Package org.openscience.cdk.io.pubchemxml

Class PubChemXMLHelper

java.lang.Object

org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

public class PubChemXMLHelper
extends Object

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

Fields

Modifier and Type	Field	Description
static final String	EL_ATOM_CONFORMER
static final String	EL_ATOM_CONFORMER_X
static final String	EL_ATOM_CONFORMER_XE
static final String	EL_ATOM_CONFORMER_Y
static final String	EL_ATOM_CONFORMER_YE
static final String	EL_ATOM_CONFORMER_Z
static final String	EL_ATOM_CONFORMER_ZE
static final String	EL_ATOMBLOCK
static final String	EL_ATOMINT
static final String	EL_ATOMINT_AID
static final String	EL_ATOMINT_VALUE
static final String	EL_ATOMSCHARGE
static final String	EL_ATOMSELEMENT
static final String	EL_BONDBLOCK
static final String	EL_BONDID1
static final String	EL_BONDID2
static final String	EL_BONDORDER
static final String	EL_COORDINATES_AID
static final String	EL_COORDINATES_AIDE
static final String	EL_COORDINATESBLOCK
static final String	EL_ELEMENT
static final String	EL_PCCOMPOUND
static final String	EL_PCCOMPOUND_CID
static final String	EL_PCCOMPOUND_ID
static final String	EL_PCCOMPOUNDS
static final String	EL_PCID_ID
static final String	EL_PCSUBSTANCE
static final String	EL_PCSUBSTANCE_SID
static final String	EL_PROPS_BVAL
static final String	EL_PROPS_FVAL
static final String	EL_PROPS_INFODATA
static final String	EL_PROPS_SVAL
static final String	EL_PROPS_URNLABEL
static final String	EL_PROPS_URNNAME
static final String	EL_PROPSBLOCK

Constructor Summary

Constructors

Constructor	Description
PubChemXMLHelper(IChemObjectBuilder builder)

Method Summary

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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

EL_PCCOMPOUND

public static final String EL_PCCOMPOUND

See Also:

• Constant Field Values

EL_PCCOMPOUNDS

public static final String EL_PCCOMPOUNDS

See Also:

• Constant Field Values

EL_PCSUBSTANCE

public static final String EL_PCSUBSTANCE

See Also:

• Constant Field Values

EL_PCSUBSTANCE_SID

public static final String EL_PCSUBSTANCE_SID

See Also:

• Constant Field Values

EL_PCCOMPOUND_ID

public static final String EL_PCCOMPOUND_ID

See Also:

• Constant Field Values

EL_PCCOMPOUND_CID

public static final String EL_PCCOMPOUND_CID

See Also:

• Constant Field Values

EL_PCID_ID

public static final String EL_PCID_ID

See Also:

• Constant Field Values

EL_ATOMBLOCK

public static final String EL_ATOMBLOCK

See Also:

• Constant Field Values

EL_ATOMSELEMENT

public static final String EL_ATOMSELEMENT

See Also:

• Constant Field Values

EL_ATOMSCHARGE

public static final String EL_ATOMSCHARGE

See Also:

• Constant Field Values

EL_ATOMINT

public static final String EL_ATOMINT

See Also:

• Constant Field Values

EL_ATOMINT_AID

public static final String EL_ATOMINT_AID

See Also:

• Constant Field Values

EL_ATOMINT_VALUE

public static final String EL_ATOMINT_VALUE

See Also:

• Constant Field Values

EL_ELEMENT

public static final String EL_ELEMENT

See Also:

• Constant Field Values

EL_COORDINATESBLOCK

public static final String EL_COORDINATESBLOCK

See Also:

• Constant Field Values

EL_COORDINATES_AID

public static final String EL_COORDINATES_AID

See Also:

• Constant Field Values

EL_COORDINATES_AIDE

public static final String EL_COORDINATES_AIDE

See Also:

