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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjecttoxTree.query.FunctionalGroups
public class FunctionalGroups
This class provides static methods for various functional groups In addition there are several static methods to manipulate searching
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 |
---|
public static TTLogger logger
public static final java.lang.String MSG_HASGROUP
public static final java.lang.String MSG_MOLECULEIS
public static final java.lang.String CH3
markMaps(IAtomContainer, IAtomContainer, List)
method
public static final java.lang.String CH2
public static final java.lang.String CH
public static final java.lang.String C
public static final java.lang.String HYDROCARBON
public static final java.lang.String PRIMARY_AMINE
public static final java.lang.String SECONDARY_AMINE
public static final java.lang.String TERTIARY_AMINE
public static final java.lang.String AROMATIC_AMINE
public static final java.lang.String SECONDARY_AMINE_ALIPHATIC
public static final java.lang.String CYANO
public static final java.lang.String NITRO
public static final java.lang.String NNITROSO
public static final java.lang.String DIAZO
public static final java.lang.String TRIAZENO
public static final java.lang.String CARBOXYLIC_ACID_SALT
public static final java.lang.String CARBOXYLIC_ACID
public static final java.lang.String ACETAL
public static final java.lang.String ETHER
public static final java.lang.String METHYLETHER
public static final java.lang.String SULPHIDE
public static final java.lang.String MERCAPTAN
public static final java.lang.String ESTER
public static final java.lang.String THIOESTER
public static final java.lang.String KETONE
public static final java.lang.String KETONE_SIDECHAIN
public static final java.lang.String ALDEHYDE
public static final java.lang.String CARBONYL
public static final java.lang.String CARBONYL_ABUNSATURATED
public static final java.lang.String ALCOHOL
public static final java.lang.String SULPHONATE
public static final java.lang.String SULPHAMATE
public static final java.lang.String SULPHATE
public static final java.lang.String PHOSPHATE
public static final java.lang.String POLYOXYETHYLENE
public static final java.lang.String HYDROCHLORIDE_OF_AMINE
public static final java.lang.String SULPHATE_OF_AMINE
public static final java.lang.String ACETYLENIC
public static final java.lang.String LACTONE
public static final java.lang.String CYCLIC_DIESTER
public static final java.lang.String ISOPRENE
public static final java.lang.String HYDROXY
public static final java.lang.String METHOXY
public static final java.lang.String HYDROXY1
public static final java.lang.String HYDROXYESTERSUBSTITED
public static final java.lang.String QUATERNARY_NITROGEN
public static final java.lang.String QUATERNARY_NITROGEN_EXCEPTION
public static final java.lang.String ANHYDRIDE
public static final java.lang.String CARBONATE
public static final java.lang.String AROMATIC_N_OXIDE
public static final java.lang.String RING_NUMBERING
public static final java.lang.String DONTMARK
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
public static final java.lang.String ALLOCATED
protected static org.openscience.cdk.tools.CDKHydrogenAdder h
Constructor Detail |
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protected FunctionalGroups()
Method Detail |
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public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methyl()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methoxy()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methoxy_ring()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer noxide_aromatic()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydroxy_ring()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydroxy1()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydroxyEsterSubstituted()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ethyl()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrocarbon()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer primaryAmine(boolean aliphatic)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer secondaryAmine(boolean aliphatic)
aliphatic
-
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer tertiaryAmine()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrochlorideOfAmine(int amine)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrochlorideOfAmine3()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hydrochlorideOfAmineBreakable()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphateOfAmine(int amine)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphateOfAmineBreakable()
sulphateOfAmine(int)
with the ionic bonnd between [N+] and [O-]
marked with DONTMARK
so it can be broken by detachGroup(IAtomContainer, QueryAtomContainer)
method
