CMLCoreModule (cdk-io 2.1.1 API)

java.lang.Object
- org.openscience.cdk.io.cml.CMLCoreModule

All Implemented Interfaces:

ICMLModule

Direct Known Subclasses:

CDKConvention, CMLReactionModule, JMOLANIMATIONConvention, MDLMolConvention, PDBConvention, PMPConvention, QSARConvention
```
public class CMLCoreModule
extends Object
implements ICMLModule
```
Core CML 1.x and 2.x elements are parsed by this class (see [Willighagen, E.L., Processing CML Conventions in Java, Internet Journal of Chemistry, 2001, 4:?-?]).
Please file a bug report if this parser fails to parse a certain element or attribute value in a valid CML document.

Author:

Egon Willighagen <egonw@sci.kun.nl>

Source code:
master

Belongs to CDK module:
io

Field Summary

Fields
Modifier and Type	Field and Description
`protected List<String>`	`atomAromaticities`
`protected int`	`atomCounter`
`protected Map<Integer,List<String>>`	`atomCustomProperty`
`protected List<String>`	`atomDictRefs`
`protected Map<String,IAtom>`	`atomEnumeration`
`protected List<String>`	`atomicNumbers`
`protected List<String>`	`atomParities`
`protected List<String>`	`bondARef1`
`protected List<String>`	`bondARef2`
`protected List<Boolean>`	`bondAromaticity`
`protected int`	`bondCounter`
`protected Map<String,Map<String,String>>`	`bondCustomProperty`
`protected List<String>`	`bondDictRefs`
`protected List<String>`	`bondElid`
`protected List<String>`	`bondid`
`protected List<String>`	`bondStereo`
`protected String`	`BUILTIN`
`protected int`	`crystalScalar`
`protected int`	`curRef`
`protected IAtom`	`currentAtom`
`protected IBond`	`currentBond`
`protected String`	`currentChars`
`protected IChemFile`	`currentChemFile`
`protected IChemModel`	`currentChemModel`
`protected IChemSequence`	`currentChemSequence`
`protected int`	`CurrentElement`
`protected IAtomContainer`	`currentMolecule`
`protected IAtomContainerSet`	`currentMoleculeSet`
`protected IMonomer`	`currentMonomer`
`protected IReaction`	`currentReaction`
`protected IReactionSet`	`currentReactionSet`
`protected IStrand`	`currentStrand`
`protected String`	`DICTREF`
`protected String`	`elementTitle`
`protected List<String>`	`elid`
`protected List<String>`	`elsym`
`protected List<String>`	`eltitles`
`protected List<String>`	`exactMasses`
`protected List<String>`	`formalCharges`
`protected List<String>`	`formula`
`protected int`	`formulaCounter`
`protected List<String>`	`hCounts`
`protected String`	`inchi`
`protected List<String>`	`isotope`
`protected ILoggingTool`	`logger`
`protected List<String>`	`moleculeCustomProperty`
`protected List<String>`	`occupancies`
`protected List<String>`	`order`
`protected List<String>`	`parityARef1`
`protected List<String>`	`parityARef2`
`protected List<String>`	`parityARef3`
`protected List<String>`	`parityARef4`
`protected boolean`	`parityAtomsGiven`
`protected boolean`	`parityGiven`
`protected List<String>`	`partialCharges`
`protected List<String>`	`spinMultiplicities`
`protected boolean`	`stereoGiven`
`protected String`	`SYSTEMID`
`protected double[]`	`unitcellparams`
`protected List<String>`	`x2`
`protected List<String>`	`x3`
`protected List<String>`	`xfract`
`protected List<String>`	`y2`
`protected List<String>`	`y3`
`protected List<String>`	`yfract`
`protected List<String>`	`z3`
`protected List<String>`	`zfract`

Constructor Summary

Constructors
Constructor and Description

CMLCoreModule(IChemFile chemFile)

CMLCoreModule(ICMLModule conv)

