public class DSSR1 extends AnnotationParser
| Modifier and Type | Field and Description |
|---|---|
private static java.lang.String |
DSSR_PATHS
The paths to the unit id data within the structure.
|
| Constructor and Description |
|---|
DSSR1() |
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
calculateDSSRStructure(Viewer vwr,
javajs.util.BS bsAtoms) |
java.lang.String |
fixDSSRJSONMap(java.util.Map<java.lang.String,java.lang.Object> map)
kissingLoops and coaxStacks use index arrays instead of duplication;
|
private void |
fixIndices(java.util.Map<java.lang.String,java.lang.Object> map,
java.lang.String key,
java.lang.String root)
create a key/value pair root+"s" for all indices of root+"_indices"
|
javajs.util.BS |
getAtomBits(Viewer vwr,
java.lang.String key,
java.lang.Object dbObj,
java.util.Map<java.lang.String,java.lang.Object> annotationCache,
int type,
int modelIndex,
javajs.util.BS bsModel) |
void |
getAtomicDSSRData(ModelSet ms,
int modelIndex,
float[] dssrData,
java.lang.String dataType) |
void |
getBasePairs(Viewer vwr,
int modelIndex) |
private java.lang.String |
getDSSRForModel(Viewer vwr,
int modelIndex) |
javajs.util.P3[] |
getDSSRFrame(java.util.Map<java.lang.String,java.lang.Object> nt) |
java.lang.String |
getHBonds(ModelSet ms,
int modelIndex,
javajs.util.Lst<Bond> vHBonds,
boolean doReport) |
private void |
getPoint(java.util.Map<java.lang.String,java.lang.Object> frame,
java.lang.String item,
javajs.util.P3 pt) |
private void |
setBioPolymers(BioModel m,
boolean b) |
void |
setGroup1(ModelSet ms,
int modelIndex) |
private NucleicMonomer |
setRes(Atom atom) |
catalogStructureUnits, catalogValidations, fixAtoms, getAnnotationInfo, getAtomValidation, getAttachedAtomForPDBH, initializeAnnotationprivate static final java.lang.String DSSR_PATHS
public java.lang.String calculateDSSRStructure(Viewer vwr, javajs.util.BS bsAtoms)
calculateDSSRStructure in interface JmolAnnotationParsercalculateDSSRStructure in class AnnotationParserprivate java.lang.String getDSSRForModel(Viewer vwr, int modelIndex)
public java.lang.String fixDSSRJSONMap(java.util.Map<java.lang.String,java.lang.Object> map)
fixDSSRJSONMap in interface JmolAnnotationParserfixDSSRJSONMap in class AnnotationParsermap - private void fixIndices(java.util.Map<java.lang.String,java.lang.Object> map,
java.lang.String key,
java.lang.String root)
map - key - root - public void getBasePairs(Viewer vwr, int modelIndex)
getBasePairs in interface JmolAnnotationParsergetBasePairs in class AnnotationParserprivate void setBioPolymers(BioModel m, boolean b)
private NucleicMonomer setRes(Atom atom)
public javajs.util.BS getAtomBits(Viewer vwr, java.lang.String key, java.lang.Object dbObj, java.util.Map<java.lang.String,java.lang.Object> annotationCache, int type, int modelIndex, javajs.util.BS bsModel)
getAtomBits in interface JmolAnnotationParsergetAtomBits in class AnnotationParserpublic java.lang.String getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport)
getHBonds in interface JmolAnnotationParsergetHBonds in class AnnotationParserpublic void setGroup1(ModelSet ms, int modelIndex)
setGroup1 in interface JmolAnnotationParsersetGroup1 in class AnnotationParserpublic void getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData, java.lang.String dataType)
getAtomicDSSRData in interface JmolAnnotationParsergetAtomicDSSRData in class AnnotationParserpublic javajs.util.P3[] getDSSRFrame(java.util.Map<java.lang.String,java.lang.Object> nt)
getDSSRFrame in interface JmolAnnotationParsergetDSSRFrame in class AnnotationParserprivate void getPoint(java.util.Map<java.lang.String,java.lang.Object> frame,
java.lang.String item,
javajs.util.P3 pt)