public class AnnotationParser extends java.lang.Object implements JmolAnnotationParser
| Modifier and Type | Field and Description |
|---|---|
private static java.util.Map<java.lang.String,java.lang.String> |
pdbAtomForH |
| Constructor and Description |
|---|
AnnotationParser() |
| Modifier and Type | Method and Description |
|---|---|
private void |
assignPDBH(java.lang.String group3,
java.lang.String sNames) |
java.lang.String |
calculateDSSRStructure(Viewer vwr,
javajs.util.BS bsAtoms) |
java.lang.String |
catalogStructureUnits(Viewer viewer,
SV map0,
int[] modelAtomIndices,
java.util.Map<java.lang.String,int[]> resMap,
java.lang.Object object,
java.util.Map<java.lang.String,java.lang.Integer> modelMap) |
private boolean |
catalogUnit(Viewer viewer,
float[][] vals,
java.lang.String unitID,
float val,
javajs.util.BS bsAtoms,
int[] modelAtomIndices,
java.util.Map<java.lang.String,int[]> resMap,
java.util.Map<java.lang.String,java.lang.Integer> atomMap,
java.util.Map<java.lang.String,java.lang.Integer> modelMap)
Carried out for each unit
|
javajs.util.Lst<java.lang.Object> |
catalogValidations(Viewer viewer,
SV map0,
int[] modelAtomIndices,
java.util.Map<java.lang.String,int[]> resMap,
java.util.Map<java.lang.String,java.lang.Integer> atomMap,
java.util.Map<java.lang.String,java.lang.Integer> modelMap)
Returns a Lst
|
private void |
findAnnotationAtoms(Viewer vwr,
java.lang.String name,
javajs.util.Lst<SV> _list,
java.lang.String key,
javajs.util.BS bs)
find annotations; allows for wild cards InterPro.* where .....
|
void |
fixAtoms(int modelIndex,
SV dbObj,
javajs.util.BS bsAddedMask,
int type,
int margin)
Adjusts _atoms bitset to account for added hydrogen atoms.
|
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)
Get a string report of annotation data
|
private void |
getAnnotationKVPairs(SV a,
java.lang.String match,
java.lang.String dotPath,
javajs.util.SB sb,
java.lang.String pre,
boolean showDetail,
boolean isMappingOnly,
int type)
Construct a nice listing for this annotation, including validation
|
javajs.util.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,
javajs.util.BS bsModel) |
void |
getAtomicDSSRData(ModelSet ms,
int modelIndex,
float[] dssrData,
java.lang.String dataType) |
javajs.util.Lst<java.lang.Float> |
getAtomValidation(Viewer vwr,
java.lang.String type,
Atom atom)
Get all validation values corresponding to a specific validation type.
|
java.lang.String |
getAttachedAtomForPDBH(java.lang.String group3,
java.lang.String name)
Finds the standard attached heavy atom for a PDB H atom; used in EBI clash
validation.
|
void |
getBasePairs(Viewer vwr,
int modelIndex) |
private java.lang.String |
getDataKey(int type) |
javajs.util.P3[] |
getDSSRFrame(java.util.Map<java.lang.String,java.lang.Object> dssrNT) |
java.lang.String |
getHBonds(ModelSet ms,
int modelIndex,
javajs.util.Lst<Bond> vHBonds,
boolean doReport) |
private SV |
getMainItem(java.util.Map<java.lang.String,SV> data) |
javajs.util.Lst<SV> |
initializeAnnotation(SV objAnn,
int type,
int modelIndex)
We create a main list of mappings, where each mapping has _atoms and _path
|
private javajs.util.BS |
setAnnotationAtoms(Viewer vwr,
java.util.Map<java.lang.String,SV> mapping,
int i) |
void |
setGroup1(ModelSet ms,
int modelIndex) |
private static java.util.Map<java.lang.String,java.lang.String> pdbAtomForH
private void getAnnotationKVPairs(SV a, java.lang.String match, java.lang.String dotPath, javajs.util.SB sb, java.lang.String pre, boolean showDetail, boolean isMappingOnly, int type)
a - match - dotPath - sb - pre - showDetail - isMappingOnly - type - private java.lang.String getDataKey(int type)
public java.lang.String catalogStructureUnits(Viewer viewer, SV map0, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.lang.Object object, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
catalogStructureUnits in interface JmolAnnotationParserpublic javajs.util.Lst<java.lang.Object> catalogValidations(Viewer viewer, SV map0, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.util.Map<java.lang.String,java.lang.Integer> atomMap, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
catalogValidations in interface JmolAnnotationParserpublic javajs.util.Lst<SV> initializeAnnotation(SV objAnn, int type, int modelIndex)
initializeAnnotation in interface JmolAnnotationParserobjAnn - private void findAnnotationAtoms(Viewer vwr, java.lang.String name, javajs.util.Lst<SV> _list, java.lang.String key, javajs.util.BS bs)
vwr - name - _list - key - bs - private javajs.util.BS setAnnotationAtoms(Viewer vwr, java.util.Map<java.lang.String,SV> mapping, int i)
private boolean catalogUnit(Viewer viewer, float[][] vals, java.lang.String unitID, float val, javajs.util.BS bsAtoms, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.util.Map<java.lang.String,java.lang.Integer> atomMap, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
viewer - vals - model-based array of float values for a given validation typeunitID - val - bsAtoms - modelAtomIndices - resMap - atomMap - modelMap - TODOpublic javajs.util.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, javajs.util.BS bsModel)
getAtomBits in interface JmolAnnotationParserpublic javajs.util.Lst<java.lang.Float> getAtomValidation(Viewer vwr, java.lang.String type, Atom atom)
getAtomValidation in interface JmolAnnotationParservwr - type - e.g. "clashes"atom - public java.lang.String getAnnotationInfo(Viewer vwr, SV a, java.lang.String match, int type, int modelIndex)
getAnnotationInfo in interface JmolAnnotationParsera - an annotation structure wrapped as a script variablematch - can contain "mappings" to get those specificallypublic java.lang.String getAttachedAtomForPDBH(java.lang.String group3,
java.lang.String name)
group3 - name - private void assignPDBH(java.lang.String group3,
java.lang.String sNames)
public void fixAtoms(int modelIndex,
SV dbObj,
javajs.util.BS bsAddedMask,
int type,
int margin)
fixAtoms in interface JmolAnnotationParserpublic void getBasePairs(Viewer vwr, int modelIndex)
getBasePairs in interface JmolAnnotationParserpublic java.lang.String calculateDSSRStructure(Viewer vwr, javajs.util.BS bsAtoms)
calculateDSSRStructure in interface JmolAnnotationParserpublic java.lang.String fixDSSRJSONMap(java.util.Map<java.lang.String,java.lang.Object> map)
fixDSSRJSONMap in interface JmolAnnotationParserpublic java.lang.String getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport)
getHBonds in interface JmolAnnotationParserpublic void getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData, java.lang.String dataType)
getAtomicDSSRData in interface JmolAnnotationParserpublic void setGroup1(ModelSet ms, int modelIndex)
setGroup1 in interface JmolAnnotationParserpublic javajs.util.P3[] getDSSRFrame(java.util.Map<java.lang.String,java.lang.Object> dssrNT)
getDSSRFrame in interface JmolAnnotationParser