Package org.openscience.cdk.io.cml
Class PDBConvention
- java.lang.Object
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- org.openscience.cdk.io.cml.CMLCoreModule
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- org.openscience.cdk.io.cml.PDBConvention
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- 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
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Field Summary
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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
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Constructor Summary
Constructors Constructor Description PDBConvention(IChemFile chemFile)
PDBConvention(ICMLModule conv)
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Method Summary
All Methods Instance Methods Concrete Methods 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()
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Methods inherited from class org.openscience.cdk.io.cml.CMLCoreModule
addArrayElementsTo, inherit, newAtomData, newBondData, newCrystalData, newFormulaData, newMolecule, newMoleculeData, notify, returnChemFile, startDocument, storeBondData
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Constructor Detail
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PDBConvention
public PDBConvention(IChemFile chemFile)
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PDBConvention
public PDBConvention(ICMLModule conv)
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Method Detail
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endDocument
public void endDocument()
- Specified by:
endDocument
in interfaceICMLModule
- Overrides:
endDocument
in classCMLCoreModule
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startElement
public void startElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw, Attributes atts)
- Specified by:
startElement
in interfaceICMLModule
- Overrides:
startElement
in classCMLCoreModule
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newSequence
public void newSequence()
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endElement
public void endElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw)
- Specified by:
endElement
in interfaceICMLModule
- Overrides:
endElement
in classCMLCoreModule
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characterData
public void characterData(org.openscience.cdk.io.cml.CMLStack xpath, char[] ch, int start, int length)
- Specified by:
characterData
in interfaceICMLModule
- Overrides:
characterData
in classCMLCoreModule
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storeData
protected void storeData()
- Overrides:
storeData
in classCMLCoreModule
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storeAtomData
protected void storeAtomData()
- Overrides:
storeAtomData
in classCMLCoreModule
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