable()
          This is sulphateOfAmine(int) with the ionic bonnd between [N+] and [O-] marked with DONTMARK so it can be broken by detachGroup(IAtomContainer, QueryAtomContainer) method
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphide()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphonate(java.lang.String[] metals)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphonate(java.lang.String[] metals, boolean bonded)
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer tertiaryAmine()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer thioester()
           
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer triAzeno()
          SMARTS: [#6][#7]=[#7][#7;H2]
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer vicinalDiKetone()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

logger

public static TTLogger logger

MSG_HASGROUP

public static final java.lang.String MSG_HASGROUP
Messages

See Also:
Constant Field Values

MSG_MOLECULEIS

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

CH3

public static final java.lang.String CH3
These constants are used in Atom.setProperty(CH3,true) fashion in order to mark which atoms/bonds belong to the corresponding group Used by markMaps(IAtomContainer, IAtomContainer, List) method

See Also:
Constant Field Values

CH2

public static final java.lang.String CH2
See Also:
Constant Field Values

CH

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

C

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

HYDROCARBON

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

PRIMARY_AMINE

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

SECONDARY_AMINE

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

TERTIARY_AMINE

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

AROMATIC_AMINE

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

SECONDARY_AMINE_ALIPHATIC

public static final java.lang.String SECONDARY_AMINE_ALIPHATIC
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Constant Field Values

CYANO

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

NITRO

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

NNITROSO

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

DIAZO

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

TRIAZENO

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

CARBOXYLIC_ACID_SALT

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

CARBOXYLIC_ACID

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

ACETAL

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

ETHER

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

METHYLETHER

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

SULPHIDE

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

MERCAPTAN

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

ESTER

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

THIOESTER

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

KETONE

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

KETONE_SIDECHAIN

public static final java.lang.String KETONE_SIDECHAIN
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Constant Field Values

ALDEHYDE

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

CARBONYL

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

CARBONYL_ABUNSATURATED

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

ALCOHOL

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

SULPHONATE

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

SULPHAMATE

public static final java.lang.String SULPHAMATE
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Constant Field Values

SULPHATE

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

PHOSPHATE

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

POLYOXYETHYLENE

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

HYDROCHLORIDE_OF_AMINE

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

SULPHATE_OF_AMINE

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

ACETYLENIC

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

LACTONE

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

CYCLIC_DIESTER

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

ISOPRENE

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

HYDROXY

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

METHOXY

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

HYDROXY1

public static final java.lang.String HYDROXY1
See Also:
Constant Field Values

HYDROXYESTERSUBSTITED

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

QUATERNARY_NITROGEN

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

QUATERNARY_NITROGEN_EXCEPTION

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

ANHYDRIDE

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

CARBONATE

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

AROMATIC_N_OXIDE

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

RING_NUMBERING

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

DONTMARK

public static final java.lang.String DONTMARK
Use DONTMARK constant when building a query QueryAtom atom; atom.setProperty(DONTMARK,query.getID()); This is used as a flag that the atom belongs not to the group but to the neighboring radicals It is also essential for the detachGroup(IAtomContainer, QueryAtomContainer) procedure to work, as the bond to break is the one with one atom having the property set, while the other has the property unset

See Also:
Constant Field Values

ALLOCATED

public static final java.lang.String ALLOCATED
The intention is to use this property to mark if an atom/bond was already associated with a functional group. It will help to avoid wrong overlapping allocation of different group to the same atom Finally, marking by setProperty(query.getID(),new Boolean(true)) may be replaced with setProperty(ALLOCATED,query.getID()) perhaps in v0.04 release :)

See Also:
Constant Field Values

h

protected static org.openscience.cdk.tools.CDKHydrogenAdder h
Constructor Detail

FunctionalGroups

protected FunctionalGroups()
Method Detail

methyl

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methyl()
Query for Methyl group.

Returns:

methoxy

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methoxy()
Query for methoxy group.

