src/programs/legacymodules.cpp

   1 /*
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  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 #include "gromacs/tools/report-methods.h"
  60
  61 #include "mdrun/mdrun_main.h"
  62 #include "view/view.h"
  63
  64 namespace
  65 {
  66
  67 /*! \brief
  68  * Command line module that provides information about obsolescence.
  69  *
  70  * Prints a message directing the user to a wiki page describing replacement
  71  * options.
  72  */
  73 class ObsoleteToolModule : public gmx::ICommandLineModule
  74 {
  75     public:
  76         //! Creates an obsolete tool module for a tool with the given name.
  77         explicit ObsoleteToolModule(const char *name)
  78             : name_(name)
  79         {
  80         }
  81
  82         const char *name() const override
  83         {
  84             return name_;
  85         }
  86         const char *shortDescription() const override
  87         {
  88             return nullptr;
  89         }
  90
  91         void init(gmx::CommandLineModuleSettings * /*settings*/) override
  92         {
  93         }
  94         int run(int /*argc*/, char * /*argv*/[]) override
  95         {
  96             printMessage();
  97             return 0;
  98         }
  99         void writeHelp(const gmx::CommandLineHelpContext & /*context*/) const override
 100         {
 101             printMessage();
 102         }
 103
 104     private:
 105         void printMessage() const
 106         {
 107             std::fprintf(stderr,
 108                          "This tool is no longer present in GROMACS. Please see\n"
 109                          "  http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/user-guide/cmdline.html#command-changes\n"
 110                          "for ideas how to perform the same tasks with the "
 111                          "new tools.\n");
 112         }
 113
 114         const char             *name_;
 115 };
 116
 117 //! Initializer for a module that defaults to nice level zero.
 118 void initSettingsNoNice(gmx::CommandLineModuleSettings *settings)
 119 {
 120     settings->setDefaultNiceLevel(0);
 121 }
 122
 123 /*! \brief
 124  * Convenience function for creating and registering a module.
 125  *
 126  * \param[in] manager          Module manager to which to register the module.
 127  * \param[in] mainFunction     Main function to wrap.
 128  * \param[in] name             Name for the new module.
 129  * \param[in] shortDescription One-line description for the new module.
 130  */
 131 void registerModule(gmx::CommandLineModuleManager                *manager,
 132                     gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 133                     const char *name, const char *shortDescription)
 134 {
 135     manager->addModuleCMain(name, shortDescription, mainFunction);
 136 }
 137
 138 /*! \brief
 139  * Convenience function for creating and registering a module that defaults to
 140  * -nice 0.
 141  *
 142  * \param[in] manager          Module manager to which to register the module.
 143  * \param[in] mainFunction     Main function to wrap.
 144  * \param[in] name             Name for the new module.
 145  * \param[in] shortDescription One-line description for the new module.
 146  */
 147 void registerModuleNoNice(gmx::CommandLineModuleManager                *manager,
 148                           gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 149                           const char *name, const char *shortDescription)
 150 {
 151     manager->addModuleCMainWithSettings(name, shortDescription, mainFunction,
 152                                         &initSettingsNoNice);
 153 }
 154
 155 /*! \brief
 156  * Convenience function for registering a module for an obsolete tool.
 157  *
 158  * \param[in] manager          Module manager to which to register the module.
 159  * \param[in] name             Name for the obsolete tool.
 160  */
 161 void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
 162                           const char                    *name)
 163 {
 164     gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
 165     manager->addModule(std::move(module));
 166 }
 167
 168 } // namespace
 169
 170 void registerLegacyModules(gmx::CommandLineModuleManager *manager)
 171 {
 172     // Modules from this directory (were in src/kernel/).
