src/programs/legacymodules.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \internal \brief
  36  * Registers command-line modules for pre-5.0 binaries.
  37  *
  38  * \author Teemu Murtola <teemu.murtola@gmail.com>
  39  */
  40 #include "gmxpre.h"
  41
  42 #include "legacymodules.h"
  43
  44 #include <cstdio>
  45
  46 #include "gromacs/commandline/cmdlinemodule.h"
  47 #include "gromacs/commandline/cmdlinemodulemanager.h"
  48 #include "gromacs/commandline/cmdlineoptionsmodule.h"
  49 #include "gromacs/gmxana/gmx_ana.h"
  50 #include "gromacs/gmxpreprocess/genconf.h"
  51 #include "gromacs/gmxpreprocess/grompp.h"
  52 #include "gromacs/gmxpreprocess/insert-molecules.h"
  53 #include "gromacs/gmxpreprocess/pdb2gmx.h"
  54 #include "gromacs/gmxpreprocess/solvate.h"
  55 #include "gromacs/gmxpreprocess/x2top.h"
  56 #include "gromacs/tools/check.h"
  57 #include "gromacs/tools/convert_tpr.h"
  58 #include "gromacs/tools/dump.h"
  59
  60 #include "mdrun/mdrun_main.h"
  61 #include "view/view.h"
  62
  63 namespace
  64 {
  65
  66 /*! \brief
  67  * Command line module that provides information about obsolescence.
  68  *
  69  * Prints a message directing the user to a wiki page describing replacement
  70  * options.
  71  */
  72 class ObsoleteToolModule : public gmx::ICommandLineModule
  73 {
  74     public:
  75         //! Creates an obsolete tool module for a tool with the given name.
  76         explicit ObsoleteToolModule(const char *name)
  77             : name_(name)
  78         {
  79         }
  80
  81         virtual const char *name() const
  82         {
  83             return name_;
  84         }
  85         virtual const char *shortDescription() const
  86         {
  87             return nullptr;
  88         }
  89
  90         virtual void init(gmx::CommandLineModuleSettings * /*settings*/)
  91         {
  92         }
  93         virtual int run(int /*argc*/, char * /*argv*/[])
  94         {
  95             printMessage();
  96             return 0;
  97         }
  98         virtual void writeHelp(const gmx::CommandLineHelpContext & /*context*/) const
  99         {
 100             printMessage();
 101         }
 102
 103     private:
 104         void printMessage() const
 105         {
 106             std::fprintf(stderr,
 107                          "This tool is no longer present in GROMACS. Please see\n"
 108                          "  http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/user-guide/cmdline.html#command-changes\n"
 109                          "for ideas how to perform the same tasks with the "
 110                          "new tools.\n");
 111         }
 112
 113         const char             *name_;
 114 };
 115
 116 //! Initializer for a module that defaults to nice level zero.
 117 void initSettingsNoNice(gmx::CommandLineModuleSettings *settings)
 118 {
 119     settings->setDefaultNiceLevel(0);
 120 }
 121
 122 /*! \brief
 123  * Convenience function for creating and registering a module.
 124  *
 125  * \param[in] manager          Module manager to which to register the module.
 126  * \param[in] mainFunction     Main function to wrap.
 127  * \param[in] name             Name for the new module.
 128  * \param[in] shortDescription One-line description for the new module.
 129  */
 130 void registerModule(gmx::CommandLineModuleManager                *manager,
 131                     gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 132                     const char *name, const char *shortDescription)
 133 {
 134     manager->addModuleCMain(name, shortDescription, mainFunction);
 135 }
 136
 137 /*! \brief
 138  * Convenience function for creating and registering a module that defaults to
 139  * -nice 0.
 140  *
 141  * \param[in] manager          Module manager to which to register the module.
 142  * \param[in] mainFunction     Main function to wrap.
 143  * \param[in] name             Name for the new module.
 144  * \param[in] shortDescription One-line description for the new module.
 145  */
 146 void registerModuleNoNice(gmx::CommandLineModuleManager                *manager,
 147                           gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 148                           const char *name, const char *shortDescription)
 149 {
 150     manager->addModuleCMainWithSettings(name, shortDescription, mainFunction,
 151                                         &initSettingsNoNice);
 152 }
 153
 154 /*! \brief
 155  * Convenience function for registering a module for an obsolete tool.
 156  *
 157  * \param[in] manager          Module manager to which to register the module.
 158  * \param[in] name             Name for the obsolete tool.
