Class FoldingXyzReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader
    Direct Known Subclasses:
    TinkerReader

    public class FoldingXyzReader
    extends AtomSetCollectionReader
    This reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format. I used source code from fpd from Dick Howell to analyze the file format. (see http://boston.quik.com/rph) -- Nico Vervelle Extended by Bob Hanson 2/2014: - adds support for newer Tinker files (see data/folding) - adds desired model options - adds atom type if available
    • Constructor Detail

      • FoldingXyzReader

        public FoldingXyzReader()
    • Method Detail

      • checkLine

        protected boolean checkLine()
                             throws java.lang.Exception
        Overrides:
        checkLine in class AtomSetCollectionReader
        Returns:
        true if next line needs to be read. Note that just a single token on line 1 is NOT possible. If that were the case, the xyz reader would have captured this.
        Throws:
        java.lang.Exception
      • readAtoms

        boolean readAtoms​(int ac,
                          boolean addAtoms)
                   throws java.lang.Exception
        Lots of possibilities here: atom count is real; atom count is one less than true atom count sixth column is atom type; sixth column is first bond
        Parameters:
        ac -
        addAtoms -
        Returns:
        true if next line needs to be read
        Throws:
        java.lang.Exception
      • makeBonds

        private void makeBonds​(java.lang.String[][] bonds,
                               boolean haveAtomTypes)
      • getElement

        private java.lang.String getElement​(java.lang.String name)