 173     registerModule(manager, &gmx_check, "check",
 174                    "Check and compare files");
 175     registerModule(manager, &gmx_dump, "dump",
 176                    "Make binary files human readable");
 177     registerModule(manager, &gmx_grompp, "grompp",
 178                    "Make a run input file");
 179     registerModule(manager, &gmx_convert_tpr, "convert-tpr",
 180                    "Make a modifed run-input file");
 181     registerObsoleteTool(manager, "tpbconv");
 182     registerModule(manager, &gmx_x2top, "x2top",
 183                    "Generate a primitive topology from coordinates");
 184
 185     registerModuleNoNice(manager, &gmx::gmx_mdrun, "mdrun",
 186                          "Perform a simulation, do a normal mode analysis or an energy minimization");
 187
 188     gmx::ICommandLineOptionsModule::registerModuleFactory(
 189             manager, gmx::InsertMoleculesInfo::name(),
 190             gmx::InsertMoleculesInfo::shortDescription(),
 191             &gmx::InsertMoleculesInfo::create);
 192
 193     gmx::ICommandLineOptionsModule::registerModuleFactory(
 194             manager, gmx::ReportMethodsInfo::name,
 195             gmx::ReportMethodsInfo::shortDescription,
 196             &gmx::ReportMethodsInfo::create);
 197
 198     gmx::ICommandLineOptionsModule::registerModuleFactory(
 199             manager, gmx::pdb2gmxInfo::name,
 200             gmx::pdb2gmxInfo::shortDescription,
 201             &gmx::pdb2gmxInfo::create);
 202
 203     // Modules from gmx_ana.h.
 204     registerModule(manager, &gmx_do_dssp, "do_dssp",
 205                    "Assign secondary structure and calculate solvent accessible surface area");
 206     registerModule(manager, &gmx_editconf, "editconf",
 207                    "Convert and manipulates structure files");
 208     registerModule(manager, &gmx_eneconv, "eneconv",
 209                    "Convert energy files");
 210     registerModule(manager, &gmx_solvate, "solvate",
 211                    "Solvate a system");
 212     registerObsoleteTool(manager, "genbox");
 213     registerModule(manager, &gmx_genconf, "genconf",
 214                    "Multiply a conformation in 'random' orientations");
 215     registerModule(manager, &gmx_genion, "genion",
 216                    "Generate monoatomic ions on energetically favorable positions");
 217     registerModule(manager, &gmx_genpr, "genrestr",
 218                    "Generate position restraints or distance restraints for index groups");
 219     registerModule(manager, &gmx_make_edi, "make_edi",
 220                    "Generate input files for essential dynamics sampling");
 221     registerModule(manager, &gmx_make_ndx, "make_ndx",
 222                    "Make index files");
 223     registerModule(manager, &gmx_mk_angndx, "mk_angndx",
 224                    "Generate index files for 'gmx angle'");
 225     registerModule(manager, &gmx_trjcat, "trjcat",
 226                    "Concatenate trajectory files");
 227     registerModule(manager, &gmx_trjconv, "trjconv",
 228                    "Convert and manipulates trajectory files");
 229     registerModule(manager, &gmx_trjorder, "trjorder",
 230                    "Order molecules according to their distance to a group");
 231     registerModule(manager, &gmx_xpm2ps, "xpm2ps",
 232                    "Convert XPM (XPixelMap) matrices to postscript or XPM");
 233
 234     registerModule(manager, &gmx_anadock, "anadock",
 235                    "Cluster structures from Autodock runs");
 236     registerModule(manager, &gmx_anaeig, "anaeig",
 237                    "Analyze eigenvectors/normal modes");
 238     registerModule(manager, &gmx_analyze, "analyze",
 239                    "Analyze data sets");
 240     registerModule(manager, &gmx_g_angle, "angle",
 241                    "Calculate distributions and correlations for angles and dihedrals");
 242     registerModule(manager, &gmx_awh, "awh",
 243                    "Extract data from an accelerated weight histogram (AWH) run");
 244     registerModule(manager, &gmx_bar, "bar",
 245                    "Calculate free energy difference estimates through Bennett's acceptance ratio");
 246     registerObsoleteTool(manager, "bond");
 247     registerObsoleteTool(manager, "dist");
 248     registerObsoleteTool(manager, "sas");
 249     registerObsoleteTool(manager, "sgangle");
 250
 251     registerModule(manager, &gmx_bundle, "bundle",
 252                    "Analyze bundles of axes, e.g., helices");
 253     registerModule(manager, &gmx_chi, "chi",
 254                    "Calculate everything you want to know about chi and other dihedrals");
 255     registerModule(manager, &gmx_cluster, "cluster",
 256                    "Cluster structures");
 257     registerModule(manager, &gmx_clustsize, "clustsize",
