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
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
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
characterData
(org.openscience.cdk.io.cml.CMLStack xpath, char[] ch, int start, int length) void
void
endElement
(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw) void
void
startElement
(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw, Attributes atts) protected void
protected void
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 Details
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PDBConvention
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PDBConvention
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Method Details
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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() -
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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