Class FoldingXyzReader

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.simple.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 Details

    • FoldingXyzReader

      public FoldingXyzReader()
  • Method Details

    • initializeReader

      protected void initializeReader()
      Overrides:
      initializeReader in class AtomSetCollectionReader
    • finalizeSubclassReader

      protected void finalizeSubclassReader() throws Exception
      Description copied from class: AtomSetCollectionReader
      optional reader-specific method run first.
      Overrides:
      finalizeSubclassReader in class AtomSetCollectionReader
      Throws:
      Exception
    • checkLine

      protected boolean checkLine() throws 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:
      Exception
    • readAtoms

      boolean readAtoms(int ac, boolean addAtoms) throws 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:
      Exception
    • makeBonds

      private void makeBonds(String[][] bonds, boolean haveAtomTypes)
    • getElement

      private String getElement(String name)