Returns:

methoxy_ring

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

noxide_aromatic

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

hydroxy_ring

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

hydroxy1

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydroxy1()

hydroxyEsterSubstituted

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

ethyl

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

hydrocarbon

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

primaryAmine

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer primaryAmine(boolean aliphatic)

secondaryAmine

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer secondaryAmine(boolean aliphatic)
SMARTS: [C;R0]-;!@[N;R0;H1]-;!@[C;R0]

Parameters:
aliphatic -
Returns:

tertiaryAmine

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

hydrochlorideOfAmine

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrochlorideOfAmine(int amine)

hydrochlorideOfAmine3

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrochlorideOfAmine3()

hydrochlorideOfAmineBreakable

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

sulphateOfAmine

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphateOfAmine(int amine)

sulphateOfAmineBreakable

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphateOfAmineBreakable()
This is sulphateOfAmine(int) with the ionic bonnd between [N+] and [O-] marked with DONTMARK so it can be broken by detachGroup(IAtomContainer, QueryAtomContainer) method

Returns:
QueryAtomContainer the query

cyano

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer cyano()
SMARTS: C(#N)([C,#1])

Returns:

nitro2double

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer nitro2double()
SMARTS: N(=O)(=O)([!#1])

Returns:

nitro1double

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer nitro1double()
SMARTS: [N+](=O)([O-])([!#1])

Returns:

Nnitroso

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer Nnitroso()
SMARTS: O=NN([!#1])([!#1])

Returns:

diAzo

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

triAzeno

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer triAzeno()
SMARTS: [#6][#7]=[#7][#7;H2]

Returns:

quaternaryNitrogen1

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer quaternaryNitrogen1(boolean charged)

quaternaryNitrogen2

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer quaternaryNitrogen2(boolean charged)

quarternaryNitrogenException

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

carboxylicAcid

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

acyclic_acetal

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

acetal

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

ether

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

alkoxy

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

methylether

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

sulphide

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

mercaptan

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

thioester

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

ester

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

carbonate

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

anhydride

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

lactone

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer lactone(boolean abUnsaturated)
Parameters:
abUnsaturated - if true, this will be alpha -beta unsaturated lactone
Returns:

lactoneBreakable

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

isCyclicDiester

public static boolean isCyclicDiester(org.openscience.cdk.interfaces.IAtomContainer mol,
                                      org.openscience.cdk.interfaces.IRingSet rings)

isopreneUnit

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

ketone

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

ketone_ring

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

sidechain_ketone

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

aldehyde

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer aldehyde()
RC(=O)H An aldehyde is either a functional group consisting of a terminal carbonyl group, or a compound containing a terminal carbonyl group. (Where -R represents the carbon chain.)


carbonyl

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

ab_unsaturated_carbonyl

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

alcohol

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer alcohol(boolean aliphatic)
Parameters:
aliphatic - - if true looks for aliphatic alcohols, if not for any alcohols
Returns:

sulphamate

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

saltOfCarboxylicAcid

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

saltOfCarboxylicAcid1

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcid1(java.lang.String[] metals)

saltOfCarboxylicAcid2

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcid2(java.lang.String[] metals)

saltOfCarboxylicAcidBreakable

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

saltOfCarboxylicAcidBreakable1

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcidBreakable1(java.lang.String[] metals)

saltOfCarboxylicAcidBreakable2

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcidBreakable2(java.lang.String[] metals)

sulphonate

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

sulphonate

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphonate(java.lang.String[] metals,
                                                                                     boolean bonded)

sulphate

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

phosphate

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

polyoxyethylene

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer polyoxyethylene(int n)

cloneDiscardRingAtomAndBonds

public static org.openscience.cdk.interfaces.IAtomContainer cloneDiscardRingAtomAndBonds(org.openscience.cdk.interfaces.IAtomContainer ac,
                                                                                         org.openscience.cdk.interfaces.IRing ring)

getBondMap

public static java.util.List getBondMap(org.openscience.cdk.interfaces.IAtomContainer mol,
                                        org.openscience.cdk.interfaces.IAtomContainer q,
                                        boolean isPreprocessed)
Parameters:
mol - - The molecule to be searched AtomContainer
q - - The query AtomContainer
isPreprocessed - - whether the molecule was preprocessed by preProcess(IAtomContainer)
Returns:
List List

getKeyFromMap

protected static java.lang.String getKeyFromMap(org.openscience.cdk.isomorphism.mcss.RMap rmap)

isOverlapped

protected static boolean isOverlapped(org.openscience.cdk.interfaces.IAtomContainer mol,
                                      org.openscience.cdk.interfaces.IAtomContainer q,
                                      java.util.List first)

getUniqueBondMap

public static java.util.List getUniqueBondMap(org.openscience.cdk.interfaces.IAtomContainer mol,
                                              org.openscience.cdk.interfaces.IAtomContainer q,
                                              boolean isPreprocessed)

