Class PubChemXMLHelper
- java.lang.Object
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- org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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Field Summary
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Constructor Summary
Constructors Constructor Description PubChemXMLHelper(IChemObjectBuilder builder)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getCID(XMLStreamReader parser)
String
getSID(XMLStreamReader parser)
void
parseAtomCharges(XMLStreamReader parser, IAtomContainer molecule)
void
parseAtomElements(XMLStreamReader parser, IAtomContainer molecule)
IAtomContainerSet
parseCompoundsBlock(XMLStreamReader parser)
IAtomContainer
parseMolecule(XMLStreamReader parser, IChemObjectBuilder builder)
void
parserAtomBlock(XMLStreamReader parser, IAtomContainer molecule)
void
parserBondBlock(XMLStreamReader parser, IAtomContainer molecule)
void
parserCompoundInfoData(XMLStreamReader parser, IAtomContainer molecule)
void
parserCoordBlock(XMLStreamReader parser, IAtomContainer molecule)
IChemModel
parseSubstance(XMLStreamReader parser)
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Field Detail
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EL_PCCOMPOUND
public static final String EL_PCCOMPOUND
- See Also:
- Constant Field Values
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EL_PCCOMPOUNDS
public static final String EL_PCCOMPOUNDS
- See Also:
- Constant Field Values
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EL_PCSUBSTANCE
public static final String EL_PCSUBSTANCE
- See Also:
- Constant Field Values
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EL_PCSUBSTANCE_SID
public static final String EL_PCSUBSTANCE_SID
- See Also:
- Constant Field Values
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EL_PCCOMPOUND_ID
public static final String EL_PCCOMPOUND_ID
- See Also:
- Constant Field Values
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EL_PCCOMPOUND_CID
public static final String EL_PCCOMPOUND_CID
- See Also:
- Constant Field Values
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EL_PCID_ID
public static final String EL_PCID_ID
- See Also:
- Constant Field Values
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EL_ATOMBLOCK
public static final String EL_ATOMBLOCK
- See Also:
- Constant Field Values
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EL_ATOMSELEMENT
public static final String EL_ATOMSELEMENT
- See Also:
- Constant Field Values
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EL_ATOMSCHARGE
public static final String EL_ATOMSCHARGE
- See Also:
- Constant Field Values
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EL_ATOMINT
public static final String EL_ATOMINT
- See Also:
- Constant Field Values
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EL_ATOMINT_AID
public static final String EL_ATOMINT_AID
- See Also:
- Constant Field Values
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EL_ATOMINT_VALUE
public static final String EL_ATOMINT_VALUE
- See Also:
- Constant Field Values
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EL_ELEMENT
public static final String EL_ELEMENT
- See Also:
- Constant Field Values
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EL_COORDINATESBLOCK
public static final String EL_COORDINATESBLOCK
- See Also:
- Constant Field Values
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EL_COORDINATES_AID
public static final String EL_COORDINATES_AID
- See Also:
- Constant Field Values
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EL_COORDINATES_AIDE
public static final String EL_COORDINATES_AIDE
- See Also:
- Constant Field Values
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EL_ATOM_CONFORMER
public static final String EL_ATOM_CONFORMER
- See Also:
- Constant Field Values
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EL_ATOM_CONFORMER_X
public static final String EL_ATOM_CONFORMER_X
- See Also:
- Constant Field Values
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EL_ATOM_CONFORMER_XE
public static final String EL_ATOM_CONFORMER_XE
- See Also:
- Constant Field Values
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EL_ATOM_CONFORMER_Y
public static final String EL_ATOM_CONFORMER_Y
- See Also:
- Constant Field Values
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EL_ATOM_CONFORMER_YE
public static final String EL_ATOM_CONFORMER_YE
- See Also:
- Constant Field Values
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EL_ATOM_CONFORMER_Z
public static final String EL_ATOM_CONFORMER_Z
- See Also:
- Constant Field Values
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EL_ATOM_CONFORMER_ZE
public static final String EL_ATOM_CONFORMER_ZE
- See Also:
- Constant Field Values
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EL_BONDBLOCK
public static final String EL_BONDBLOCK
- See Also:
- Constant Field Values
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EL_BONDID1
public static final String EL_BONDID1
- See Also:
- Constant Field Values
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EL_BONDID2
public static final String EL_BONDID2
- See Also:
- Constant Field Values
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EL_BONDORDER
public static final String EL_BONDORDER
- See Also:
- Constant Field Values
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EL_PROPSBLOCK
public static final String EL_PROPSBLOCK
- See Also:
- Constant Field Values
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EL_PROPS_INFODATA
public static final String EL_PROPS_INFODATA
- See Also:
- Constant Field Values
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EL_PROPS_URNLABEL
public static final String EL_PROPS_URNLABEL
- See Also:
- Constant Field Values
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EL_PROPS_URNNAME
public static final String EL_PROPS_URNNAME
- See Also:
- Constant Field Values
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EL_PROPS_SVAL
public static final String EL_PROPS_SVAL
- See Also:
- Constant Field Values
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EL_PROPS_FVAL
public static final String EL_PROPS_FVAL
- See Also:
- Constant Field Values
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EL_PROPS_BVAL
public static final String EL_PROPS_BVAL
- See Also:
- Constant Field Values
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Constructor Detail
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PubChemXMLHelper
public PubChemXMLHelper(IChemObjectBuilder builder) throws IOException
- Throws:
IOException
- if there is error in getting theIsotopeFactory
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Method Detail
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parseCompoundsBlock
public IAtomContainerSet parseCompoundsBlock(XMLStreamReader parser) throws Exception
- Throws:
Exception
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parseSubstance
public IChemModel parseSubstance(XMLStreamReader parser) throws Exception
- Throws:
Exception
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getSID
public String getSID(XMLStreamReader parser) throws Exception
- Throws:
Exception
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getCID
public String getCID(XMLStreamReader parser) throws Exception
- Throws:
Exception
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parseAtomElements
public void parseAtomElements(XMLStreamReader parser, IAtomContainer molecule) throws Exception
- Throws:
Exception
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parserAtomBlock
public void parserAtomBlock(XMLStreamReader parser, IAtomContainer molecule) throws Exception
- Throws:
Exception
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parserCompoundInfoData
public void parserCompoundInfoData(XMLStreamReader parser, IAtomContainer molecule) throws Exception
- Throws:
Exception
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parseAtomCharges
public void parseAtomCharges(XMLStreamReader parser, IAtomContainer molecule) throws Exception
- Throws:
Exception
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parseMolecule
public IAtomContainer parseMolecule(XMLStreamReader parser, IChemObjectBuilder builder) throws Exception
- Throws:
Exception
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parserBondBlock
public void parserBondBlock(XMLStreamReader parser, IAtomContainer molecule) throws Exception
- Throws:
Exception
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parserCoordBlock
public void parserCoordBlock(XMLStreamReader parser, IAtomContainer molecule) throws Exception
- Throws:
Exception
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