• Constant Field Values

EL_ATOM_CONFORMER

public static final String EL_ATOM_CONFORMER

See Also:

• Constant Field Values

EL_ATOM_CONFORMER_X

public static final String EL_ATOM_CONFORMER_X

See Also:

• Constant Field Values

EL_ATOM_CONFORMER_XE

public static final String EL_ATOM_CONFORMER_XE

See Also:

• Constant Field Values

EL_ATOM_CONFORMER_Y

public static final String EL_ATOM_CONFORMER_Y

See Also:

• Constant Field Values

EL_ATOM_CONFORMER_YE

public static final String EL_ATOM_CONFORMER_YE

See Also:

• Constant Field Values

EL_ATOM_CONFORMER_Z

public static final String EL_ATOM_CONFORMER_Z

See Also:

• Constant Field Values

EL_ATOM_CONFORMER_ZE

public static final String EL_ATOM_CONFORMER_ZE

See Also:

• Constant Field Values

EL_BONDBLOCK

public static final String EL_BONDBLOCK

See Also:

• Constant Field Values

EL_BONDID1

public static final String EL_BONDID1

See Also:

• Constant Field Values

EL_BONDID2

public static final String EL_BONDID2

See Also:

• Constant Field Values

EL_BONDORDER

public static final String EL_BONDORDER

See Also:

• Constant Field Values

EL_PROPSBLOCK

public static final String EL_PROPSBLOCK

See Also:

• Constant Field Values

EL_PROPS_INFODATA

public static final String EL_PROPS_INFODATA

See Also:

• Constant Field Values

EL_PROPS_URNLABEL

public static final String EL_PROPS_URNLABEL

See Also:

• Constant Field Values

EL_PROPS_URNNAME

public static final String EL_PROPS_URNNAME

See Also:

• Constant Field Values

EL_PROPS_SVAL

public static final String EL_PROPS_SVAL

See Also:

• Constant Field Values

EL_PROPS_FVAL

public static final String EL_PROPS_FVAL

See Also:

• Constant Field Values

EL_PROPS_BVAL

public static final String EL_PROPS_BVAL

See Also:

• Constant Field Values

Constructor Details

PubChemXMLHelper

public PubChemXMLHelper(IChemObjectBuilder builder)
                 throws IOException

Throws:

IOException - if there is error in getting the IsotopeFactory

Method Details

parseCompoundsBlock

public IAtomContainerSet parseCompoundsBlock(XMLStreamReader parser)
                                      throws Exception

Throws:

Exception

parseSubstance

public IChemModel parseSubstance(XMLStreamReader parser)
                          throws Exception

Throws:

Exception

getSID

public String getSID(XMLStreamReader parser)
              throws Exception

Throws:

Exception

getCID

public String getCID(XMLStreamReader parser)
              throws Exception

Throws:

Exception

parseAtomElements

public void parseAtomElements(XMLStreamReader parser,
 IAtomContainer molecule)
                       throws Exception

Throws:

Exception

parserAtomBlock

public void parserAtomBlock(XMLStreamReader parser,
 IAtomContainer molecule)
                     throws Exception

Throws:

Exception

parserCompoundInfoData

public void parserCompoundInfoData(XMLStreamReader parser,
 IAtomContainer molecule)
                            throws Exception

Throws:

Exception

parseAtomCharges

public void parseAtomCharges(XMLStreamReader parser,
 IAtomContainer molecule)
                      throws Exception

Throws:

Exception

parseMolecule

public IAtomContainer parseMolecule(XMLStreamReader parser,
 IChemObjectBuilder builder)
                             throws Exception

Throws:

Exception

parserBondBlock

public void parserBondBlock(XMLStreamReader parser,
 IAtomContainer molecule)
                     throws Exception

Throws:

Exception

parserCoordBlock

public void parserCoordBlock(XMLStreamReader parser,
 IAtomContainer molecule)
                      throws Exception

Throws:

Exception