 258                    "Calculate size distributions of atomic clusters");
 259     registerModule(manager, &gmx_confrms, "confrms",
 260                    "Fit two structures and calculates the RMSD");
 261     registerModule(manager, &gmx_covar, "covar",
 262                    "Calculate and diagonalize the covariance matrix");
 263     registerModule(manager, &gmx_current, "current",
 264                    "Calculate dielectric constants and current autocorrelation function");
 265     registerModule(manager, &gmx_density, "density",
 266                    "Calculate the density of the system");
 267     registerModule(manager, &gmx_densmap, "densmap",
 268                    "Calculate 2D planar or axial-radial density maps");
 269     registerModule(manager, &gmx_densorder, "densorder",
 270                    "Calculate surface fluctuations");
 271     registerModule(manager, &gmx_dielectric, "dielectric",
 272                    "Calculate frequency dependent dielectric constants");
 273     registerModule(manager, &gmx_dipoles, "dipoles",
 274                    "Compute the total dipole plus fluctuations");
 275     registerModule(manager, &gmx_disre, "disre",
 276                    "Analyze distance restraints");
 277     registerModule(manager, &gmx_dos, "dos",
 278                    "Analyze density of states and properties based on that");
 279     registerModule(manager, &gmx_dyecoupl, "dyecoupl",
 280                    "Extract dye dynamics from trajectories");
 281     registerModule(manager, &gmx_dyndom, "dyndom",
 282                    "Interpolate and extrapolate structure rotations");
 283     registerModule(manager, &gmx_enemat, "enemat",
 284                    "Extract an energy matrix from an energy file");
 285     registerModule(manager, &gmx_energy, "energy",
 286                    "Writes energies to xvg files and display averages");
 287     registerModule(manager, &gmx_filter, "filter",
 288                    "Frequency filter trajectories, useful for making smooth movies");
 289     registerModule(manager, &gmx_gyrate, "gyrate",
 290                    "Calculate the radius of gyration");
 291     registerModule(manager, &gmx_h2order, "h2order",
 292                    "Compute the orientation of water molecules");
 293     registerModule(manager, &gmx_hbond, "hbond",
 294                    "Compute and analyze hydrogen bonds");
 295     registerModule(manager, &gmx_helix, "helix",
 296                    "Calculate basic properties of alpha helices");
 297     registerModule(manager, &gmx_helixorient, "helixorient",
 298                    "Calculate local pitch/bending/rotation/orientation inside helices");
 299     registerModule(manager, &gmx_hydorder, "hydorder",
 300                    "Compute tetrahedrality parameters around a given atom");
 301     registerModule(manager, &gmx_lie, "lie",
 302                    "Estimate free energy from linear combinations");
 303     registerModule(manager, &gmx_mdmat, "mdmat",
 304                    "Calculate residue contact maps");
 305     registerModule(manager, &gmx_mindist, "mindist",
 306                    "Calculate the minimum distance between two groups");
 307     registerModule(manager, &gmx_morph, "morph",
 308                    "Interpolate linearly between conformations");
 309     registerModule(manager, &gmx_msd, "msd",
 310                    "Calculates mean square displacements");
 311     registerModule(manager, &gmx_nmeig, "nmeig",
 312                    "Diagonalize the Hessian for normal mode analysis");
 313     registerModule(manager, &gmx_nmens, "nmens",
 314                    "Generate an ensemble of structures from the normal modes");
 315     registerModule(manager, &gmx_nmr, "nmr",
 316                    "Analyze nuclear magnetic resonance properties from an energy file");
 317     registerModule(manager, &gmx_nmtraj, "nmtraj",
 318                    "Generate a virtual oscillating trajectory from an eigenvector");
 319     registerModule(manager, &gmx_order, "order",
 320                    "Compute the order parameter per atom for carbon tails");
 321     registerModule(manager, &gmx_pme_error, "pme_error",
 322                    "Estimate the error of using PME with a given input file");
 323     registerModule(manager, &gmx_polystat, "polystat",
 324                    "Calculate static properties of polymers");
 325     registerModule(manager, &gmx_potential, "potential",
 326                    "Calculate the electrostatic potential across the box");
 327     registerModule(manager, &gmx_principal, "principal",
 328                    "Calculate principal axes of inertia for a group of atoms");
 329     registerModule(manager, &gmx_rama, "rama",
 330                    "Compute Ramachandran plots");
 331     registerModule(manager, &gmx_rms, "rms",
