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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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncalculateDSSRStructure
(Viewer vwr, BS bsAtoms) catalogStructureUnits
(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Object object, Map<String, Integer> modelMap) catalogValidations
(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Map<String, Integer> atomMap, Map<String, Integer> modelMap) Returns a Lstvoid
Adjusts _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 datagetAtomBits
(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, BS bsModel) void
getAtomicDSSRData
(ModelSet ms, int modelIndex, float[] dssrData, String dataType) 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.void
getBasePairs
(Viewer vwr, int modelIndex) P3[]
getDSSRFrame
(Map<String, Object> dssrNT) initializeAnnotation
(SV objAnn, int type, int modelIndex) We create a main list of mappings, where each mapping has _atoms and _pathvoid
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Constructor Details
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AnnotationParser
public AnnotationParser()
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Method Details
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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:
catalogStructureUnits
in interfaceJmolAnnotationParser
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catalogValidations
public 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:
catalogValidations
in interfaceJmolAnnotationParser
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initializeAnnotation
We create a main list of mappings, where each mapping has _atoms and _path- Specified by:
initializeAnnotation
in interfaceJmolAnnotationParser
- Parameters:
objAnn
-- Returns:
- Lst of mappings
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getAtomBits
public BS getAtomBits(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, BS bsModel) - Specified by:
getAtomBits
in interfaceJmolAnnotationParser
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getAtomValidation
Get all validation values corresponding to a specific validation type. Used by label %[validation.clashes]- Specified by:
getAtomValidation
in 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:
getAnnotationInfo
in 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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fixAtoms
Adjusts _atoms bitset to account for added hydrogen atoms. A margin of 20 allows for 20 added H atoms per group- Specified by:
fixAtoms
in interfaceJmolAnnotationParser
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getBasePairs
- Specified by:
getBasePairs
in interfaceJmolAnnotationParser
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calculateDSSRStructure
- Specified by:
calculateDSSRStructure
in interfaceJmolAnnotationParser
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fixDSSRJSONMap
- Specified by:
fixDSSRJSONMap
in interfaceJmolAnnotationParser
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getHBonds
- Specified by:
getHBonds
in interfaceJmolAnnotationParser
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getAtomicDSSRData
- Specified by:
getAtomicDSSRData
in interfaceJmolAnnotationParser
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setGroup1
- Specified by:
setGroup1
in interfaceJmolAnnotationParser
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getDSSRFrame
- Specified by:
getDSSRFrame
in interfaceJmolAnnotationParser
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