Class MMCifValidationParser

java.lang.Object
org.jmol.adapter.readers.cif.MMCifValidationParser

public class MMCifValidationParser extends Object
  • Field Details

  • Constructor Details

    • MMCifValidationParser

      public MMCifValidationParser()
  • Method Details

    • set

    • finalizeValidations

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

      public String finalizeRna3d(Map<String,Integer> modelMap)
    • getRna3dMap

      private SV getRna3dMap(String addedData)
    • mapAtomResIDs

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