DSSR1

java.lang.Object
- org.jmol.dssx.AnnotationParser
- - org.jmol.dssx.DSSR1

All Implemented Interfaces:

JmolAnnotationParser
```
public class DSSR1
extends AnnotationParser
```
A parser for output from 3DNA web service. load =1d66/dssr also other annotations now, load *1cbs/dom calls EBI for the mmCIF file and also retrieves the domains mapping JSON report. load *1cbs/val calls EBI for the mmCIF file and also retrieves the validation outliers JSON report. Bob Hanson July 2014

Author:

Bob Hanson hansonr@stolaf.edu

Field Summary

Fields
Modifier and Type Field Description

private static java.lang.String DSSR_PATHS
The paths to the unit id data within the structure.

Fields
Modifier and Type	Field	Description
`private static java.lang.String`	`DSSR_PATHS`	The paths to the unit id data within the structure.

Constructor Summary

Constructors
Constructor Description

DSSR1()

Constructors
Constructor	Description
`DSSR1()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.String`	`calculateDSSRStructure(Viewer vwr, 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"
`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, BS bsModel)`
`void`	`getBasePairs(Viewer vwr, int modelIndex)`
`private java.lang.String`	`getDSSRForModel(Viewer vwr, int modelIndex)`
`java.lang.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)`

Methods inherited from class org.jmol.dssx.AnnotationParser
catalogStructureUnits, catalogValidations, fixAtoms, getAnnotationInfo, getAtomValidation, getAttachedAtomForPDBH, initializeAnnotation

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- DSSR_PATHS
```
private static final java.lang.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 java.lang.String calculateDSSRStructure(Viewer vwr,
                                               BS bsAtoms)

Specified by:: calculateDSSRStructure in interface JmolAnnotationParser
Overrides:: calculateDSSRStructure in class AnnotationParser

getDSSRForModel

private java.lang.String getDSSRForModel(Viewer vwr,
                                         int modelIndex)

fixDSSRJSONMap
```
public java.lang.String fixDSSRJSONMap(java.util.Map<java.lang.String,java.lang.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(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"

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,
                      java.lang.String key,
                      java.lang.Object dbObj,
                      java.util.Map<java.lang.String,java.lang.Object> annotationCache,
                      int type,
                      int modelIndex,
                      BS bsModel)

Specified by:: getAtomBits in interface JmolAnnotationParser
Overrides:: getAtomBits in class AnnotationParser

getHBonds

public java.lang.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

Class DSSR1

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.jmol.dssx.AnnotationParser

Methods inherited from class java.lang.Object

Field Detail

DSSR_PATHS

Constructor Detail

DSSR1

Method Detail

calculateDSSRStructure

getDSSRForModel

fixDSSRJSONMap

fixIndices

getBasePairs

setBioPolymers

setRes

getAtomBits

getHBonds

setGroup1