public class DSSR1 extends AnnotationParser
Modifier and Type | Field and Description |
---|---|
private static String |
DSSR_PATHS
The paths to the unit id data within the structure.
|
Constructor and Description |
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DSSR1() |
Modifier and Type | Method and Description |
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String |
calculateDSSRStructure(Viewer vwr,
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"
|
BS |
getAtomBits(Viewer vwr,
String key,
Object dbObj,
Map<String,Object> annotationCache,
int type,
int modelIndex,
BS bsModel) |
void |
getBasePairs(Viewer vwr,
int modelIndex) |
private String |
getDSSRForModel(Viewer vwr,
int modelIndex) |
String |
getHBonds(ModelSet ms,
int modelIndex,
javajs.util.Lst<Bond> vHBonds,
boolean doReport) |
private void |
setBioPolymers(BioModel m,
boolean b) |
void |
setGroup1(ModelSet ms,
int modelIndex) |
private NucleicMonomer |
setRes(Atom atom) |
catalogStructureUnits, catalogValidations, fixAtoms, getAnnotationInfo, getAtomValidation, getAttachedAtomForPDBH, initializeAnnotation
private static final String DSSR_PATHS
public String calculateDSSRStructure(Viewer vwr, BS bsAtoms)
calculateDSSRStructure
in interface JmolAnnotationParser
calculateDSSRStructure
in class AnnotationParser
public String fixDSSRJSONMap(Map<String,Object> map)
fixDSSRJSONMap
in interface JmolAnnotationParser
fixDSSRJSONMap
in class AnnotationParser
map
- private void fixIndices(Map<String,Object> map, String key, String root)
map
- key
- root
- public void getBasePairs(Viewer vwr, int modelIndex)
getBasePairs
in interface JmolAnnotationParser
getBasePairs
in class AnnotationParser
private void setBioPolymers(BioModel m, boolean b)
private NucleicMonomer setRes(Atom atom)
public BS getAtomBits(Viewer vwr, String key, Object dbObj, Map<String,Object> annotationCache, int type, int modelIndex, BS bsModel)
getAtomBits
in interface JmolAnnotationParser
getAtomBits
in class AnnotationParser
public String getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport)
getHBonds
in interface JmolAnnotationParser
getHBonds
in class AnnotationParser
public void setGroup1(ModelSet ms, int modelIndex)
setGroup1
in interface JmolAnnotationParser
setGroup1
in class AnnotationParser