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

Constructor Summary

Constructors

Constructor

Description

DSSR1()
Method Summary

Modifier and Type

Method

Description

String

calculateDSSRStructure(Viewer vwr, BS bsAtoms)

String

fixDSSRJSONMap(Map<String,Object> map)

kissingLoops and coaxStacks use index arrays instead of duplication;

BS

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

////////////////// general post-load processing ////////////////

void

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

void

getBasePairs(Viewer vwr, int modelIndex)

P3[]

getDSSRFrame(Map<String,Object> nt)

String

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

void

setGroup1(ModelSet ms, int modelIndex)

Methods inherited from class AnnotationParser
catalogStructureUnits, catalogValidations, fixAtoms, getAnnotationInfo, getAtomValidation, getAttachedAtomForPDBH, initializeAnnotation

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

Constructor Details
- DSSR1
  
  public DSSR1()
Method Details
- calculateDSSRStructure
  
  public String calculateDSSRStructure(Viewer vwr, BS bsAtoms)
  
  Specified by:
  
  calculateDSSRStructure in interface JmolAnnotationParser
  
  Overrides:
  
  calculateDSSRStructure in class AnnotationParser
- 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
- getBasePairs
  
  public void getBasePairs(Viewer vwr, int modelIndex)
  
  Specified by:
  
  getBasePairs in interface JmolAnnotationParser
  
  Overrides:
  
  getBasePairs in class AnnotationParser
- getAtomBits
  
  public BS getAtomBits(Viewer vwr, String key, Object dbObj, Map<String,Object> annotationCache, int type, int modelIndex, BS bsModel)
  
  Description copied from class: AnnotationParser
  
  ////////////////// general post-load processing ////////////////
  
  Specified by:
  
  getAtomBits in interface JmolAnnotationParser
  
  Overrides:
  
  getAtomBits in class AnnotationParser
- getHBonds
  
  public String getHBonds(ModelSet ms, int modelIndex, 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 P3[] getDSSRFrame(Map<String,Object> nt)
  
  Specified by:
  
  getDSSRFrame in interface JmolAnnotationParser
  
  Overrides:
  
  getDSSRFrame in class AnnotationParser

Class DSSR1

Constructor Summary

Method Summary

Methods inherited from class AnnotationParser

Methods inherited from class Object

Constructor Details

DSSR1

Method Details

calculateDSSRStructure

fixDSSRJSONMap

getBasePairs

getAtomBits

getHBonds

setGroup1

getAtomicDSSRData

getDSSRFrame