 332                    "Calculate RMSDs with a reference structure and RMSD matrices");
 333     registerModule(manager, &gmx_rmsdist, "rmsdist",
 334                    "Calculate atom pair distances averaged with power -2, -3 or -6");
 335     registerModule(manager, &gmx_rmsf, "rmsf",
 336                    "Calculate atomic fluctuations");
 337     registerModule(manager, &gmx_rotacf, "rotacf",
 338                    "Calculate the rotational correlation function for molecules");
 339     registerModule(manager, &gmx_rotmat, "rotmat",
 340                    "Plot the rotation matrix for fitting to a reference structure");
 341     registerModule(manager, &gmx_saltbr, "saltbr",
 342                    "Compute salt bridges");
 343     registerModule(manager, &gmx_sans, "sans",
 344                    "Compute small angle neutron scattering spectra");
 345     registerModule(manager, &gmx_saxs, "saxs",
 346                    "Compute small angle X-ray scattering spectra");
 347     registerModule(manager, &gmx_sham, "sham",
 348                    "Compute free energies or other histograms from histograms");
 349     registerModule(manager, &gmx_sigeps, "sigeps",
 350                    "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
 351     registerModule(manager, &gmx_sorient, "sorient",
 352                    "Analyze solvent orientation around solutes");
 353     registerModule(manager, &gmx_spatial, "spatial",
 354                    "Calculate the spatial distribution function");
 355     registerModule(manager, &gmx_spol, "spol",
 356                    "Analyze solvent dipole orientation and polarization around solutes");
 357     registerModule(manager, &gmx_tcaf, "tcaf",
 358                    "Calculate viscosities of liquids");
 359     registerModule(manager, &gmx_traj, "traj",
 360                    "Plot x, v, f, box, temperature and rotational energy from trajectories");
 361     registerModule(manager, &gmx_tune_pme, "tune_pme",
 362                    "Time mdrun as a function of PME ranks to optimize settings");
 363     registerModule(manager, &gmx_vanhove, "vanhove",
 364                    "Compute Van Hove displacement and correlation functions");
 365     registerModule(manager, &gmx_velacc, "velacc",
 366                    "Calculate velocity autocorrelation functions");
 367     registerModule(manager, &gmx_wham, "wham",
 368                    "Perform weighted histogram analysis after umbrella sampling");
 369     registerModule(manager, &gmx_wheel, "wheel",
 370                    "Plot helical wheels");
 371     registerModuleNoNice(manager, &gmx_view, "view",
 372                          "View a trajectory on an X-Windows terminal");
 373
 374     {
 375         gmx::CommandLineModuleGroup group =
 376             manager->addModuleGroup("Generating topologies and coordinates");
 377         group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
 378         group.addModule("x2top");
 379         group.addModule("solvate");
 380         group.addModule("insert-molecules");
 381         group.addModule("genconf");
 382         group.addModule("genion");
 383         group.addModule("genrestr");
 384         group.addModule("pdb2gmx");
 385     }
 386     {
 387         gmx::CommandLineModuleGroup group =
 388             manager->addModuleGroup("Running a simulation");
 389         group.addModule("grompp");
 390         group.addModule("mdrun");
 391         group.addModule("convert-tpr");
 392     }
 393     {
 394         gmx::CommandLineModuleGroup group =
 395             manager->addModuleGroup("Viewing trajectories");
 396         group.addModule("nmtraj");
 397         group.addModule("view");
 398     }
 399     {
 400         gmx::CommandLineModuleGroup group =
 401             manager->addModuleGroup("Processing energies");
 402         group.addModule("enemat");
 403         group.addModule("energy");
 404         group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
 405     }
 406     {
 407         gmx::CommandLineModuleGroup group =
 408             manager->addModuleGroup("Converting files");
 409         group.addModule("editconf");
 410         group.addModule("eneconv");
 411         group.addModule("sigeps");
 412         group.addModule("trjcat");
 413         group.addModule("trjconv");
 414         group.addModule("xpm2ps");
 415     }
 416     {
 417         gmx::CommandLineModuleGroup group =
 418             manager->addModuleGroup("Tools");
 419         group.addModule("analyze");
 420         group.addModule("awh");
 421         group.addModule("dyndom");
 422         group.addModule("filter");
 423         group.addModule("lie");
 424         group.addModule("morph");
 425         group.addModule("pme_error");
 426         group.addModule("sham");
 427         group.addModule("spatial");