 159  */
 160 void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
 161                           const char                    *name)
 162 {
 163     gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
 164     manager->addModule(std::move(module));
 165 }
 166
 167 } // namespace
 168
 169 void registerLegacyModules(gmx::CommandLineModuleManager *manager)
 170 {
 171     // Modules from this directory (were in src/kernel/).
 172     registerModule(manager, &gmx_check, "check",
 173                    "Check and compare files");
 174     registerModule(manager, &gmx_dump, "dump",
 175                    "Make binary files human readable");
 176     registerModule(manager, &gmx_grompp, "grompp",
 177                    "Make a run input file");
 178     registerModule(manager, &gmx_pdb2gmx, "pdb2gmx",
 179                    "Convert coordinate files to topology and FF-compliant coordinate files");
 180     registerModule(manager, &gmx_convert_tpr, "convert-tpr",
 181                    "Make a modifed run-input file");
 182     registerObsoleteTool(manager, "tpbconv");
 183     registerModule(manager, &gmx_x2top, "x2top",
 184                    "Generate a primitive topology from coordinates");
 185
 186     registerModuleNoNice(manager, &gmx_mdrun, "mdrun",
 187                          "Perform a simulation, do a normal mode analysis or an energy minimization");
 188
 189     gmx::ICommandLineOptionsModule::registerModuleFactory(
 190             manager, gmx::InsertMoleculesInfo::name,
 191             gmx::InsertMoleculesInfo::shortDescription,
 192             &gmx::InsertMoleculesInfo::create);
 193
 194     // Modules from gmx_ana.h.
 195     registerModule(manager, &gmx_do_dssp, "do_dssp",
 196                    "Assign secondary structure and calculate solvent accessible surface area");
 197     registerModule(manager, &gmx_editconf, "editconf",
 198                    "Convert and manipulates structure files");
 199     registerModule(manager, &gmx_eneconv, "eneconv",
 200                    "Convert energy files");
 201     registerModule(manager, &gmx_solvate, "solvate",
 202                    "Solvate a system");
 203     registerObsoleteTool(manager, "genbox");
 204     registerModule(manager, &gmx_genconf, "genconf",
 205                    "Multiply a conformation in 'random' orientations");
 206     registerModule(manager, &gmx_genion, "genion",
 207                    "Generate monoatomic ions on energetically favorable positions");
 208     registerModule(manager, &gmx_genpr, "genrestr",
 209                    "Generate position restraints or distance restraints for index groups");
 210     registerModule(manager, &gmx_make_edi, "make_edi",
 211                    "Generate input files for essential dynamics sampling");
 212     registerModule(manager, &gmx_make_ndx, "make_ndx",
 213                    "Make index files");
 214     registerModule(manager, &gmx_mk_angndx, "mk_angndx",
 215                    "Generate index files for 'gmx angle'");
 216     registerModule(manager, &gmx_trjcat, "trjcat",
 217                    "Concatenate trajectory files");
 218     registerModule(manager, &gmx_trjconv, "trjconv",
 219                    "Convert and manipulates trajectory files");
 220     registerModule(manager, &gmx_trjorder, "trjorder",
 221                    "Order molecules according to their distance to a group");
 222     registerModule(manager, &gmx_xpm2ps, "xpm2ps",
 223                    "Convert XPM (XPixelMap) matrices to postscript or XPM");
 224
 225     registerModule(manager, &gmx_anadock, "anadock",
 226                    "Cluster structures from Autodock runs");
 227     registerModule(manager, &gmx_anaeig, "anaeig",
 228                    "Analyze eigenvectors/normal modes");
 229     registerModule(manager, &gmx_analyze, "analyze",
 230                    "Analyze data sets");
 231     registerModule(manager, &gmx_g_angle, "angle",
 232                    "Calculate distributions and correlations for angles and dihedrals");
 233     registerModule(manager, &gmx_bar, "bar",
 234                    "Calculate free energy difference estimates through Bennett's acceptance ratio");
 235     registerObsoleteTool(manager, "bond");
 236     registerObsoleteTool(manager, "dist");
 237     registerObsoleteTool(manager, "sas");
 238     registerObsoleteTool(manager, "sgangle");
 239
 240     registerModule(manager, &gmx_bundle, "bundle",
 241                    "Analyze bundles of axes, e.g., helices");
 242     registerModule(manager, &gmx_chi, "chi",
 243                    "Calculate everything you want to know about chi and other dihedrals");
 244     registerModule(manager, &gmx_cluster, "cluster",
 245                    "Cluster structures");
 246     registerModule(manager, &gmx_clustsize, "clustsize",
