Package org.jmol.dssx
Class AnnotationParser
java.lang.Object
org.jmol.dssx.AnnotationParser
- All Implemented Interfaces:
JmolAnnotationParser
- Direct Known Subclasses:
DSSR1
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
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate voidassignPDBH(String group3, String sNames) calculateDSSRStructure(Viewer vwr, javajs.util.BS bsAtoms) catalogStructureUnits(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Object object, Map<String, Integer> modelMap) private booleancatalogUnit(Viewer viewer, float[][] vals, String unitID, float val, javajs.util.BS bsAtoms, int[] modelAtomIndices, Map<String, int[]> resMap, Map<String, Integer> atomMap, Map<String, Integer> modelMap) Carried out for each unitjavajs.util.Lst<Object>catalogValidations(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Map<String, Integer> atomMap, Map<String, Integer> modelMap) Returns a Lstprivate voidfindAnnotationAtoms(Viewer vwr, String name, javajs.util.Lst<SV> _list, String key, javajs.util.BS bs) find annotations; allows for wild cards InterPro.* where .....voidAdjusts _atoms bitset to account for added hydrogen atoms.fixDSSRJSONMap(Map<String, Object> map) getAnnotationInfo(Viewer vwr, SV a, String match, int type, int modelIndex) Get a string report of annotation dataprivate voidgetAnnotationKVPairs(SV a, String match, String dotPath, javajs.util.SB sb, String pre, boolean showDetail, boolean isMappingOnly, int type) Construct a nice listing for this annotation, including validationjavajs.util.BSgetAtomBits(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, javajs.util.BS bsModel) voidgetAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData, String dataType) javajs.util.Lst<Float>getAtomValidation(Viewer vwr, String type, Atom atom) Get all validation values corresponding to a specific validation type.getAttachedAtomForPDBH(String group3, String name) Finds the standard attached heavy atom for a PDB H atom; used in EBI clash validation.voidgetBasePairs(Viewer vwr, int modelIndex) private StringgetDataKey(int type) javajs.util.P3[]getDSSRFrame(Map<String, Object> dssrNT) private SVgetMainItem(Map<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 _pathprivate javajs.util.BSsetAnnotationAtoms(Viewer vwr, Map<String, SV> mapping, int i) void
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Field Details
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pdbAtomForH
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Constructor Details
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AnnotationParser
public AnnotationParser()
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Method Details
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getAnnotationKVPairs
private void getAnnotationKVPairs(SV a, String match, String dotPath, javajs.util.SB sb, String pre, boolean showDetail, boolean isMappingOnly, int type) Construct a nice listing for this annotation, including validation- Parameters:
a-match-dotPath-sb-pre-showDetail-isMappingOnly-type-
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getDataKey
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catalogStructureUnits
public String catalogStructureUnits(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Object object, Map<String, Integer> modelMap) - Specified by:
catalogStructureUnitsin interfaceJmolAnnotationParser
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catalogValidations
public javajs.util.Lst<Object> catalogValidations(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Map<String, Integer> atomMap, Map<String, Integer> modelMap) Returns a Lst- Specified by:
catalogValidationsin interfaceJmolAnnotationParser
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getMainItem
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initializeAnnotation
We create a main list of mappings, where each mapping has _atoms and _path- Specified by:
initializeAnnotationin interfaceJmolAnnotationParser- Parameters:
objAnn-- Returns:
- Lst of mappings
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findAnnotationAtoms
private void findAnnotationAtoms(Viewer vwr, String name, javajs.util.Lst<SV> _list, String key, javajs.util.BS bs) find annotations; allows for wild cards InterPro.* where .....- Parameters:
vwr-name-_list-key-bs-
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setAnnotationAtoms
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catalogUnit
private boolean catalogUnit(Viewer viewer, float[][] vals, String unitID, float val, javajs.util.BS bsAtoms, int[] modelAtomIndices, Map<String, int[]> resMap, Map<String, Integer> atomMap, Map<String, Integer> modelMap) Carried out for each unit- Parameters:
viewer-vals- model-based array of float values for a given validation typeunitID-val-bsAtoms-modelAtomIndices-resMap-atomMap-modelMap- TODO- Returns:
- true if this is residue-based validation (to be added to H atoms when pdbAddHydrogens is set
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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:
getAtomBitsin interfaceJmolAnnotationParser
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getAtomValidation
Get all validation values corresponding to a specific validation type. Used by label %[validation.clashes]- Specified by:
getAtomValidationin interfaceJmolAnnotationParser- Parameters:
vwr-type- e.g. "clashes"atom-- Returns:
- a list of Float values associated with this atom and this type of validation
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getAnnotationInfo
Get a string report of annotation data- Specified by:
getAnnotationInfoin interfaceJmolAnnotationParser- Parameters:
a- an annotation structure wrapped as a script variablematch- can contain "mappings" to get those specifically- Returns:
- tab-separated line-based listing
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getAttachedAtomForPDBH
Finds the standard attached heavy atom for a PDB H atom; used in EBI clash validation.- Parameters:
group3-name-- Returns:
- name of attached atom or hName
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assignPDBH
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fixAtoms
Adjusts _atoms bitset to account for added hydrogen atoms. A margin of 20 allows for 20 added H atoms per group- Specified by:
fixAtomsin interfaceJmolAnnotationParser
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getBasePairs
- Specified by:
getBasePairsin interfaceJmolAnnotationParser
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calculateDSSRStructure
- Specified by:
calculateDSSRStructurein interfaceJmolAnnotationParser
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fixDSSRJSONMap
- Specified by:
fixDSSRJSONMapin interfaceJmolAnnotationParser
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getHBonds
public String getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport) - Specified by:
getHBondsin interfaceJmolAnnotationParser
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getAtomicDSSRData
- Specified by:
getAtomicDSSRDatain interfaceJmolAnnotationParser
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setGroup1
- Specified by:
setGroup1in interfaceJmolAnnotationParser
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getDSSRFrame
- Specified by:
getDSSRFramein interfaceJmolAnnotationParser
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