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 final String

DSSR_PATHS

The paths to the unit id data within the structure.
Constructor Summary

Constructors

Constructor

Description

DSSR1()
Method Summary

Modifier and Type

Method

Description

String

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

String

fixDSSRJSONMap(Map<String,Object> map)

kissingLoops and coaxStacks use index arrays instead of duplication;

private void

fixIndices(Map<String,Object> map, String key, String root)

create a key/value pair root+"s" for all indices of root+"_indices"

javajs.util.BS

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

void

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

void

getBasePairs(Viewer vwr, int modelIndex)

private String

getDSSRForModel(Viewer vwr, int modelIndex)

javajs.util.P3[]

getDSSRFrame(Map<String,Object> nt)

String

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

private void

getPoint(Map<String,Object> frame, String item, javajs.util.P3 pt)

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 Details
- 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 Details
- DSSR1
  
  public DSSR1()
Method Details
- calculateDSSRStructure
  
  public String calculateDSSRStructure(Viewer vwr, javajs.util.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 javajs.util.BS getAtomBits(Viewer vwr, String key, Object dbObj, Map<String,Object> annotationCache, int type, int modelIndex, javajs.util.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
- getAtomicDSSRData
  
  public void getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData, String dataType)
  
  Specified by:
  
  getAtomicDSSRData in interface JmolAnnotationParser
  
  Overrides:
  
  getAtomicDSSRData in class AnnotationParser
- getDSSRFrame
  
  public javajs.util.P3[] getDSSRFrame(Map<String,Object> nt)
  
  Specified by:
  
  getDSSRFrame in interface JmolAnnotationParser
  
  Overrides:
  
  getDSSRFrame in class AnnotationParser
- getPoint
  
  private void getPoint(Map<String,Object> frame, String item, javajs.util.P3 pt)

Class DSSR1

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.jmol.dssx.AnnotationParser

Methods inherited from class java.lang.Object

Field Details

DSSR_PATHS

Constructor Details

DSSR1

Method Details

calculateDSSRStructure

getDSSRForModel

fixDSSRJSONMap

fixIndices

getBasePairs

setBioPolymers

setRes

getAtomBits

getHBonds

setGroup1

getAtomicDSSRData

getDSSRFrame

getPoint