Move non-analysis tools from gmxana to gmxpreprocess

Renamed genpr to genrestr to align with actual gmx <tool> call

refs #2727

Change-Id: I83a1dc6b39915372c4178768354d334c7e911ae2

diff --git a/src/gromacs/gmxana/gmx_ana.h b/src/gromacs/gmxana/gmx_ana.h
index 0924f04f19940a4167b967195aec831925f51299..756865dc5cae80efe6161562b5250922d7272391 100644 (file)
--- a/src/gromacs/gmxana/gmx_ana.h
+++ b/src/gromacs/gmxana/gmx_ana.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -98,9 +98,6 @@ gmx_dos(int argc, char *argv[]);
 int
 gmx_dyecoupl(int argc, char *argv[]);
 
-int
-gmx_editconf(int argc, char *argv[]);
-
 int
 gmx_eneconv(int argc, char *argv[]);
 
@@ -116,12 +113,6 @@ gmx_lie(int argc, char *argv[]);
 int
 gmx_filter(int argc, char *argv[]);
 
-int
-gmx_genion(int argc, char *argv[]);
-
-int
-gmx_genpr(int argc, char *argv[]);
-
 int
 gmx_gyrate(int argc, char *argv[]);
 

diff --git a/src/gromacs/gmxana/gmx_editconf.cpp b/src/gromacs/gmxpreprocess/editconf.cpp
similarity index 99%
rename from src/gromacs/gmxana/gmx_editconf.cpp
rename to src/gromacs/gmxpreprocess/editconf.cpp
index 933b718c65d581cddca883a5068a7226cba65acf..58347b87a82f80534a51f6bc0380419df97bc4f7 100644 (file)
--- a/src/gromacs/gmxana/gmx_editconf.cpp
+++ b/src/gromacs/gmxpreprocess/editconf.cpp
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "editconf.h"
+
 #include <cmath>
 #include <cstring>
 
@@ -48,7 +50,6 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/princ.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
 #include "gromacs/math/functions.h"

diff --git a/src/gromacs/gmxpreprocess/editconf.h b/src/gromacs/gmxpreprocess/editconf.h
new file mode 100644 (file)
index 0000000..c1122c8
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/editconf.h
@@ -0,0 +1,40 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
+ * 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 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 research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_GMXPREPROCESS_EDITCONF_H
+#define GMX_GMXPREPROCESS_EDITCONF_H
+
+int gmx_editconf(int argc, char *argv[]);
+
+#endif

diff --git a/src/gromacs/gmxana/gmx_genion.cpp b/src/gromacs/gmxpreprocess/genion.cpp
similarity index 99%
rename from src/gromacs/gmxana/gmx_genion.cpp
rename to src/gromacs/gmxpreprocess/genion.cpp
index 1190caa175b0457bc5d85e4580303b81d2543395..297b2190e9606cb57a3db683f44d4b4e0b3f6c53 100644 (file)
--- a/src/gromacs/gmxana/gmx_genion.cpp
+++ b/src/gromacs/gmxpreprocess/genion.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "genion.h"
+
 #include <cctype>
 #include <cmath>
 #include <cstdlib>
@@ -43,7 +45,6 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxpreprocess/genion.h b/src/gromacs/gmxpreprocess/genion.h
new file mode 100644 (file)
index 0000000..1ce7f9b
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/genion.h
@@ -0,0 +1,40 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
+ * 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 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 research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_GMXPREPROCESS_GENION_H
+#define GMX_GMXPREPROCESS_GENION_H
+
+int gmx_genion(int argc, char *argv[]);
+
+#endif

diff --git a/src/gromacs/gmxana/gmx_genpr.cpp b/src/gromacs/gmxpreprocess/genrestr.cpp
similarity index 98%
rename from src/gromacs/gmxana/gmx_genpr.cpp
rename to src/gromacs/gmxpreprocess/genrestr.cpp
index e22380046e84d8064489dd7f532b21bdcabaef5b..a70cbb5c1c1b4b161996583a57422c318bf664ab 100644 (file)
--- a/src/gromacs/gmxana/gmx_genpr.cpp
+++ b/src/gromacs/gmxpreprocess/genrestr.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018,2019, 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.
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "genrestr.h"
+
 #include <cmath>
 #include <cstring>
 
@@ -43,7 +45,6 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/topology/topology.h"
@@ -53,7 +54,7 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
-int gmx_genpr(int argc, char *argv[])
+int gmx_genrestr(int argc, char *argv[])
 {
     const char        *desc[] = {
         "[THISMODULE] produces an #include file for a topology containing",

diff --git a/src/gromacs/gmxpreprocess/genrestr.h b/src/gromacs/gmxpreprocess/genrestr.h
new file mode 100644 (file)
index 0000000..d7264fe
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/genrestr.h
@@ -0,0 +1,40 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
+ * 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 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 research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_GMXPREPROCESS_GENPR_H
+#define GMX_GMXPREPROCESS_GENPR_H
+
+int gmx_genrestr(int argc, char *argv[]);
+
+#endif

diff --git a/src/programs/legacymodules.cpp b/src/programs/legacymodules.cpp
index 24606ce58a52708647b03b7b943ea142259d3889..4e3381216633846c9ab428bee8b6dbd17b85f823 100644 (file)
--- a/src/programs/legacymodules.cpp
+++ b/src/programs/legacymodules.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, 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.
@@ -47,7 +47,10 @@
 #include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/commandline/cmdlineoptionsmodule.h"
 #include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxpreprocess/editconf.h"
 #include "gromacs/gmxpreprocess/genconf.h"
+#include "gromacs/gmxpreprocess/genion.h"
+#include "gromacs/gmxpreprocess/genrestr.h"
 #include "gromacs/gmxpreprocess/grompp.h"
 #include "gromacs/gmxpreprocess/insert-molecules.h"
 #include "gromacs/gmxpreprocess/pdb2gmx.h"
@@ -214,7 +217,7 @@ void registerLegacyModules(gmx::CommandLineModuleManager *manager)
                    "Multiply a conformation in 'random' orientations");
     registerModule(manager, &gmx_genion, "genion",
                    "Generate monoatomic ions on energetically favorable positions");
-    registerModule(manager, &gmx_genpr, "genrestr",
+    registerModule(manager, &gmx_genrestr, "genrestr",
                    "Generate position restraints or distance restraints for index groups");
     registerModule(manager, &gmx_make_edi, "make_edi",
                    "Generate input files for essential dynamics sampling");