Class BilbaoReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader

    public class BilbaoReader
    extends AtomSetCollectionReader
    Bilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML. Keys for Bilbao format data are a given bit of text such as "High symmetry structure". Any changes to that (including capitalization) will cause this reader to fail. The space group number is read immediately after the "pre" tag on that line. filter options include: HIGH include high-symmetry structure; preliminary only
    Author:
    Bob Hanson
    • Field Detail

      • getHigh

        private boolean getHigh
      • getSym

        private boolean getSym
      • normDispl

        private boolean normDispl
      • doDisplace

        private boolean doDisplace
      • kvec

        private java.lang.String kvec
      • i0

        private int i0
      • nAtoms

        private int nAtoms
      • isBCSfile

        private boolean isBCSfile
    • Constructor Detail

      • BilbaoReader

        public BilbaoReader()
    • Method Detail

      • checkLine

        protected boolean checkLine()
                             throws java.lang.Exception
        Overrides:
        checkLine in class AtomSetCollectionReader
        Returns:
        true if need to read new line
        Throws:
        java.lang.Exception
      • readBilbaoDataFile

        private void readBilbaoDataFile()
                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • checkComment

        private boolean checkComment()
      • readBilbaoFormat

        private void readBilbaoFormat​(java.lang.String title,
                                      float fAmp)
                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readDisplacements

        private void readDisplacements​(float fAmp)
                                throws java.lang.Exception
        Throws:
        java.lang.Exception
      • setTitle

        private void setTitle​(java.lang.String title)
      • rdLine

        private java.lang.String rdLine()
                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readVirtual

        private void readVirtual()
                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getAttr

        private java.lang.String getAttr​(java.lang.String s,
                                         java.lang.String key)
      • getLinesUntil

        private java.lang.String getLinesUntil​(java.lang.String key)
                                        throws java.lang.Exception
        Throws:
        java.lang.Exception