toxTree.query

Class FunctionalGroups

java.lang.Object

toxTree.query.FunctionalGroups

Direct Known Subclasses:

FunctionalGroups

public class FunctionalGroups
extends 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

Fields

Modifier and Type	Field and Description
static String	ACETAL
static String	ACETYLENIC
static String	ALCOHOL
static String	ALDEHYDE
static String	ALLOCATED The intention is to use this property to mark if an atom/bond was already associated with a functional group.
static String	ANHYDRIDE
static String	AROMATIC_AMINE
static String	AROMATIC_N_OXIDE
static String	C
static String	CARBONATE
static String	CARBONYL
static String	CARBONYL_ABUNSATURATED
static String	CARBOXYLIC_ACID
static String	CARBOXYLIC_ACID_SALT
static String	CH
static String	CH2
static 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 String	CYANO
static String	CYCLIC_DIESTER
static String	DIAZO
static 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 String	ESTER
static String	ETHER
protected static org.openscience.cdk.tools.CDKHydrogenAdder	h
static String	HYDROCARBON
static String	HYDROCHLORIDE_OF_AMINE
static String	HYDROXY
static String	HYDROXY1
static String	HYDROXYESTERSUBSTITED
static String	ISOPRENE
static String	KETONE
static String	KETONE_SIDECHAIN
static String	LACTONE
static Logger	logger
static String	MERCAPTAN
static String	METHOXY
static String	METHYLETHER
static String	MSG_HASGROUP Messages
static String	MSG_MOLECULEIS
static String	NITRO
static String	NNITROSO
static String	PHOSPHATE
static String	POLYOXYETHYLENE
static String	PRIMARY_AMINE
static String	QUATERNARY_NITROGEN
static String	QUATERNARY_NITROGEN_EXCEPTION
static String	RING_NUMBERING
static String	SECONDARY_AMINE
static String	SECONDARY_AMINE_ALIPHATIC
static String	SULPHAMATE
static String	SULPHATE
static String	SULPHATE_OF_AMINE
static String	SULPHIDE
static String	SULPHONATE
static String	TERTIARY_AMINE
static String	THIOESTER
static String	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	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, 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(String smiles)
static org.openscience.cdk.interfaces.IAtomContainer	createAtomContainer(String smiles, boolean addHydrogens)
static org.openscience.cdk.interfaces.IAtomContainer	createAtomContainer(String smiles, boolean addHydrogens, String id)
static org.openscience.cdk.interfaces.IAtomContainer	createAtomContainer(String smiles, boolean addHydrogens, String id, ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
static org.openscience.cdk.interfaces.IAtomContainer	createAtomContainer(String smiles, ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
static org.openscience.cdk.interfaces.IAtomContainer	createAtomContainer(String smiles, String id)
static org.openscience.cdk.interfaces.IAtomContainer	createAtomContainer(String smiles, String id, ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	createQuery(String smiles)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	createQuery(String smiles, String id)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	cyano() SMARTS: C(#N)([C,#1])
static org.openscience.cdk.interfaces.IAtomContainerSet	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 List	getBondMap(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, boolean isPreprocessed)
protected static String	getKeyFromMap(org.openscience.cdk.isomorphism.mcss.RMap rmap)
static int	getLongestCarbonChainLength(org.openscience.cdk.interfaces.IAtomContainer mol)
static 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, ArrayList query, boolean isPreprocessed)
static boolean	hasAnySubstructure(org.openscience.cdk.interfaces.IAtomContainer mol, ArrayList query)
static boolean	hasAnySubstructure(org.openscience.cdk.interfaces.IAtomContainer mol, 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, String id)
static boolean	hasGroupMarked(org.openscience.cdk.interfaces.IAtomContainer mol, 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, Collection id) Has to be preprocessed with getBondMap or getUniqueBondMap and markMaps
static boolean	hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, 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, Collection ids, boolean isPreprocessed)
static boolean	hasOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, QueryAtomContainers query, 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, 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.IAtomContainer mol)
static StringBuilder	mapToString(org.openscience.cdk.interfaces.IAtomContainer mol)
static StringBuffer	mapToString(org.openscience.cdk.interfaces.IAtomContainer mol, Collection id)
static StringBuffer	mapToString(org.openscience.cdk.interfaces.IAtomContainer mol, String id)
static int	mark(org.openscience.cdk.interfaces.IAtomContainer mol, 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, List list)
static void	markOneMap(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, List first, int j)
static boolean	markUniqueBondMap(org.openscience.cdk.interfaces.IAtomContainer mol, 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(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(String[] metals)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	saltOfCarboxylicAcid1(String[] metals)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	saltOfCarboxylicAcid2(String[] metals)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	saltOfCarboxylicAcidBreakable(String[] metals)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	saltOfCarboxylicAcidBreakable1(String[] metals)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	saltOfCarboxylicAcidBreakable2(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(String[] metals)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	sulphate(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(String[] metals)
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	sulphonate(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 Logger logger