Constructors
Constructor and Description
`CMLCoreModule(IChemFile chemFile)`
`CMLCoreModule(ICMLModule conv)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected int`	`addArrayElementsTo(List<String> toAddto, String array)`
`void`	`characterData(org.openscience.cdk.io.cml.CMLStack xpath, char[] ch, int start, int length)`
`void`	`endDocument()`
`void`	`endElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String name, String raw)`
`void`	`inherit(ICMLModule convention)`
`protected void`	`newAtomData()` Clean all data about read atoms.
`protected void`	`newBondData()` Clean all data about read bonds.
`protected void`	`newCrystalData()` Clean all data about read bonds.
`protected void`	`newFormulaData()` Clean all data about read formulas.
`protected void`	`newMolecule()` Clean all data about parsed data.
`protected void`	`newMoleculeData()` Clean all data about the molecule itself.
`protected void`	`notify(String message, String systemId, int line, int column)`
`IChemFile`	`returnChemFile()`
`void`	`startDocument()`
`void`	`startElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw, Attributes atts)`
`protected void`	`storeAtomData()`
`protected void`	`storeBondData()`
`protected void`	`storeData()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger
```
protected ILoggingTool logger
```

SYSTEMID
```
protected final String SYSTEMID
```
See Also:

Constant Field Values

currentChemFile
```
protected IChemFile currentChemFile
```

currentMolecule

protected IAtomContainer currentMolecule

currentMoleculeSet

protected IAtomContainerSet currentMoleculeSet

currentChemModel
```
protected IChemModel currentChemModel
```

currentChemSequence

protected IChemSequence currentChemSequence

currentReactionSet

protected IReactionSet currentReactionSet

currentReaction
```
protected IReaction currentReaction
```

currentAtom
```
protected IAtom currentAtom
```

currentBond
```
protected IBond currentBond
```

currentStrand
```
protected IStrand currentStrand
```

currentMonomer
```
protected IMonomer currentMonomer
```

atomEnumeration

protected Map<String,IAtom> atomEnumeration

moleculeCustomProperty

protected List<String> moleculeCustomProperty

formulaCounter
```
protected int formulaCounter
```

atomCounter
```
protected int atomCounter
```

elsym
```
protected List<String> elsym
```

eltitles
```
protected List<String> eltitles
```

elid
```
protected List<String> elid
```

formula
```
protected List<String> formula
```

formalCharges
```
protected List<String> formalCharges
```

partialCharges
```
protected List<String> partialCharges
```

isotope
```
protected List<String> isotope
```

atomicNumbers
```
protected List<String> atomicNumbers
```

exactMasses
```
protected List<String> exactMasses
```

x3
```
protected List<String> x3
```

y3
```
protected List<String> y3
```

z3
```
protected List<String> z3
```

x2
```
protected List<String> x2
```

y2
```
protected List<String> y2
```

xfract
```
protected List<String> xfract
```

yfract
```
protected List<String> yfract
```

zfract
```
protected List<String> zfract
```

hCounts
```
protected List<String> hCounts
```

atomParities
```
protected List<String> atomParities
```

parityARef1
```
protected List<String> parityARef1
```

parityARef2
```
protected List<String> parityARef2
```

parityARef3
```
protected List<String> parityARef3
```

parityARef4
```
protected List<String> parityARef4
```

atomDictRefs
```
protected List<String> atomDictRefs
```

atomAromaticities

protected List<String> atomAromaticities

spinMultiplicities

protected List<String> spinMultiplicities

occupancies
```
protected List<String> occupancies
```

atomCustomProperty

protected Map<Integer,List<String>> atomCustomProperty

parityAtomsGiven
```
protected boolean parityAtomsGiven
```

parityGiven
```
protected boolean parityGiven
```

bondCounter
```
protected int bondCounter
```

bondid
```
protected List<String> bondid
```

bondARef1
```
protected List<String> bondARef1
```

bondARef2
```
protected List<String> bondARef2
```

order
```
protected List<String> order
```

bondStereo
```
