Field Detail

• asResidues

  private boolean asResidues

• reader

  private AtomSetCollectionReader reader

• 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

• set

  public MMCifValidationParser set​(AtomSetCollectionReader reader)

• 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