--- trunk/src/io/RestReader.hpp	2006/06/28 14:35:14	996
+++ trunk/src/io/RestReader.hpp	2009/09/07 16:31:51	1360
@@ -1,89 +1,69 @@
-/*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
- *
- * The University of Notre Dame grants you ("Licensee") a
- * non-exclusive, royalty free, license to use, modify and
- * redistribute this software in source and binary code form, provided
- * that the following conditions are met:
- *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
- *    notice, this list of conditions and the following disclaimer.
- *
- * 3. Redistributions in binary form must reproduce the above copyright
- *    notice, this list of conditions and the following disclaimer in the
- *    documentation and/or other materials provided with the
- *    distribution.
- *
- * This software is provided "AS IS," without a warranty of any
- * kind. All express or implied conditions, representations and
- * warranties, including any implied warranty of merchantability,
- * fitness for a particular purpose or non-infringement, are hereby
- * excluded.  The University of Notre Dame and its licensors shall not
- * be liable for any damages suffered by licensee as a result of
- * using, modifying or distributing the software or its
- * derivatives. In no event will the University of Notre Dame or its
- * licensors be liable for any lost revenue, profit or data, or for
- * direct, indirect, special, consequential, incidental or punitive
- * damages, however caused and regardless of the theory of liability,
- * arising out of the use of or inability to use software, even if the
- * University of Notre Dame has been advised of the possibility of
- * such damages.
- */
-#ifndef IO_RESTREADER_HPP
-#define IO_RESTREADER_HPP
+/* 
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. 
+ * 
+ * The University of Notre Dame grants you ("Licensee") a 
+ * non-exclusive, royalty free, license to use, modify and 
+ * redistribute this software in source and binary code form, provided 
+ * that the following conditions are met: 
+ * 
+ * 1. Acknowledgement of the program authors must be made in any 
+ *    publication of scientific results based in part on use of the 
+ *    program.  An acceptable form of acknowledgement is citation of 
+ *    the article in which the program was described (Matthew 
+ *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher 
+ *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented 
+ *    Parallel Simulation Engine for Molecular Dynamics," 
+ *    J. Comput. Chem. 26, pp. 252-271 (2005)) 
+ * 
+ * 2. Redistributions of source code must retain the above copyright 
+ *    notice, this list of conditions and the following disclaimer. 
+ * 
+ * 3. Redistributions in binary form must reproduce the above copyright 
+ *    notice, this list of conditions and the following disclaimer in the 
+ *    documentation and/or other materials provided with the 
+ *    distribution. 
+ * 
+ * This software is provided "AS IS," without a warranty of any 
+ * kind. All express or implied conditions, representations and 
+ * warranties, including any implied warranty of merchantability, 
+ * fitness for a particular purpose or non-infringement, are hereby 
+ * excluded.  The University of Notre Dame and its licensors shall not 
+ * be liable for any damages suffered by licensee as a result of 
+ * using, modifying or distributing the software or its 
+ * derivatives. In no event will the University of Notre Dame or its 
+ * licensors be liable for any lost revenue, profit or data, or for 
+ * direct, indirect, special, consequential, incidental or punitive 
+ * damages, however caused and regardless of the theory of liability, 
+ * arising out of the use of or inability to use software, even if the 
+ * University of Notre Dame has been advised of the possibility of 
+ * such damages. 
+ */ 
+  
+/** 
+ * @file RestReader.hpp 
+ */ 
+ 
+#ifndef IO_RESTREADER_HPP 
+#define IO_RESTREADER_HPP 
+ 
+#include "io/DumpReader.hpp"
 
-#define _LARGEFILE_SOURCE64
-#ifndef _FILE_OFFSET_BITS
-#define _FILE_OFFSET_BITS 64
-#endif
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <stdio.h>
-#include <stdlib.h>
-#include <unistd.h>
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#include "brains/SimInfo.hpp"
-#include "primitives/StuntDouble.hpp"
-
-namespace oopse {
-    
-
-  /**
-   * @class RestReader RestReader.hpp "io/RestReader.hpp"
-   * @for extra file reading when using thermodynamic integration
-   */
-  class RestReader {
-    
-  public:
-    RestReader( SimInfo* theInfo );
-    ~RestReader();
-    
-    void readIdealCrystal();
-    void readZangle();
-    void zeroZangle();
-    
-  private:
-    char* parseIdealLine(char* readLine, StuntDouble* sd);
-    std::string angFile;
-    std::string idealName;
-    std::istream* inIdealFile;
-    std::istream* inAngFile;
-
-    RealType angleTransfer;
-    SimInfo *info_;
+namespace oopse { 
+ 
+  /** 
+   * @class RestReader RestReader.hpp "io/RestReader.hpp" 
+   */ 
+  class RestReader : public DumpReader { 
+  public: 
+    RestReader(SimInfo* info, const std::string &filename) : DumpReader(info, filename){}
+    void readReferenceStructure();
+  protected: 
+    virtual void parseDumpLine(const std::string&);  
+    virtual void readFrameProperties(std::istream& inputStream);
+  private: 
+    std::vector<Vector3d> all_pos_;
   };
-
-} //end namespace oopse
-#endif
+ 
+}      //end namespace oopse 
+ 
+#endif //IO_RESTREADER_HPP