MSG_HASGROUP

public static final String MSG_HASGROUP

Messages

See Also:

Constant Field Values

MSG_MOLECULEIS

public static final String MSG_MOLECULEIS

See Also:

Constant Field Values

CH3

public static final 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

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Constant Field Values

CH2

public static final String CH2

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Constant Field Values

CH

public static final String CH

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Constant Field Values

C

public static final String C

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Constant Field Values

HYDROCARBON

public static final String HYDROCARBON

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Constant Field Values

PRIMARY_AMINE

public static final String PRIMARY_AMINE

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Constant Field Values

SECONDARY_AMINE

public static final String SECONDARY_AMINE

See Also:

Constant Field Values

TERTIARY_AMINE

public static final String TERTIARY_AMINE

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Constant Field Values

AROMATIC_AMINE

public static final String AROMATIC_AMINE

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Constant Field Values

SECONDARY_AMINE_ALIPHATIC

public static final String SECONDARY_AMINE_ALIPHATIC

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Constant Field Values

CYANO

public static final String CYANO

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Constant Field Values

NITRO

public static final String NITRO

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Constant Field Values

NNITROSO

public static final String NNITROSO

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Constant Field Values

DIAZO

public static final String DIAZO

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Constant Field Values

TRIAZENO

public static final String TRIAZENO

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Constant Field Values

CARBOXYLIC_ACID_SALT

public static final String CARBOXYLIC_ACID_SALT

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Constant Field Values

CARBOXYLIC_ACID

public static final String CARBOXYLIC_ACID

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Constant Field Values

ACETAL

public static final String ACETAL

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Constant Field Values

ETHER

public static final String ETHER

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Constant Field Values

METHYLETHER

public static final String METHYLETHER

See Also:

Constant Field Values

SULPHIDE

public static final String SULPHIDE

See Also:

Constant Field Values

MERCAPTAN

public static final String MERCAPTAN

See Also:

