Package org.jmol.adapter.readers.cif
Class MMCifValidationParser
- java.lang.Object
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- org.jmol.adapter.readers.cif.MMCifValidationParser
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public class MMCifValidationParser extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description private boolean
asResidues
private java.util.Map<java.lang.String,java.lang.Integer>
atomMap
private AtomSetCollectionReader
reader
private java.util.Map<java.lang.String,int[]>
resMap
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Constructor Summary
Constructors Constructor Description MMCifValidationParser()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
finalizeRna3d(java.util.Map<java.lang.String,java.lang.Integer> modelMap)
java.lang.String
finalizeValidations(Viewer vwr, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
Create property_xxxx for each validation category.private int[]
getModelAtomIndices()
prepare a list of starting atom indices for each model, adding one additional one to indicate 1 + last atom indexprivate SV
getRna3dMap(java.lang.String addedData)
private void
mapAtomResIDs(java.util.Map<java.lang.String,java.lang.Integer> modelMap)
Map all atom and residue unit ids to atom indexesMMCifValidationParser
set(AtomSetCollectionReader reader)
private java.lang.String
setProperties(javajs.util.Lst<java.lang.Object> propList)
Set property_xxx for atoms from list of name, data, modelIndex series.
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Field Detail
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asResidues
private boolean asResidues
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reader
private AtomSetCollectionReader reader
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resMap
private java.util.Map<java.lang.String,int[]> resMap
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atomMap
private java.util.Map<java.lang.String,java.lang.Integer> atomMap
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Method Detail
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set
public MMCifValidationParser set(AtomSetCollectionReader reader)
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finalizeValidations
public java.lang.String finalizeValidations(Viewer vwr, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
Create property_xxxx for each validation category.- Parameters:
vwr
-modelMap
-- Returns:
- loading note
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finalizeRna3d
public java.lang.String finalizeRna3d(java.util.Map<java.lang.String,java.lang.Integer> modelMap)
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getRna3dMap
private SV getRna3dMap(java.lang.String addedData)
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mapAtomResIDs
private void mapAtomResIDs(java.util.Map<java.lang.String,java.lang.Integer> modelMap)
Map all atom and residue unit ids to atom indexes- Parameters:
modelMap
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getModelAtomIndices
private int[] getModelAtomIndices()
prepare a list of starting atom indices for each model, adding one additional one to indicate 1 + last atom index- Returns:
- array
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setProperties
private java.lang.String setProperties(javajs.util.Lst<java.lang.Object> propList)
Set property_xxx for atoms from list of name, data, modelIndex series.- Parameters:
propList
-- Returns:
- note string
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