mark

public static int mark(org.openscience.cdk.interfaces.IAtomContainer mol,
                       java.util.ArrayList elements)

markCHn

public static int markCHn(org.openscience.cdk.interfaces.IAtomContainer mol)

markOneMap

public static void markOneMap(org.openscience.cdk.interfaces.IAtomContainer mol,
                              org.openscience.cdk.interfaces.IAtomContainer q,
                              java.util.List first,
                              int j)

markMaps

public static void markMaps(org.openscience.cdk.interfaces.IAtomContainer mol,
                            org.openscience.cdk.interfaces.IAtomContainer q,
                            java.util.List list)

mapHydrocarbon

public static void mapHydrocarbon(org.openscience.cdk.interfaces.IMolecule mol)

mapToString

public static java.lang.StringBuffer mapToString(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                 java.lang.String id)

mapToString

public static java.lang.StringBuffer mapToString(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                 java.util.Collection id)

mapToString

public static java.lang.StringBuffer mapToString(org.openscience.cdk.interfaces.IAtomContainer mol)

hasAnySubstructure

public static boolean hasAnySubstructure(org.openscience.cdk.interfaces.IAtomContainer mol,
                                         java.util.ArrayList query)
                                  throws org.openscience.cdk.exception.CDKException
Parameters:
mol -
query - ArrayList of AtomContainer - - the list of substructures to be searched for
Returns:
true if any of the fragments are a substructure of mol
Throws:
org.openscience.cdk.exception.CDKException

hasAnySubstructure

public static boolean hasAnySubstructure(org.openscience.cdk.interfaces.IAtomContainer mol,
                                         java.util.ArrayList query,
                                         org.openscience.cdk.interfaces.IAtomContainer selected)
                                  throws org.openscience.cdk.exception.CDKException
Throws:
org.openscience.cdk.exception.CDKException

hasAllSubstructure

public static boolean hasAllSubstructure(org.openscience.cdk.interfaces.IAtomContainer mol,
                                         java.util.ArrayList query,
                                         boolean isPreprocessed)
                                  throws org.openscience.cdk.exception.CDKException
Parameters:
mol -
query - ArrayList of AtomContainer - - the list of substructures to be searched for
Returns:
true if all of the fragments are a substructure of mol
Throws:
org.openscience.cdk.exception.CDKException

needsPreprocessing

protected static boolean needsPreprocessing(org.openscience.cdk.interfaces.IAtomContainer query)

preProcess

public static void preProcess(org.openscience.cdk.interfaces.IAtomContainer mol)

markUniqueBondMap

public static boolean markUniqueBondMap(org.openscience.cdk.interfaces.IMolecule mol,
                                        java.util.ArrayList query,
                                        boolean isPreprocessed)

hasOnlyTheseGroups

public static boolean hasOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol,
                                         QueryAtomContainers query,
                                         java.util.Collection ids,
                                         boolean isPreprocessed)

hasOnlyTheseGroups

public static boolean hasOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol,
                                         QueryAtomContainers query,
                                         java.util.Collection ids,
                                         boolean isPreprocessed,
                                         org.openscience.cdk.interfaces.IAtomContainer selected)

hasMarkedOnlyTheseGroups

public static boolean hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol,
                                               java.util.Collection id)
Has to be preprocessed with getBondMap or getUniqueBondMap and markMaps

Parameters:
mol -
id - Collection of functional group identifiers as used by the procedures listed above
Returns:
true if mol contains only specified groups (i.e. there are no unmarked atoms)

hasMarkedOnlyTheseGroups

public static boolean hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol,
                                               java.util.Collection id,
                                               org.openscience.cdk.interfaces.IAtomContainer selection,
                                               org.openscience.cdk.interfaces.IAtomContainer selectionOther)

hasGroupMarked

public static boolean hasGroupMarked(org.openscience.cdk.interfaces.IAtomContainer mol,
                                     java.lang.String id)

hasGroupMarked

public static boolean hasGroupMarked(org.openscience.cdk.interfaces.IAtomContainer mol,
                                     java.lang.String id,
                                     org.openscience.cdk.interfaces.IAtomContainer selection)

hasMarkedOnlyTheseGroups

public static boolean hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol,
                                               QueryAtomContainers query)

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles,
                                                                                java.lang.String id)

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles,
                                                                                java.lang.String id,
                                                                                ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles)