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer cyano()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer nitro2double()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer nitro1double()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer Nnitroso()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer diAzo()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer triAzeno()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer quaternaryNitrogen1(boolean charged)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer quaternaryNitrogen2(boolean charged)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer quarternaryNitrogenException()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer carboxylicAcid()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer acyclic_acetal()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer acetal()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ether()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer alkoxy()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer methylether()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphide()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer mercaptan()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer thioester()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ester()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer carbonate()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer anhydride()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer lactone(boolean abUnsaturated)
abUnsaturated
- if true, this will be alpha -beta unsaturated lactone
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer lactoneBreakable()
public static boolean isCyclicDiester(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IRingSet rings)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer isopreneUnit()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ketone()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ketone_ring()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sidechain_ketone()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer aldehyde()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer carbonyl()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ab_unsaturated_carbonyl()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer alcohol(boolean aliphatic)
aliphatic
- - if true looks for aliphatic alcohols, if not for any alcohols
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphamate(java.lang.String[] metals)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcid(java.lang.String[] metals)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcid1(java.lang.String[] metals)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcid2(java.lang.String[] metals)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcidBreakable(java.lang.String[] metals)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcidBreakable1(java.lang.String[] metals)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer saltOfCarboxylicAcidBreakable2(java.lang.String[] metals)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphonate(java.lang.String[] metals)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphonate(java.lang.String[] metals, boolean bonded)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphate(java.lang.String[] setOfAtoms)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer phosphate(java.lang.String[] setOfAtoms)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer polyoxyethylene(int n)
public static org.openscience.cdk.interfaces.IAtomContainer cloneDiscardRingAtomAndBonds(org.openscience.cdk.interfaces.IAtomContainer ac, org.openscience.cdk.interfaces.IRing ring)
public static java.util.List getBondMap(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, boolean isPreprocessed)
mol
- - The molecule to be searched AtomContainer
q
- - The query AtomContainer
isPreprocessed
- - whether the molecule was preprocessed by preProcess(IAtomContainer)
List
protected static java.lang.String getKeyFromMap(org.openscience.cdk.isomorphism.mcss.RMap rmap)
protected static boolean isOverlapped(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, java.util.List first)
public static java.util.List getUniqueBondMap(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, boolean isPreprocessed)
public static int mark(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.ArrayList elements)
public static int markCHn(org.openscience.cdk.interfaces.IAtomContainer mol)
public static void markOneMap(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, java.util.List first, int j)
public static void markMaps(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, java.util.List list)
public static void mapHydrocarbon(org.openscience.cdk.interfaces.IMolecule mol)
public static java.lang.StringBuffer mapToString(org.openscience.cdk.interfaces.IAtomContainer mol, java.lang.String id)
public static java.lang.StringBuffer mapToString(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.Collection id)
public static java.lang.StringBuffer mapToString(org.openscience.cdk.interfaces.IAtomContainer mol)
public static boolean hasAnySubstructure(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.ArrayList query) throws org.openscience.cdk.exception.CDKException
mol
- query
- ArrayList of AtomContainer - - the list of substructures to be searched for
org.openscience.cdk.exception.CDKException
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
org.openscience.cdk.exception.CDKException
public static boolean hasAllSubstructure(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.ArrayList query, boolean isPreprocessed) throws org.openscience.cdk.exception.CDKException
mol
- query
- ArrayList of AtomContainer - - the list of substructures to be searched for
org.openscience.cdk.exception.CDKException
protected static boolean needsPreprocessing(org.openscience.cdk.interfaces.IAtomContainer query)
public static void preProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
public static boolean markUniqueBondMap(org.openscience.cdk.interfaces.IMolecule mol, java.util.ArrayList query, boolean isPreprocessed)