 247                    "Calculate size distributions of atomic clusters");
 248     registerModule(manager, &gmx_confrms, "confrms",
 249                    "Fit two structures and calculates the RMSD");
 250     registerModule(manager, &gmx_covar, "covar",
 251                    "Calculate and diagonalize the covariance matrix");
 252     registerModule(manager, &gmx_current, "current",
 253                    "Calculate dielectric constants and current autocorrelation function");
 254     registerModule(manager, &gmx_density, "density",
 255                    "Calculate the density of the system");
 256     registerModule(manager, &gmx_densmap, "densmap",
 257                    "Calculate 2D planar or axial-radial density maps");
 258     registerModule(manager, &gmx_densorder, "densorder",
 259                    "Calculate surface fluctuations");
 260     registerModule(manager, &gmx_dielectric, "dielectric",
 261                    "Calculate frequency dependent dielectric constants");
 262     registerModule(manager, &gmx_dipoles, "dipoles",
 263                    "Compute the total dipole plus fluctuations");
 264     registerModule(manager, &gmx_disre, "disre",
 265                    "Analyze distance restraints");
 266     registerModule(manager, &gmx_dos, "dos",
 267                    "Analyze density of states and properties based on that");
 268     registerModule(manager, &gmx_dyecoupl, "dyecoupl",
 269                    "Extract dye dynamics from trajectories");
 270     registerModule(manager, &gmx_dyndom, "dyndom",
 271                    "Interpolate and extrapolate structure rotations");
 272     registerModule(manager, &gmx_enemat, "enemat",
 273                    "Extract an energy matrix from an energy file");
 274     registerModule(manager, &gmx_energy, "energy",
 275                    "Writes energies to xvg files and display averages");
 276     registerModule(manager, &gmx_filter, "filter",
 277                    "Frequency filter trajectories, useful for making smooth movies");
 278     registerModule(manager, &gmx_gyrate, "gyrate",
 279                    "Calculate the radius of gyration");
 280     registerModule(manager, &gmx_h2order, "h2order",
 281                    "Compute the orientation of water molecules");
 282     registerModule(manager, &gmx_hbond, "hbond",
 283                    "Compute and analyze hydrogen bonds");
 284     registerModule(manager, &gmx_helix, "helix",
 285                    "Calculate basic properties of alpha helices");
 286     registerModule(manager, &gmx_helixorient, "helixorient",
 287                    "Calculate local pitch/bending/rotation/orientation inside helices");
 288     registerModule(manager, &gmx_hydorder, "hydorder",
 289                    "Compute tetrahedrality parameters around a given atom");
 290     registerModule(manager, &gmx_lie, "lie",
 291                    "Estimate free energy from linear combinations");
 292     registerModule(manager, &gmx_mdmat, "mdmat",
 293                    "Calculate residue contact maps");
 294     registerModule(manager, &gmx_mindist, "mindist",
 295                    "Calculate the minimum distance between two groups");
 296     registerModule(manager, &gmx_morph, "morph",
 297                    "Interpolate linearly between conformations");
 298     registerModule(manager, &gmx_msd, "msd",
 299                    "Calculates mean square displacements");
 300     registerModule(manager, &gmx_nmeig, "nmeig",
 301                    "Diagonalize the Hessian for normal mode analysis");
 302     registerModule(manager, &gmx_nmens, "nmens",
 303                    "Generate an ensemble of structures from the normal modes");
 304     registerModule(manager, &gmx_nmr, "nmr",
 305                    "Analyze nuclear magnetic resonance properties from an energy file");
 306     registerModule(manager, &gmx_nmtraj, "nmtraj",
 307                    "Generate a virtual oscillating trajectory from an eigenvector");
 308     registerModule(manager, &gmx_order, "order",
 309                    "Compute the order parameter per atom for carbon tails");
 310     registerModule(manager, &gmx_pme_error, "pme_error",
 311                    "Estimate the error of using PME with a given input file");
 312     registerModule(manager, &gmx_polystat, "polystat",
 313                    "Calculate static properties of polymers");
 314     registerModule(manager, &gmx_potential, "potential",
 315                    "Calculate the electrostatic potential across the box");
 316     registerModule(manager, &gmx_principal, "principal",
 317                    "Calculate principal axes of inertia for a group of atoms");
 318     registerModule(manager, &gmx_rama, "rama",
 319                    "Compute Ramachandran plots");
