Class MMCifValidationParser


  • public class MMCifValidationParser
    extends java.lang.Object
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.String finalizeRna3d​(java.util.Map<java.lang.String,​java.lang.Integer> modelMap)  
      java.lang.String finalizeValidations​(Viewer vwr, java.util.Map<java.lang.String,​java.lang.Integer> modelMap)
      Create property_xxxx for each validation category.
      private int[] getModelAtomIndices()
      prepare a list of starting atom indices for each model, adding one additional one to indicate 1 + last atom index
      private SV getRna3dMap​(java.lang.String addedData)  
      private void mapAtomResIDs​(java.util.Map<java.lang.String,​java.lang.Integer> modelMap)
      Map all atom and residue unit ids to atom indexes
      MMCifValidationParser set​(AtomSetCollectionReader reader)  
      private java.lang.String setProperties​(javajs.util.Lst<java.lang.Object> propList)
      Set property_xxx for atoms from list of name, data, modelIndex series.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • asResidues

        private boolean asResidues
      • resMap

        private java.util.Map<java.lang.String,​int[]> resMap
      • atomMap

        private java.util.Map<java.lang.String,​java.lang.Integer> atomMap
    • Constructor Detail

      • MMCifValidationParser

        public MMCifValidationParser()
    • Method Detail

      • finalizeValidations

        public java.lang.String finalizeValidations​(Viewer vwr,
                                                    java.util.Map<java.lang.String,​java.lang.Integer> modelMap)
        Create property_xxxx for each validation category.
        Parameters:
        vwr -
        modelMap -
        Returns:
        loading note
      • finalizeRna3d

        public java.lang.String finalizeRna3d​(java.util.Map<java.lang.String,​java.lang.Integer> modelMap)
      • getRna3dMap

        private SV getRna3dMap​(java.lang.String addedData)
      • mapAtomResIDs

        private void mapAtomResIDs​(java.util.Map<java.lang.String,​java.lang.Integer> modelMap)
        Map all atom and residue unit ids to atom indexes
        Parameters:
        modelMap -
      • getModelAtomIndices

        private int[] getModelAtomIndices()
        prepare a list of starting atom indices for each model, adding one additional one to indicate 1 + last atom index
        Returns:
        array
      • setProperties

        private java.lang.String setProperties​(javajs.util.Lst<java.lang.Object> propList)
        Set property_xxx for atoms from list of name, data, modelIndex series.
        Parameters:
        propList -
        Returns:
        note string