Package biotransformer.utils
Class ChemicalClassFinder
- java.lang.Object
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- biotransformer.utils.ChemicalClassFinder
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public class ChemicalClassFinder extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
ChemicalClassFinder.ChemicalClassName
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Field Summary
Fields Modifier and Type Field Description static java.util.LinkedHashMap<ChemicalClassFinder.ChemicalClassName,java.util.LinkedHashMap<java.lang.String,java.lang.String[]>>
chemicalClassDefinitions
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Constructor Summary
Constructors Constructor Description ChemicalClassFinder()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.util.ArrayList<ChemicalClassFinder.ChemicalClassName>
AssignChemicalClasses(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
compoundMatchesClassSmartsDefinitions(org.openscience.cdk.interfaces.IAtomContainer molecule, ChemicalClassFinder.ChemicalClassName className)
static ChemicalClassFinder.ChemicalClassName
findChemicalClass(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isAcylCoAConjugate(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isAlphaHydroxyFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isBetaHydroxyFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isC23BileAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isC24BileAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isEtherLipid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isGlutathioneConjugate(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isGlycerol_3_PhosphateInositol(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isGlyceroLipid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isGlycerophosphoLipid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isGlycinatedCompound(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isGlycosylatedCompound(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isOligoOrPolysaccharide(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isOmegaHydroxyFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isSaturatedFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isSphingoLipid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isSulfatedCompound(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isSulfateEster(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isTetrapyrrole(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isUnsaturatedFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static boolean
isUnsubstitutedSatudatedFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
static void
main(java.lang.String[] args)
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Field Detail
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chemicalClassDefinitions
public static java.util.LinkedHashMap<ChemicalClassFinder.ChemicalClassName,java.util.LinkedHashMap<java.lang.String,java.lang.String[]>> chemicalClassDefinitions
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Method Detail
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compoundMatchesClassSmartsDefinitions
public static boolean compoundMatchesClassSmartsDefinitions(org.openscience.cdk.interfaces.IAtomContainer molecule, ChemicalClassFinder.ChemicalClassName className) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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findChemicalClass
public static ChemicalClassFinder.ChemicalClassName findChemicalClass(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException, java.lang.CloneNotSupportedException, org.openscience.cdk.exception.CDKException
- Throws:
ambit2.smarts.query.SMARTSException
java.lang.CloneNotSupportedException
org.openscience.cdk.exception.CDKException
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AssignChemicalClasses
public static java.util.ArrayList<ChemicalClassFinder.ChemicalClassName> AssignChemicalClasses(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException, java.lang.CloneNotSupportedException, org.openscience.cdk.exception.CDKException
- Throws:
ambit2.smarts.query.SMARTSException
java.lang.CloneNotSupportedException
org.openscience.cdk.exception.CDKException
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isUnsubstitutedSatudatedFattyAcid
public static boolean isUnsubstitutedSatudatedFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
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isFattyAcid
public static boolean isFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
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isUnsaturatedFattyAcid
public static boolean isUnsaturatedFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
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isSaturatedFattyAcid
public static boolean isSaturatedFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isAlphaHydroxyFattyAcid
public static boolean isAlphaHydroxyFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
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isBetaHydroxyFattyAcid
public static boolean isBetaHydroxyFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
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isOmegaHydroxyFattyAcid
public static boolean isOmegaHydroxyFattyAcid(org.openscience.cdk.interfaces.IAtomContainer molecule)
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isEtherLipid
public static boolean isEtherLipid(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isGlyceroLipid
public static boolean isGlyceroLipid(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isGlycerophosphoLipid
public static boolean isGlycerophosphoLipid(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isSphingoLipid
public static boolean isSphingoLipid(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isGlycerol_3_PhosphateInositol
public static boolean isGlycerol_3_PhosphateInositol(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isC23BileAcid
public static boolean isC23BileAcid(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isC24BileAcid
public static boolean isC24BileAcid(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isSulfateEster
public static boolean isSulfateEster(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isTetrapyrrole
public static boolean isTetrapyrrole(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isOligoOrPolysaccharide
public static boolean isOligoOrPolysaccharide(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException, org.openscience.cdk.exception.CDKException
- Throws:
ambit2.smarts.query.SMARTSException
org.openscience.cdk.exception.CDKException
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isGlycosylatedCompound
public static boolean isGlycosylatedCompound(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isSulfatedCompound
public static boolean isSulfatedCompound(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isGlutathioneConjugate
public static boolean isGlutathioneConjugate(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isAcylCoAConjugate
public static boolean isAcylCoAConjugate(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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isGlycinatedCompound
public static boolean isGlycinatedCompound(org.openscience.cdk.interfaces.IAtomContainer molecule) throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
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main
public static void main(java.lang.String[] args) throws ambit2.smarts.query.SMARTSException, java.lang.CloneNotSupportedException, org.openscience.cdk.exception.CDKException
- Throws:
ambit2.smarts.query.SMARTSException
java.lang.CloneNotSupportedException
org.openscience.cdk.exception.CDKException
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