Constant Field Values

ESTER

public static final String ESTER

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Constant Field Values

THIOESTER

public static final String THIOESTER

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Constant Field Values

KETONE

public static final String KETONE

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Constant Field Values

KETONE_SIDECHAIN

public static final String KETONE_SIDECHAIN

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Constant Field Values

ALDEHYDE

public static final String ALDEHYDE

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Constant Field Values

CARBONYL

public static final String CARBONYL

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Constant Field Values

CARBONYL_ABUNSATURATED

public static final String CARBONYL_ABUNSATURATED

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Constant Field Values

ALCOHOL

public static final String ALCOHOL

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Constant Field Values

SULPHONATE

public static final String SULPHONATE

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Constant Field Values

SULPHAMATE

public static final String SULPHAMATE

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Constant Field Values

SULPHATE

public static final String SULPHATE

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Constant Field Values

PHOSPHATE

public static final String PHOSPHATE

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Constant Field Values

POLYOXYETHYLENE

public static final String POLYOXYETHYLENE

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Constant Field Values

HYDROCHLORIDE_OF_AMINE

public static final String HYDROCHLORIDE_OF_AMINE

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Constant Field Values

SULPHATE_OF_AMINE

public static final String SULPHATE_OF_AMINE

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Constant Field Values

ACETYLENIC

public static final String ACETYLENIC

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Constant Field Values

LACTONE

public static final String LACTONE

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Constant Field Values

CYCLIC_DIESTER

public static final String CYCLIC_DIESTER

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Constant Field Values

ISOPRENE

public static final String ISOPRENE

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Constant Field Values

HYDROXY

public static final String HYDROXY

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Constant Field Values

METHOXY

public static final String METHOXY

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Constant Field Values

HYDROXY1

public static final String HYDROXY1

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Constant Field Values

HYDROXYESTERSUBSTITED

public static final String HYDROXYESTERSUBSTITED

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Constant Field Values

QUATERNARY_NITROGEN

public static final String QUATERNARY_NITROGEN

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Constant Field Values

QUATERNARY_NITROGEN_EXCEPTION

public static final String QUATERNARY_NITROGEN_EXCEPTION

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Constant Field Values

ANHYDRIDE

public static final String ANHYDRIDE

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Constant Field Values

CARBONATE

public static final String CARBONATE

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Constant Field Values

AROMATIC_N_OXIDE

public static final String AROMATIC_N_OXIDE

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Constant Field Values

RING_NUMBERING

public static final String RING_NUMBERING

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Constant Field Values

DONTMARK

public static final 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

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Constant Field Values

ALLOCATED

public static final 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(String[] metals)

saltOfCarboxylicAcid

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

saltOfCarboxylicAcid1

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

saltOfCarboxylicAcid2

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

saltOfCarboxylicAcidBreakable

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

saltOfCarboxylicAcidBreakable1

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

saltOfCarboxylicAcidBreakable2

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

sulphonate

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

sulphonate

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

sulphate

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

phosphate

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer phosphate(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 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 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,
                                      List first)

getUniqueBondMap

public static 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,
                       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,
                              List first,
                              int j)

markMaps

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

mapHydrocarbon

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

mapToString

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

mapToString

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

mapToString

public static StringBuilder mapToString(org.openscience.cdk.interfaces.IAtomContainer mol)

hasAnySubstructure

public static boolean hasAnySubstructure(org.openscience.cdk.interfaces.IAtomContainer mol,
                                         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,
                                         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,
                                         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.IAtomContainer mol,
                                        ArrayList query,
                                        boolean isPreprocessed)

hasOnlyTheseGroups

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

hasOnlyTheseGroups

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

hasMarkedOnlyTheseGroups

public static boolean hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol,
                                               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,
                                               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,
                                     String id)

hasGroupMarked

public static boolean hasGroupMarked(org.openscience.cdk.interfaces.IAtomContainer mol,
                                     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(String smiles,
                                                                                String id)
                                                                         throws org.openscience.cdk.exception.CDKException,
                                                                                org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.CDKException

org.openscience.cdk.exception.InvalidSmilesException

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(String smiles,
                                                                                String id,
                                                                                ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
                                                                         throws org.openscience.cdk.exception.CDKException,
                                                                                org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.CDKException

org.openscience.cdk.exception.InvalidSmilesException

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(String smiles)
                                                                         throws org.openscience.cdk.exception.CDKException,
                                                                                org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.CDKException

org.openscience.cdk.exception.InvalidSmilesException

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(String smiles,
                                                                                ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
                                                                         throws org.openscience.cdk.exception.CDKException,
                                                                                org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.CDKException

org.openscience.cdk.exception.InvalidSmilesException

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(String smiles,
                                                                                boolean addHydrogens)
                                                                         throws org.openscience.cdk.exception.CDKException,
                                                                                org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.CDKException

org.openscience.cdk.exception.InvalidSmilesException

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(String smiles,
                                                                                boolean addHydrogens,
                                                                                String id)
                                                                         throws org.openscience.cdk.exception.CDKException,
                                                                                org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.CDKException

org.openscience.cdk.exception.InvalidSmilesException

createAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(String smiles,
                                                                                boolean addHydrogens,
                                                                                String id,
                                                                                ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
                                                                         throws org.openscience.cdk.exception.CDKException,
                                                                                org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.CDKException

org.openscience.cdk.exception.InvalidSmilesException

createQuery

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

Throws:

Exception

createQuery

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createQuery(String smiles,
                                                                                      String id)
                                                                               throws org.openscience.cdk.exception.CDKException,
                                                                                      org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.CDKException

org.openscience.cdk.exception.InvalidSmilesException

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.IAtomContainerSet 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,
                             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()