Package org.jmol.adapter.readers.cif
Class MMCifValidationParser
java.lang.Object
org.jmol.adapter.readers.cif.MMCifValidationParser
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionfinalizeRna3d
(Map<String, Integer> modelMap) finalizeValidations
(Viewer vwr, Map<String, Integer> modelMap) Create property_xxxx for each validation category.private int[]
prepare a list of starting atom indices for each model, adding one additional one to indicate 1 + last atom indexprivate SV
getRna3dMap
(String addedData) private void
mapAtomResIDs
(Map<String, Integer> modelMap) Map all atom and residue unit ids to atom indexesset
(AtomSetCollectionReader reader) private String
setProperties
(javajs.util.Lst<Object> propList) Set property_xxx for atoms from list of name, data, modelIndex series.
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Field Details
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asResidues
private boolean asResidues -
reader
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resMap
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atomMap
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Constructor Details
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MMCifValidationParser
public MMCifValidationParser()
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Method Details
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set
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finalizeValidations
Create property_xxxx for each validation category.- Parameters:
vwr
-modelMap
-- Returns:
- loading note
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finalizeRna3d
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getRna3dMap
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mapAtomResIDs
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
Set property_xxx for atoms from list of name, data, modelIndex series.- Parameters:
propList
-- Returns:
- note string
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