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles,
                                                                                ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles,
                                                                                boolean addHydrogens)

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles,
                                                                                boolean addHydrogens,
                                                                                java.lang.String id)

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles,
                                                                                boolean addHydrogens,
                                                                                java.lang.String id,
                                                                                ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)

createQuery

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

createQuery

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createQuery(java.lang.String smiles,
                                                                                      java.lang.String id)

vicinalDiKetone

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

ketoneAttachedToTerminalVinyl

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

ketalAttachedToTerminalVinyl

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

alcoholSecondaryAttachedToTerminalVinyl

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

esterOfalcoholSecondaryAttachedToTerminalVinyl

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

allylAlcohol

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

allylAlcoholAcetal

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

allylAlcoholEsterDerivative

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

allylMercaptan

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

allylAmine

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

allylSulphide

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

allylThioester

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

acrolein

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

methacrolein

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

methacroleinAcetal

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

acrylicAcid

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

methacrylicAcid

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

isAcetylenic

public static boolean isAcetylenic(org.openscience.cdk.interfaces.IAtomContainer mol)

stericallyHindered

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

hasSubstituents

public static boolean hasSubstituents(org.openscience.cdk.interfaces.IAtomContainer mol,
                                      org.openscience.cdk.interfaces.IRingSet rings)

isCommonTerpene

public static boolean isCommonTerpene(org.openscience.cdk.interfaces.IAtomContainer mol)

isCommonTerpene

public static boolean isCommonTerpene(org.openscience.cdk.interfaces.IAtomContainer mol,
                                      org.openscience.cdk.interfaces.IRingSet rings)

singleFusedRing

public static boolean singleFusedRing(org.openscience.cdk.interfaces.IAtomContainer mol,
                                      org.openscience.cdk.interfaces.IRingSet rings)

hasGroup

public static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol,
                               org.openscience.cdk.interfaces.IAtomContainer q)

hasGroup

public static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol,
                               org.openscience.cdk.interfaces.IAtomContainer q,
                               org.openscience.cdk.interfaces.IAtomContainer selected)

hasGroup

public static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol,
                               org.openscience.cdk.interfaces.IAtomContainer q,
                               boolean preprocess)

hasGroup

public static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol,
                               org.openscience.cdk.interfaces.IAtomContainer q,
                               boolean preprocess,
                               org.openscience.cdk.interfaces.IAtomContainer selected)

isSubstance

public static boolean isSubstance(org.openscience.cdk.interfaces.IAtomContainer mol,
                                  org.openscience.cdk.interfaces.IAtomContainer q)

hasManyDifferentFunctionalGroups

public static boolean hasManyDifferentFunctionalGroups(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                       int threshold)

associateIonic

public static int associateIonic(org.openscience.cdk.interfaces.IAtomContainer a)
                          throws org.openscience.cdk.exception.CDKException
Throws:
org.openscience.cdk.exception.CDKException

detachGroup

public static org.openscience.cdk.interfaces.IMoleculeSet detachGroup(org.openscience.cdk.interfaces.IAtomContainer a,
                                                                      org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
Identifies the fragment to be detached and breaks the relevant bonds In order to function properly, the group has to be defined with at least one atom marked with setProperty(DONTMARK,dontMark). This defined the bond to break. See DONTMARK

Parameters:
a - AtomContainer to be processed
q - QueryAtomContainer defines the group to be detached
Returns:
SetOfAtomContainers set of AtomContainer resulted by breaking bonds as above. Hydrogens are added on the broken end of each bond TODO care for bond orders!

clearMark

public static void clearMark(org.openscience.cdk.interfaces.IAtomContainer a,
                             org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)

clearMark

public static void clearMark(org.openscience.cdk.interfaces.IAtomContainer a,
                             java.lang.Object id)

clearMarks

public static void clearMarks(org.openscience.cdk.interfaces.IAtomContainer a)

ring

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ring(int size)
Parameters:
size -
Returns:
ring

markAtomsInRing

public static void markAtomsInRing(org.openscience.cdk.interfaces.IAtomContainer mol,
                                   org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
Parameters:
mol -
q -

getLongestCarbonChainLength

public static int getLongestCarbonChainLength(org.openscience.cdk.interfaces.IAtomContainer mol)
Parameters:
mol - AtomContainer
Returns:
the length of the longest carbon chain

getAllGroups

public static QueryAtomContainers getAllGroups()


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