Package org.jmol.api
Interface JmolAnnotationParser
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AnnotationParser
,DSSR1
public interface JmolAnnotationParser
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String
calculateDSSRStructure(Viewer vwr, BS bsAtoms)
java.lang.String
catalogStructureUnits(Viewer vwr, SV svMap, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.lang.Object object, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
javajs.util.Lst<java.lang.Object>
catalogValidations(Viewer vwr, SV validation, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> valResMap, java.util.Map<java.lang.String,java.lang.Integer> map, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
void
fixAtoms(int modelIndex, SV v, BS bsAddedMask, int type, int margin)
java.lang.String
fixDSSRJSONMap(java.util.Map<java.lang.String,java.lang.Object> map)
java.lang.String
getAnnotationInfo(Viewer vwr, SV a, java.lang.String match, int type, int modelIndex)
BS
getAtomBits(Viewer vwr, java.lang.String key, java.lang.Object dssr, java.util.Map<java.lang.String,java.lang.Object> cache, int type, int modelIndex, BS bsModel)
javajs.util.Lst<java.lang.Float>
getAtomValidation(Viewer vwr, java.lang.String type, Atom atom)
void
getBasePairs(Viewer vwr, int modelIndex)
java.lang.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)
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Method Detail
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fixDSSRJSONMap
java.lang.String fixDSSRJSONMap(java.util.Map<java.lang.String,java.lang.Object> map)
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getAtomBits
BS getAtomBits(Viewer vwr, java.lang.String key, java.lang.Object dssr, java.util.Map<java.lang.String,java.lang.Object> cache, int type, int modelIndex, BS bsModel)
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getBasePairs
void getBasePairs(Viewer vwr, int modelIndex)
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getHBonds
java.lang.String getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport)
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getAnnotationInfo
java.lang.String getAnnotationInfo(Viewer vwr, SV a, java.lang.String match, int type, int modelIndex)
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catalogValidations
javajs.util.Lst<java.lang.Object> catalogValidations(Viewer vwr, SV validation, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> valResMap, java.util.Map<java.lang.String,java.lang.Integer> map, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
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getAtomValidation
javajs.util.Lst<java.lang.Float> getAtomValidation(Viewer vwr, java.lang.String type, Atom atom)
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catalogStructureUnits
java.lang.String catalogStructureUnits(Viewer vwr, SV svMap, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.lang.Object object, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
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setGroup1
void setGroup1(ModelSet ms, int modelIndex)
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