Field Detail

• 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

Constructor Detail

• DSSR1

  public DSSR1()

Method Detail

• calculateDSSRStructure

  public String calculateDSSRStructure(Viewer vwr,
                                       BS bsAtoms)

  Specified by:

  calculateDSSRStructure in interface JmolAnnotationParser

  Overrides:

  calculateDSSRStructure in class AnnotationParser

• getDSSRForModel

  private String getDSSRForModel(Viewer vwr,
                                 int modelIndex)

• fixDSSRJSONMap

  public String fixDSSRJSONMap(Map<String,Object> map)

  kissingLoops and coaxStacks use index arrays instead of duplication;

  Specified by:

  fixDSSRJSONMap in interface JmolAnnotationParser

  Overrides:

  fixDSSRJSONMap in class AnnotationParser

  Parameters:

  map -

  Returns:

  msg

• 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 -

• getBasePairs

  public void getBasePairs(Viewer vwr,
                           int modelIndex)

  Specified by:

  getBasePairs in interface JmolAnnotationParser

  Overrides:

  getBasePairs in class AnnotationParser

• setBioPolymers

  private void setBioPolymers(BioModel m,
                              boolean b)

• setRes

  private NucleicMonomer setRes(Atom atom)

• getAtomBits

  public BS getAtomBits(Viewer vwr,
                        String key,
                        Object dbObj,
                        Map<String,Object> annotationCache,
                        int type,
                        int modelIndex,
                        BS bsModel)

  Specified by:

  getAtomBits in interface JmolAnnotationParser

  Overrides:

  getAtomBits in class AnnotationParser

• getHBonds

  public String getHBonds(ModelSet ms,
                          int modelIndex,
                          javajs.util.Lst<Bond> vHBonds,
                          boolean doReport)

  Specified by:

  getHBonds in interface JmolAnnotationParser

  Overrides:

  getHBonds in class AnnotationParser

• setGroup1

  public void setGroup1(ModelSet ms,
                        int modelIndex)

  Specified by:

  setGroup1 in interface JmolAnnotationParser

  Overrides:

  setGroup1 in class AnnotationParser