 320     registerModule(manager, &gmx_rms, "rms",
 321                    "Calculate RMSDs with a reference structure and RMSD matrices");
 322     registerModule(manager, &gmx_rmsdist, "rmsdist",
 323                    "Calculate atom pair distances averaged with power -2, -3 or -6");
 324     registerModule(manager, &gmx_rmsf, "rmsf",
 325                    "Calculate atomic fluctuations");
 326     registerModule(manager, &gmx_rotacf, "rotacf",
 327                    "Calculate the rotational correlation function for molecules");
 328     registerModule(manager, &gmx_rotmat, "rotmat",
 329                    "Plot the rotation matrix for fitting to a reference structure");
 330     registerModule(manager, &gmx_saltbr, "saltbr",
 331                    "Compute salt bridges");
 332     registerModule(manager, &gmx_sans, "sans",
 333                    "Compute small angle neutron scattering spectra");
 334     registerModule(manager, &gmx_saxs, "saxs",
 335                    "Compute small angle X-ray scattering spectra");
 336     registerModule(manager, &gmx_sham, "sham",
 337                    "Compute free energies or other histograms from histograms");
 338     registerModule(manager, &gmx_sigeps, "sigeps",
 339                    "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
 340     registerModule(manager, &gmx_sorient, "sorient",
 341                    "Analyze solvent orientation around solutes");
 342     registerModule(manager, &gmx_spatial, "spatial",
 343                    "Calculate the spatial distribution function");
 344     registerModule(manager, &gmx_spol, "spol",
 345                    "Analyze solvent dipole orientation and polarization around solutes");
 346     registerModule(manager, &gmx_tcaf, "tcaf",
 347                    "Calculate viscosities of liquids");
 348     registerModule(manager, &gmx_traj, "traj",
 349                    "Plot x, v, f, box, temperature and rotational energy from trajectories");
 350     registerModule(manager, &gmx_tune_pme, "tune_pme",
 351                    "Time mdrun as a function of PME ranks to optimize settings");
 352     registerModule(manager, &gmx_vanhove, "vanhove",
 353                    "Compute Van Hove displacement and correlation functions");
 354     registerModule(manager, &gmx_velacc, "velacc",
 355                    "Calculate velocity autocorrelation functions");
 356     registerModule(manager, &gmx_wham, "wham",
 357                    "Perform weighted histogram analysis after umbrella sampling");
 358     registerModule(manager, &gmx_wheel, "wheel",
 359                    "Plot helical wheels");
 360     registerModuleNoNice(manager, &gmx_view, "view",
 361                          "View a trajectory on an X-Windows terminal");
 362
 363     {
 364         gmx::CommandLineModuleGroup group =
 365             manager->addModuleGroup("Generating topologies and coordinates");
 366         group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
 367         group.addModule("x2top");
 368         group.addModule("solvate");
 369         group.addModule("insert-molecules");
 370         group.addModule("genconf");
 371         group.addModule("genion");
 372         group.addModule("genrestr");
 373         group.addModule("pdb2gmx");
 374     }
 375     {
 376         gmx::CommandLineModuleGroup group =
 377             manager->addModuleGroup("Running a simulation");
 378         group.addModule("grompp");
 379         group.addModule("mdrun");
 380         group.addModule("convert-tpr");
 381     }
 382     {
 383         gmx::CommandLineModuleGroup group =
 384             manager->addModuleGroup("Viewing trajectories");
 385         group.addModule("nmtraj");
 386         group.addModule("view");
 387     }
 388     {
 389         gmx::CommandLineModuleGroup group =
 390             manager->addModuleGroup("Processing energies");
 391         group.addModule("enemat");
 392         group.addModule("energy");
 393         group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
 394     }
 395     {
 396         gmx::CommandLineModuleGroup group =
 397             manager->addModuleGroup("Converting files");
 398         group.addModule("editconf");
 399         group.addModule("eneconv");
 400         group.addModule("sigeps");
 401         group.addModule("trjcat");
 402         group.addModule("trjconv");
 403         group.addModule("xpm2ps");
 404     }
 405     {
 406         gmx::CommandLineModuleGroup group =
 407             manager->addModuleGroup("Tools");
 408         group.addModule("analyze");
 409         group.addModule("dyndom");
 410         group.addModule("filter");
 411         group.addModule("lie");
 412         group.addModule("morph");
 413         group.addModule("pme_error");
 414         group.addModule("sham");
