Package org.openscience.cdk.io.cml

Class PDBConvention

java.lang.Object

org.openscience.cdk.io.cml.CMLCoreModule

org.openscience.cdk.io.cml.PDBConvention

All Implemented Interfaces:

ICMLModule

public class PDBConvention
extends CMLCoreModule

Implements the PDB convention used by PDB2CML.

This is a lousy implementation, though. Problems that will arise:

• when this new convention is adopted in the root element no currentFrame was set. This is done when <list sequence=""> is found
• multiple sequences are not yet supported
• the frame is now added when the doc is ended, which will result in problems but work for one sequence files made by PDB2CML v.??

What is does:

• work for now
• give an idea on the API of the plugable CML import filter (a real one will be made)
• read CML files generated with Steve Zara's PDB 2 CML converter (of which version 1999 produces invalid CML 1.0)

Author:

Egon Willighagen <egonw@sci.kun.nl>

Source code:

main

Belongs to CDK module:

io

Field Summary

Fields inherited from class org.openscience.cdk.io.cml.CMLCoreModule

atomAromaticities, atomCounter, atomCustomProperty, atomDictRefs, atomEnumeration, atomicNumbers, atomParities, bondARef1, bondARef2, bondAromaticity, bondCounter, bondCustomProperty, bondDictRefs, bondElid, bondid, bondStereo, BUILTIN, crystalScalar, curRef, currentAtom, currentBond, currentChars, currentChemFile, currentChemModel, currentChemSequence, CurrentElement, currentMolecule, currentMoleculeSet, currentMonomer, currentReaction, currentReactionSet, currentStrand, DICTREF, elementTitle, elid, elsym, eltitles, exactMasses, formalCharges, formula, formulaCounter, hCounts, inchi, isotope, logger, moleculeCustomProperty, occupancies, order, parityARef1, parityARef2, parityARef3, parityARef4, parityAtomsGiven, parityGiven, partialCharges, spinMultiplicities, stereoGiven, SYSTEMID, unitcellparams, x2, x3, xfract, y2, y3, yfract, z3, zfract

Constructor Summary

Constructors

Constructor	Description
PDBConvention(IChemFile chemFile)
PDBConvention(ICMLModule conv)

Method Summary

Modifier and Type	Method	Description
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 local, String raw)
void	newSequence()
void	startElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw, Attributes atts)
protected void	storeAtomData()
protected void	storeData()

Methods inherited from class org.openscience.cdk.io.cml.CMLCoreModule

addArrayElementsTo, inherit, newAtomData, newBondData, newCrystalData, newFormulaData, newMolecule, newMoleculeData, notify, returnChemFile, startDocument, storeBondData

Methods inherited from class java.lang.Object

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

Constructor Detail

PDBConvention

public PDBConvention(IChemFile chemFile)

PDBConvention

public PDBConvention(ICMLModule conv)

Method Detail

endDocument

public void endDocument()

Specified by:

endDocument in interface ICMLModule

Overrides:

endDocument in class CMLCoreModule

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

Overrides:

startElement in class CMLCoreModule

newSequence

public void newSequence()

endElement

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

Specified by:

endElement in interface ICMLModule

Overrides:

endElement in class CMLCoreModule

characterData

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

Specified by:

characterData in interface ICMLModule

Overrides:

characterData in class CMLCoreModule

storeData

protected void storeData()

Overrides:

storeData in class CMLCoreModule

storeAtomData

protected void storeAtomData()

Overrides:

storeAtomData in class CMLCoreModule