Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / trajectoryanalysis / modules / distance.h

diff --git a/src/gromacs/trajectoryanalysis/modules/distance.h b/src/gromacs/trajectoryanalysis/modules/distance.h
index 78e3e2196d2a16b4142ebbac1532076fecf3156c..519176d57724559d5540486fba6c0117fa4ffc58 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/distance.h
+++ b/src/gromacs/trajectoryanalysis/modules/distance.h
@@ -1,50 +1,48 @@
 /*
+ * This file is part of the GROMACS molecular simulation package.
  *
- *                This source code is part of
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
  *
- *                 G   R   O   M   A   C   S
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
  *
- *          GROningen MAchine for Chemical Simulations
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
  *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
  *
  * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
+ * the research papers on the package. Check out http://www.gromacs.org.
  */
 /*! \internal \file
  * \brief
  * Declares trajectory analysis module for distance calculations.
  *
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_trajectoryanalysis
  */
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_DISTANCE_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_DISTANCE_H
 
-#include <string>
-
-#include "../analysismodule.h"
-#include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/average.h"
-#include "gromacs/options/options.h"
-#include "gromacs/selection/selection.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {
@@ -52,32 +50,12 @@ namespace gmx
 namespace analysismodules
 {
 
-class Distance : public TrajectoryAnalysisModule
+class DistanceInfo
 {
     public:
-        Distance();
-        virtual ~Distance();
-
+        static const char name[];
+        static const char shortDescription[];
         static TrajectoryAnalysisModulePointer create();
-
-        virtual Options &initOptions(TrajectoryAnalysisSettings *settings);
-        virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
-                                  const TopologyInformation &top);
-
-        virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
-                                  TrajectoryAnalysisModuleData *pdata);
-
-        virtual void finishAnalysis(int nframes);
-        virtual void writeOutput();
-
-    private:
-        Options                          _options;
-        std::string                      _fnDist;
-        Selection                        _sel[2];
-        AnalysisData                     _data;
-        AnalysisDataAverageModulePointer _avem;
-
-        // Copy and assign disallowed by base.
 };
 
 } // namespace analysismodules