Package org.jmol.api

Interface JmolAnnotationParser

All Known Implementing Classes:

AnnotationParser, DSSR1

public interface JmolAnnotationParser

Method Summary

Modifier and Type	Method	Description
String	calculateDSSRStructure(Viewer vwr, javajs.util.BS bsAtoms)
String	catalogStructureUnits(Viewer vwr, SV svMap, int[] modelAtomIndices, Map<String,int[]> resMap, Object object, Map<String,Integer> modelMap)
javajs.util.Lst<Object>	catalogValidations(Viewer vwr, SV validation, int[] modelAtomIndices, Map<String,int[]> valResMap, Map<String,Integer> map, Map<String,Integer> modelMap)
void	fixAtoms(int modelIndex, SV v, javajs.util.BS bsAddedMask, int type, int margin)
String	fixDSSRJSONMap(Map<String,Object> map)
String	getAnnotationInfo(Viewer vwr, SV a, String match, int type, int modelIndex)
javajs.util.BS	getAtomBits(Viewer vwr, String key, Object dssr, Map<String,Object> cache, int type, int modelIndex, javajs.util.BS bsModel)
void	getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData, String dataType)
javajs.util.Lst<Float>	getAtomValidation(Viewer vwr, String type, Atom atom)
void	getBasePairs(Viewer vwr, int modelIndex)
javajs.util.P3[]	getDSSRFrame(Map<String,Object> dssrNT)
String	getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport)
javajs.util.Lst<SV>	initializeAnnotation(SV objAnn, int type, int modelIndex)
void	setGroup1(ModelSet ms, int modelIndex)

Method Detail

fixDSSRJSONMap

String fixDSSRJSONMap(Map<String,Object> map)

getAtomBits

javajs.util.BS getAtomBits(Viewer vwr,
                           String key,
                           Object dssr,
                           Map<String,Object> cache,
                           int type,
                           int modelIndex,
                           javajs.util.BS bsModel)

getBasePairs

void getBasePairs(Viewer vwr,
                  int modelIndex)

getHBonds

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

getAtomicDSSRData

void getAtomicDSSRData(ModelSet ms,
                       int modelIndex,
                       float[] dssrData,
                       String dataType)

calculateDSSRStructure

String calculateDSSRStructure(Viewer vwr,
                              javajs.util.BS bsAtoms)

getAnnotationInfo

String getAnnotationInfo(Viewer vwr,
                         SV a,
                         String match,
                         int type,
                         int modelIndex)

catalogValidations

javajs.util.Lst<Object> catalogValidations(Viewer vwr,
                                           SV validation,
                                           int[] modelAtomIndices,
                                           Map<String,int[]> valResMap,
                                           Map<String,Integer> map,
                                           Map<String,Integer> modelMap)

initializeAnnotation

javajs.util.Lst<SV> initializeAnnotation(SV objAnn,
                                         int type,
                                         int modelIndex)

getAtomValidation

javajs.util.Lst<Float> getAtomValidation(Viewer vwr,
                                         String type,
                                         Atom atom)

fixAtoms

void fixAtoms(int modelIndex,
              SV v,
              javajs.util.BS bsAddedMask,
              int type,
              int margin)

catalogStructureUnits

String catalogStructureUnits(Viewer vwr,
                             SV svMap,
                             int[] modelAtomIndices,
                             Map<String,int[]> resMap,
                             Object object,
                             Map<String,Integer> modelMap)

setGroup1

void setGroup1(ModelSet ms,
               int modelIndex)

getDSSRFrame

javajs.util.P3[] getDSSRFrame(Map<String,Object> dssrNT)