From: Kevin Boyd Date: Thu, 17 Jan 2019 00:30:15 +0000 (-0500) Subject: Move non-analysis tools from gmxana to gmxpreprocess X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=f9c7a4ee48bf376e0be2526206ff389d88e8e011;p=alexxy%2Fgromacs.git Move non-analysis tools from gmxana to gmxpreprocess Renamed genpr to genrestr to align with actual gmx call refs #2727 Change-Id: I83a1dc6b39915372c4178768354d334c7e911ae2 --- diff --git a/src/gromacs/gmxana/gmx_ana.h b/src/gromacs/gmxana/gmx_ana.h index 0924f04f19..756865dc5c 100644 --- 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 933b718c65..58347b87a8 100644 --- a/src/gromacs/gmxana/gmx_editconf.cpp +++ b/src/gromacs/gmxpreprocess/editconf.cpp @@ -36,6 +36,8 @@ */ #include "gmxpre.h" +#include "editconf.h" + #include #include @@ -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 index 0000000000..c1122c8088 --- /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 1190caa175..297b2190e9 100644 --- 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 #include #include @@ -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 index 0000000000..1ce7f9bf66 --- /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 e22380046e..a70cbb5c1c 100644 --- 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 #include @@ -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 index 0000000000..d7264fe656 --- /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 24606ce58a..4e33812166 100644 --- 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");