public static boolean hasOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, QueryAtomContainers query, java.util.Collection ids, boolean isPreprocessed)
public static boolean hasOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, QueryAtomContainers query, java.util.Collection ids, boolean isPreprocessed, org.openscience.cdk.interfaces.IAtomContainer selected)
public static boolean hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.Collection id)
mol
- id
- Collection of functional group identifiers as used by the procedures listed above
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)
public static boolean hasGroupMarked(org.openscience.cdk.interfaces.IAtomContainer mol, java.lang.String id)
public static boolean hasGroupMarked(org.openscience.cdk.interfaces.IAtomContainer mol, java.lang.String id, org.openscience.cdk.interfaces.IAtomContainer selection)
public static boolean hasMarkedOnlyTheseGroups(org.openscience.cdk.interfaces.IAtomContainer mol, QueryAtomContainers query)
public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, java.lang.String id)
public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, java.lang.String id, ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles)
public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER mode)
public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, boolean addHydrogens)
public static org.openscience.cdk.interfaces.IAtomContainer createAtomContainer(java.lang.String smiles, boolean addHydrogens, java.lang.String id)
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)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createQuery(java.lang.String smiles)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createQuery(java.lang.String smiles, java.lang.String id)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer vicinalDiKetone()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ketoneAttachedToTerminalVinyl()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ketalAttachedToTerminalVinyl()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer alcoholSecondaryAttachedToTerminalVinyl()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer esterOfalcoholSecondaryAttachedToTerminalVinyl()
public static org.openscience.cdk.interfaces.IAtomContainer allylAlcohol()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer allylAlcoholAcetal()
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer allylAlcoholEsterDerivative()
public static org.openscience.cdk.interfaces.IAtomContainer allylMercaptan()
public static org.openscience.cdk.interfaces.IAtomContainer allylAmine()
public static org.openscience.cdk.interfaces.IAtomContainer allylSulphide()
public static org.openscience.cdk.interfaces.IAtomContainer allylThioester()
public static org.openscience.cdk.interfaces.IAtomContainer acrolein()
public static org.openscience.cdk.interfaces.IAtomContainer methacrolein()
public static org.openscience.cdk.interfaces.IAtomContainer methacroleinAcetal()
public static org.openscience.cdk.interfaces.IAtomContainer acrylicAcid()
public static org.openscience.cdk.interfaces.IAtomContainer methacrylicAcid()
public static boolean isAcetylenic(org.openscience.cdk.interfaces.IAtomContainer mol)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer stericallyHindered()
public static boolean hasSubstituents(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IRingSet rings)
public static boolean isCommonTerpene(org.openscience.cdk.interfaces.IAtomContainer mol)
public static boolean isCommonTerpene(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IRingSet rings)
public static boolean singleFusedRing(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IRingSet rings)
public static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q)
public static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, org.openscience.cdk.interfaces.IAtomContainer selected)
public static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, boolean preprocess)
public static boolean hasGroup(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q, boolean preprocess, org.openscience.cdk.interfaces.IAtomContainer selected)
public static boolean isSubstance(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer q)
public static boolean hasManyDifferentFunctionalGroups(org.openscience.cdk.interfaces.IAtomContainer mol, int threshold)
public static int associateIonic(org.openscience.cdk.interfaces.IAtomContainer a) throws org.openscience.cdk.exception.CDKException
org.openscience.cdk.exception.CDKException
public static org.openscience.cdk.interfaces.IMoleculeSet detachGroup(org.openscience.cdk.interfaces.IAtomContainer a, org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
DONTMARK
a
- AtomContainer to be processedq
- QueryAtomContainer
defines the group to be detached
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!public static void clearMark(org.openscience.cdk.interfaces.IAtomContainer a, org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
public static void clearMark(org.openscience.cdk.interfaces.IAtomContainer a, java.lang.Object id)
public static void clearMarks(org.openscience.cdk.interfaces.IAtomContainer a)
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ring(int size)
size
-
public static void markAtomsInRing(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
mol
- q
- public static int getLongestCarbonChainLength(org.openscience.cdk.interfaces.IAtomContainer mol)
mol
- AtomContainer
public static QueryAtomContainers getAllGroups()
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