 415         group.addModule("spatial");
 416         group.addModule("traj");
 417         group.addModule("tune_pme");
 418         group.addModule("wham");
 419         group.addModule("check");
 420         group.addModule("dump");
 421         group.addModule("make_ndx");
 422         group.addModule("mk_angndx");
 423         group.addModule("trjorder");
 424         group.addModule("xpm2ps");
 425     }
 426     {
 427         gmx::CommandLineModuleGroup group =
 428             manager->addModuleGroup("Distances between structures");
 429         group.addModule("cluster");
 430         group.addModule("confrms");
 431         group.addModule("rms");
 432         group.addModule("rmsf");
 433     }
 434     {
 435         gmx::CommandLineModuleGroup group =
 436             manager->addModuleGroup("Distances in structures over time");
 437         group.addModule("mindist");
 438         group.addModule("mdmat");
 439         group.addModule("polystat");
 440         group.addModule("rmsdist");
 441     }
 442     {
 443         gmx::CommandLineModuleGroup group =
 444             manager->addModuleGroup("Mass distribution properties over time");
 445         group.addModule("gyrate");
 446         group.addModule("msd");
 447         group.addModule("polystat");
 448         group.addModule("rdf");
 449         group.addModule("rotacf");
 450         group.addModule("rotmat");
 451         group.addModule("sans");
 452         group.addModule("saxs");
 453         group.addModule("traj");
 454         group.addModule("vanhove");
 455     }
 456     {
 457         gmx::CommandLineModuleGroup group =
 458             manager->addModuleGroup("Analyzing bonded interactions");
 459         group.addModule("angle");
 460         group.addModule("mk_angndx");
 461     }
 462     {
 463         gmx::CommandLineModuleGroup group =
 464             manager->addModuleGroup("Structural properties");
 465         group.addModule("anadock");
 466         group.addModule("bundle");
 467         group.addModule("clustsize");
 468         group.addModule("disre");
 469         group.addModule("hbond");
 470         group.addModule("order");
 471         group.addModule("principal");
 472         group.addModule("rdf");
 473         group.addModule("saltbr");
 474         group.addModule("sorient");
 475         group.addModule("spol");
 476     }
 477     {
 478         gmx::CommandLineModuleGroup group =
 479             manager->addModuleGroup("Kinetic properties");
 480         group.addModule("bar");
 481         group.addModule("current");
 482         group.addModule("dos");
 483         group.addModule("dyecoupl");
 484         group.addModule("principal");
 485         group.addModule("tcaf");
 486         group.addModule("traj");
 487         group.addModule("vanhove");
 488         group.addModule("velacc");
 489     }
 490     {
 491         gmx::CommandLineModuleGroup group =
 492             manager->addModuleGroup("Electrostatic properties");
 493         group.addModule("current");
 494         group.addModule("dielectric");
 495         group.addModule("dipoles");
 496         group.addModule("potential");
 497         group.addModule("spol");
 498         group.addModule("genion");
 499     }
 500     {
 501         gmx::CommandLineModuleGroup group =
 502             manager->addModuleGroup("Protein-specific analysis");
 503         group.addModule("do_dssp");
 504         group.addModule("chi");
 505         group.addModule("helix");
 506         group.addModule("helixorient");
 507         group.addModule("rama");
 508         group.addModule("wheel");
 509     }
 510     {
 511         gmx::CommandLineModuleGroup group =
 512             manager->addModuleGroup("Interfaces");
 513         group.addModule("bundle");
 514         group.addModule("density");
 515         group.addModule("densmap");
 516         group.addModule("densorder");
 517         group.addModule("h2order");
 518         group.addModule("hydorder");
 519         group.addModule("order");
 520         group.addModule("potential");
 521     }
 522     {
 523         gmx::CommandLineModuleGroup group =
 524             manager->addModuleGroup("Covariance analysis");
 525         group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
 526         group.addModule("covar");
 527         group.addModule("make_edi");
 528     }
 529     {
 530         gmx::CommandLineModuleGroup group =
 531             manager->addModuleGroup("Normal modes");
 532         group.addModuleWithDescription("anaeig", "Analyze the normal modes");
 533         group.addModule("nmeig");
 534         group.addModule("nmtraj");
 535         group.addModule("nmens");
 536         group.addModule("grompp");
 537         group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");
 538     }
 539 }