Package org.jmol.dssx

Class 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 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 Detail

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 Detail

DSSR1

public DSSR1()

Method Detail

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)