Package org.jmol.dssx
Class DSSR1
java.lang.Object
org.jmol.dssx.AnnotationParser
org.jmol.dssx.DSSR1
- All Implemented Interfaces:
JmolAnnotationParser
A parser for output from 3DNA web service.
load =1d66/dssr
also other annotations now,
load *1cbs/dom
calls EBI for the mmCIF file and also retrieves the domains mapping JSON
report.
load *1cbs/val
calls EBI for the mmCIF file and also retrieves the validation outliers JSON
report.
Bob Hanson July 2014
- Author:
- Bob Hanson hansonr@stolaf.edu
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate static final String
The paths to the unit id data within the structure. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncalculateDSSRStructure
(Viewer vwr, javajs.util.BS bsAtoms) fixDSSRJSONMap
(Map<String, Object> map) kissingLoops and coaxStacks use index arrays instead of duplication;private void
create a key/value pair root+"s" for all indices of root+"_indices"javajs.util.BS
getAtomBits
(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, javajs.util.BS bsModel) void
getAtomicDSSRData
(ModelSet ms, int modelIndex, float[] dssrData, String dataType) void
getBasePairs
(Viewer vwr, int modelIndex) private String
getDSSRForModel
(Viewer vwr, int modelIndex) javajs.util.P3[]
getDSSRFrame
(Map<String, Object> nt) private void
private void
setBioPolymers
(BioModel m, boolean b) void
private NucleicMonomer
Methods inherited from class org.jmol.dssx.AnnotationParser
catalogStructureUnits, catalogValidations, fixAtoms, getAnnotationInfo, getAtomValidation, getAttachedAtomForPDBH, initializeAnnotation
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Field Details
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DSSR_PATHS
The paths to the unit id data within the structure. This is one long string; all lowercase, each surrounded by double periods.- See Also:
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Constructor Details
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DSSR1
public DSSR1()
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Method Details
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calculateDSSRStructure
- Specified by:
calculateDSSRStructure
in interfaceJmolAnnotationParser
- Overrides:
calculateDSSRStructure
in classAnnotationParser
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getDSSRForModel
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fixDSSRJSONMap
kissingLoops and coaxStacks use index arrays instead of duplication;- Specified by:
fixDSSRJSONMap
in interfaceJmolAnnotationParser
- Overrides:
fixDSSRJSONMap
in classAnnotationParser
- Parameters:
map
-- Returns:
- msg
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fixIndices
create a key/value pair root+"s" for all indices of root+"_indices"- Parameters:
map
-key
-root
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getBasePairs
- Specified by:
getBasePairs
in interfaceJmolAnnotationParser
- Overrides:
getBasePairs
in classAnnotationParser
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setBioPolymers
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setRes
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getAtomBits
public javajs.util.BS getAtomBits(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, javajs.util.BS bsModel) - Specified by:
getAtomBits
in interfaceJmolAnnotationParser
- Overrides:
getAtomBits
in classAnnotationParser
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getHBonds
public String getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport) - Specified by:
getHBonds
in interfaceJmolAnnotationParser
- Overrides:
getHBonds
in classAnnotationParser
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setGroup1
- Specified by:
setGroup1
in interfaceJmolAnnotationParser
- Overrides:
setGroup1
in classAnnotationParser
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getAtomicDSSRData
- Specified by:
getAtomicDSSRData
in interfaceJmolAnnotationParser
- Overrides:
getAtomicDSSRData
in classAnnotationParser
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getDSSRFrame
- Specified by:
getDSSRFrame
in interfaceJmolAnnotationParser
- Overrides:
getDSSRFrame
in classAnnotationParser
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getPoint
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