Package org.jmol.dssx
Class DSSR1
- java.lang.Object
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- org.jmol.dssx.AnnotationParser
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- org.jmol.dssx.DSSR1
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- All Implemented Interfaces:
JmolAnnotationParser
public class DSSR1 extends AnnotationParser
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
Fields Modifier and Type Field Description private static String
DSSR_PATHS
The paths to the unit id data within the structure.
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Constructor Summary
Constructors Constructor Description DSSR1()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
calculateDSSRStructure(Viewer vwr, javajs.util.BS bsAtoms)
String
fixDSSRJSONMap(Map<String,Object> map)
kissingLoops and coaxStacks use index arrays instead of duplication;private void
fixIndices(Map<String,Object> map, String key, String root)
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)
String
getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport)
private void
getPoint(Map<String,Object> frame, String item, javajs.util.P3 pt)
private void
setBioPolymers(BioModel m, boolean b)
void
setGroup1(ModelSet ms, int modelIndex)
private NucleicMonomer
setRes(Atom atom)
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Methods inherited from class org.jmol.dssx.AnnotationParser
catalogStructureUnits, catalogValidations, fixAtoms, getAnnotationInfo, getAtomValidation, getAttachedAtomForPDBH, initializeAnnotation
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Field Detail
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DSSR_PATHS
private static final String 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:
- Constant Field Values
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Method Detail
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calculateDSSRStructure
public String calculateDSSRStructure(Viewer vwr, javajs.util.BS bsAtoms)
- Specified by:
calculateDSSRStructure
in interfaceJmolAnnotationParser
- Overrides:
calculateDSSRStructure
in classAnnotationParser
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fixDSSRJSONMap
public String fixDSSRJSONMap(Map<String,Object> map)
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
private void fixIndices(Map<String,Object> map, String key, String root)
create a key/value pair root+"s" for all indices of root+"_indices"- Parameters:
map
-key
-root
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getBasePairs
public void getBasePairs(Viewer vwr, int modelIndex)
- Specified by:
getBasePairs
in interfaceJmolAnnotationParser
- Overrides:
getBasePairs
in classAnnotationParser
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setBioPolymers
private void setBioPolymers(BioModel m, boolean b)
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setRes
private NucleicMonomer setRes(Atom atom)
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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
public void setGroup1(ModelSet ms, int modelIndex)
- Specified by:
setGroup1
in interfaceJmolAnnotationParser
- Overrides:
setGroup1
in classAnnotationParser
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getAtomicDSSRData
public void getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData, String dataType)
- Specified by:
getAtomicDSSRData
in interfaceJmolAnnotationParser
- Overrides:
getAtomicDSSRData
in classAnnotationParser
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getDSSRFrame
public javajs.util.P3[] getDSSRFrame(Map<String,Object> nt)
- Specified by:
getDSSRFrame
in interfaceJmolAnnotationParser
- Overrides:
getDSSRFrame
in classAnnotationParser
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