protected List<String> bondStereo
```

bondDictRefs
```
protected List<String> bondDictRefs
```

bondElid
```
protected List<String> bondElid
```

bondAromaticity

protected List<Boolean> bondAromaticity

bondCustomProperty

protected Map<String,Map<String,String>> bondCustomProperty

stereoGiven
```
protected boolean stereoGiven
```

inchi
```
protected String inchi
```

curRef
```
protected int curRef
```

CurrentElement
```
protected int CurrentElement
```

BUILTIN
```
protected String BUILTIN
```

DICTREF
```
protected String DICTREF
```

elementTitle
```
protected String elementTitle
```

currentChars
```
protected String currentChars
```

unitcellparams
```
protected double[] unitcellparams
```

crystalScalar
```
protected int crystalScalar
```

Constructor Detail

CMLCoreModule

public CMLCoreModule(IChemFile chemFile)

CMLCoreModule
```
public CMLCoreModule(ICMLModule conv)
```

Method Detail

inherit
```
public void inherit(ICMLModule convention)
```
Specified by:

inherit in interface ICMLModule

returnChemFile
```
public IChemFile returnChemFile()
```
Specified by:

returnChemFile in interface ICMLModule

newMolecule
```
protected void newMolecule()
```
Clean all data about parsed data.

newMoleculeData
```
protected void newMoleculeData()
```
Clean all data about the molecule itself.

newFormulaData
```
protected void newFormulaData()
```
Clean all data about read formulas.

newAtomData
```
protected void newAtomData()
```
Clean all data about read atoms.

newBondData
```
protected void newBondData()
```
Clean all data about read bonds.

newCrystalData
```
protected void newCrystalData()
```
Clean all data about read bonds.

startDocument
```
public void startDocument()
```
Specified by:

startDocument in interface ICMLModule

endDocument
```
public void endDocument()
```
Specified by:

endDocument in interface ICMLModule

startElement

public void startElement(org.openscience.cdk.io.cml.CMLStack xpath,
                         String uri,
                         String local,
                         String raw,
                         Attributes atts)

Specified by:: startElement in interface ICMLModule

endElement

public void endElement(org.openscience.cdk.io.cml.CMLStack xpath,
                       String uri,
                       String name,
                       String raw)

Specified by:: endElement in interface ICMLModule

characterData

public void characterData(org.openscience.cdk.io.cml.CMLStack xpath,
                          char[] ch,
                          int start,
                          int length)

Specified by:: characterData in interface ICMLModule

notify

protected void notify(String message,
                      String systemId,
                      int line,
                      int column)

storeData
```
protected void storeData()
```

storeAtomData
```
protected void storeAtomData()
```

storeBondData
```
protected void storeBondData()
```

addArrayElementsTo

protected int addArrayElementsTo(List<String> toAddto,
                                 String array)

Class CMLCoreModule

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

logger

SYSTEMID

currentChemFile

currentMolecule

currentMoleculeSet

currentChemModel

currentChemSequence

currentReactionSet

currentReaction

currentAtom

currentBond

currentStrand

currentMonomer

atomEnumeration

moleculeCustomProperty

formulaCounter

atomCounter

elsym

eltitles

elid

formula

formalCharges

partialCharges

isotope

atomicNumbers

exactMasses

x3

y3

z3

x2

y2

xfract

yfract

zfract

hCounts

atomParities

parityARef1

parityARef2

parityARef3

parityARef4

atomDictRefs

atomAromaticities

spinMultiplicities

occupancies

atomCustomProperty

parityAtomsGiven

parityGiven

bondCounter

bondid

bondARef1

bondARef2

order

bondStereo

bondDictRefs

bondElid

bondAromaticity

bondCustomProperty

stereoGiven

inchi

curRef

CurrentElement

BUILTIN

DICTREF

elementTitle

currentChars

unitcellparams

crystalScalar

Constructor Detail

CMLCoreModule

CMLCoreModule

Method Detail

inherit

returnChemFile

newMolecule