Class PubChemXMLHelper
java.lang.Object
org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
Helper class to parse PubChem XML documents.
- Author:
- Egon Willighagen <egonw@users.sf.net>
- Source code:
- main
- Belongs to CDK module:
- io
- Created on:
- 2008-05-05
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetCID
(XMLStreamReader parser) getSID
(XMLStreamReader parser) void
parseAtomCharges
(XMLStreamReader parser, IAtomContainer molecule) void
parseAtomElements
(XMLStreamReader parser, IAtomContainer molecule) parseCompoundsBlock
(XMLStreamReader parser) 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) parseSubstance
(XMLStreamReader parser)
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Field Details
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EL_PCCOMPOUND
- See Also:
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EL_PCCOMPOUNDS
- See Also:
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EL_PCSUBSTANCE
- See Also:
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EL_PCSUBSTANCE_SID
- See Also:
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EL_PCCOMPOUND_ID
- See Also:
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EL_PCCOMPOUND_CID
- See Also:
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EL_PCID_ID
- See Also:
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EL_ATOMBLOCK
- See Also:
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EL_ATOMSELEMENT
- See Also:
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EL_ATOMSCHARGE
- See Also:
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EL_ATOMINT
- See Also:
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EL_ATOMINT_AID
- See Also:
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EL_ATOMINT_VALUE
- See Also:
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EL_ELEMENT
- See Also:
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EL_COORDINATESBLOCK
- See Also:
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EL_COORDINATES_AID
- See Also:
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EL_COORDINATES_AIDE
- See Also:
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EL_ATOM_CONFORMER
- See Also:
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EL_ATOM_CONFORMER_X
- See Also:
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EL_ATOM_CONFORMER_XE
- See Also:
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EL_ATOM_CONFORMER_Y
- See Also:
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EL_ATOM_CONFORMER_YE
- See Also:
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EL_ATOM_CONFORMER_Z
- See Also:
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EL_ATOM_CONFORMER_ZE
- See Also:
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EL_BONDBLOCK
- See Also:
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EL_BONDID1
- See Also:
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EL_BONDID2
- See Also:
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EL_BONDORDER
- See Also:
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EL_PROPSBLOCK
- See Also:
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EL_PROPS_INFODATA
- See Also:
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EL_PROPS_URNLABEL
- See Also:
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EL_PROPS_URNNAME
- See Also:
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EL_PROPS_SVAL
- See Also:
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EL_PROPS_FVAL
- See Also:
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EL_PROPS_BVAL
- See Also:
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Constructor Details
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PubChemXMLHelper
- Throws:
IOException
- if there is error in getting theIsotopeFactory
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Method Details
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parseCompoundsBlock
- Throws:
Exception
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parseSubstance
- Throws:
Exception
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getSID
- Throws:
Exception
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getCID
- Throws:
Exception
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parseAtomElements
- Throws:
Exception
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parserAtomBlock
- Throws:
Exception
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parserCompoundInfoData
public void parserCompoundInfoData(XMLStreamReader parser, IAtomContainer molecule) throws Exception - Throws:
Exception
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parseAtomCharges
- Throws:
Exception
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parseMolecule
public IAtomContainer parseMolecule(XMLStreamReader parser, IChemObjectBuilder builder) throws Exception - Throws:
Exception
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parserBondBlock
- Throws:
Exception
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parserCoordBlock
- Throws:
Exception
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