Package org.jmol.dssx

Class AnnotationParser

  • All Implemented Interfaces:
    JmolAnnotationParser
    Direct Known Subclasses:
    DSSR1
    public class AnnotationParser
extends Object
implements JmolAnnotationParser
    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 Detail

      • AnnotationParser

        public AnnotationParser()

    • Method Detail

      • 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 -

      • getDataKey

        private String getDataKey​(int type)

      • getMainItem

        private SV getMainItem​(Map<String,​SV> data)

      • initializeAnnotation

        public 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
        Specified by:
        initializeAnnotation in interface JmolAnnotationParser
        Parameters:
        objAnn -
        Returns:
        Lst of mappings

      • 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 -

      • setAnnotationAtoms

        private javajs.util.BS setAnnotationAtoms​(Viewer vwr,
                                          Map<String,​SV> mapping,
                                          int i)

      • 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 type
        unitID -
        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

      • getAtomValidation

        public javajs.util.Lst<Float> getAtomValidation​(Viewer vwr,
                                                String type,
                                                Atom atom)
        Get all validation values corresponding to a specific validation type. Used by label %[validation.clashes]
        Specified by:
        getAtomValidation in interface JmolAnnotationParser
        Parameters:
        vwr -
        type - e.g. "clashes"
        atom -
        Returns:
        a list of Float values associated with this atom and this type of validation

      • getAnnotationInfo

        public String getAnnotationInfo​(Viewer vwr,
                                SV a,
                                String match,
                                int type,
                                int modelIndex)
        Get a string report of annotation data
        Specified by:
        getAnnotationInfo in interface JmolAnnotationParser
        Parameters:
        a - an annotation structure wrapped as a script variable
        match - can contain "mappings" to get those specifically
        Returns:
        tab-separated line-based listing

      • getAttachedAtomForPDBH

        public String getAttachedAtomForPDBH​(String group3,
                                     String name)
        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

      • assignPDBH

        private void assignPDBH​(String group3,
                        String sNames)

      • fixAtoms

        public void fixAtoms​(int modelIndex,
                     SV dbObj,
                     javajs.util.BS bsAddedMask,
                     int type,
                     int margin)
        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 interface JmolAnnotationParser