 428         group.addModule("traj");
 429         group.addModule("tune_pme");
 430         group.addModule("wham");
 431         group.addModule("check");
 432         group.addModule("dump");
 433         group.addModule("make_ndx");
 434         group.addModule("mk_angndx");
 435         group.addModule("trjorder");
 436         group.addModule("xpm2ps");
 437         group.addModule("report-methods");
 438     }
 439     {
 440         gmx::CommandLineModuleGroup group =
 441             manager->addModuleGroup("Distances between structures");
 442         group.addModule("cluster");
 443         group.addModule("confrms");
 444         group.addModule("rms");
 445         group.addModule("rmsf");
 446     }
 447     {
 448         gmx::CommandLineModuleGroup group =
 449             manager->addModuleGroup("Distances in structures over time");
 450         group.addModule("mindist");
 451         group.addModule("mdmat");
 452         group.addModule("polystat");
 453         group.addModule("rmsdist");
 454     }
 455     {
 456         gmx::CommandLineModuleGroup group =
 457             manager->addModuleGroup("Mass distribution properties over time");
 458         group.addModule("gyrate");
 459         group.addModule("msd");
 460         group.addModule("polystat");
 461         group.addModule("rdf");
 462         group.addModule("rotacf");
 463         group.addModule("rotmat");
 464         group.addModule("sans");
 465         group.addModule("saxs");
 466         group.addModule("traj");
 467         group.addModule("vanhove");
 468     }
 469     {
 470         gmx::CommandLineModuleGroup group =
 471             manager->addModuleGroup("Analyzing bonded interactions");
 472         group.addModule("angle");
 473         group.addModule("mk_angndx");
 474     }
 475     {
 476         gmx::CommandLineModuleGroup group =
 477             manager->addModuleGroup("Structural properties");
 478         group.addModule("anadock");
 479         group.addModule("bundle");
 480         group.addModule("clustsize");
 481         group.addModule("disre");
 482         group.addModule("hbond");
 483         group.addModule("order");
 484         group.addModule("principal");
 485         group.addModule("rdf");
 486         group.addModule("saltbr");
 487         group.addModule("sorient");
 488         group.addModule("spol");
 489     }
 490     {
 491         gmx::CommandLineModuleGroup group =
 492             manager->addModuleGroup("Kinetic properties");
 493         group.addModule("bar");
 494         group.addModule("current");
 495         group.addModule("dos");
 496         group.addModule("dyecoupl");
 497         group.addModule("principal");
 498         group.addModule("tcaf");
 499         group.addModule("traj");
 500         group.addModule("vanhove");
 501         group.addModule("velacc");
 502     }
 503     {
 504         gmx::CommandLineModuleGroup group =
 505             manager->addModuleGroup("Electrostatic properties");
 506         group.addModule("current");
 507         group.addModule("dielectric");
 508         group.addModule("dipoles");
 509         group.addModule("potential");
 510         group.addModule("spol");
 511         group.addModule("genion");
 512     }
 513     {
 514         gmx::CommandLineModuleGroup group =
 515             manager->addModuleGroup("Protein-specific analysis");
 516         group.addModule("do_dssp");
 517         group.addModule("chi");
 518         group.addModule("helix");
 519         group.addModule("helixorient");
 520         group.addModule("rama");
 521         group.addModule("wheel");
 522     }
 523     {
 524         gmx::CommandLineModuleGroup group =
 525             manager->addModuleGroup("Interfaces");
 526         group.addModule("bundle");
 527         group.addModule("density");
 528         group.addModule("densmap");
 529         group.addModule("densorder");
 530         group.addModule("h2order");
 531         group.addModule("hydorder");
 532         group.addModule("order");
 533         group.addModule("potential");
 534     }
 535     {
 536         gmx::CommandLineModuleGroup group =
 537             manager->addModuleGroup("Covariance analysis");
 538         group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
 539         group.addModule("covar");
 540         group.addModule("make_edi");
 541     }
 542     {
 543         gmx::CommandLineModuleGroup group =
 544             manager->addModuleGroup("Normal modes");
 545         group.addModuleWithDescription("anaeig", "Analyze the normal modes");
 546         group.addModule("nmeig");
 547         group.addModule("nmtraj");
 548         group.addModule("nmens");
 549         group.addModule("grompp");
 550         group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");
 551     }
 552 }