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/editconf.h"
  51 #include "gromacs/gmxpreprocess/genconf.h"
  52 #include "gromacs/gmxpreprocess/genion.h"
  53 #include "gromacs/gmxpreprocess/genrestr.h"
  54 #include "gromacs/gmxpreprocess/grompp.h"
  55 #include "gromacs/gmxpreprocess/insert_molecules.h"
  56 #include "gromacs/gmxpreprocess/pdb2gmx.h"
  57 #include "gromacs/gmxpreprocess/solvate.h"
  58 #include "gromacs/gmxpreprocess/x2top.h"
  59 #include "gromacs/tools/check.h"
  60 #include "gromacs/tools/convert_tpr.h"
  61 #include "gromacs/tools/dump.h"
  62 #include "gromacs/tools/eneconv.h"
  63 #include "gromacs/tools/make_ndx.h"
  64 #include "gromacs/tools/mk_angndx.h"
  65 #include "gromacs/tools/pme_error.h"
  66 #include "gromacs/tools/report_methods.h"
  67 #include "gromacs/tools/trjcat.h"
  68 #include "gromacs/tools/trjconv.h"
  69 #include "gromacs/tools/tune_pme.h"
  70
  71 #include "mdrun/mdrun_main.h"
  72 #include "view/view.h"
  73
  74 namespace
  75 {
  76
  77 /*! \brief
  78  * Command line module that provides information about obsolescence.
  79  *
  80  * Prints a message directing the user to a wiki page describing replacement
  81  * options.
  82  */
  83 class ObsoleteToolModule : public gmx::ICommandLineModule
  84 {
  85     public:
  86         //! Creates an obsolete tool module for a tool with the given name.
  87         explicit ObsoleteToolModule(const char *name)
  88             : name_(name)
  89         {
  90         }
  91
  92         const char *name() const override
  93         {
  94             return name_;
  95         }
  96         const char *shortDescription() const override
  97         {
  98             return nullptr;
  99         }
 100
 101         void init(gmx::CommandLineModuleSettings * /*settings*/) override
 102         {
 103         }
 104         int run(int /*argc*/, char * /*argv*/[]) override
 105         {
 106             printMessage();
 107             return 0;
 108         }
 109         void writeHelp(const gmx::CommandLineHelpContext & /*context*/) const override
 110         {
 111             printMessage();
 112         }
 113
 114     private:
 115         void printMessage() const
 116         {
 117             std::fprintf(stderr,
 118                          "This tool is no longer present in GROMACS. Please see\n"
 119                          "  http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/user-guide/cmdline.html#command-changes\n"
 120                          "for ideas how to perform the same tasks with the "
 121                          "new tools.\n");
 122         }
 123
 124         const char             *name_;
 125 };
 126
 127 //! Initializer for a module that defaults to nice level zero.
 128 void initSettingsNoNice(gmx::CommandLineModuleSettings *settings)
 129 {
 130     settings->setDefaultNiceLevel(0);
 131 }
 132
 133 /*! \brief
 134  * Convenience function for creating and registering a module.
 135  *
 136  * \param[in] manager          Module manager to which to register the module.
 137  * \param[in] mainFunction     Main function to wrap.
 138  * \param[in] name             Name for the new module.
 139  * \param[in] shortDescription One-line description for the new module.
 140  */
 141 void registerModule(gmx::CommandLineModuleManager                *manager,
 142                     gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 143                     const char *name, const char *shortDescription)
 144 {
 145     manager->addModuleCMain(name, shortDescription, mainFunction);
 146 }
 147
 148 /*! \brief
 149  * Convenience function for creating and registering a module that defaults to
 150  * -nice 0.
 151  *
 152  * \param[in] manager          Module manager to which to register the module.
 153  * \param[in] mainFunction     Main function to wrap.
 154  * \param[in] name             Name for the new module.
 155  * \param[in] shortDescription One-line description for the new module.
 156  */
 157 void registerModuleNoNice(gmx::CommandLineModuleManager                *manager,
 158                           gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 159                           const char *name, const char *shortDescription)
 160 {
 161     manager->addModuleCMainWithSettings(name, shortDescription, mainFunction,
 162                                         &initSettingsNoNice);
 163 }
 164
 165 /*! \brief
 166  * Convenience function for registering a module for an obsolete tool.
 167  *
 168  * \param[in] manager          Module manager to which to register the module.
 169  * \param[in] name             Name for the obsolete tool.
 170  */
 171 void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
 172                           const char                    *name)
 173 {
 174     gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
 175     manager->addModule(std::move(module));
 176 }
 177
 178 } // namespace
 179
 180 void registerLegacyModules(gmx::CommandLineModuleManager *manager)
 181 {
 182     registerModule(manager, &gmx_check, "check",
 183                    "Check and compare files");
 184     gmx::ICommandLineOptionsModule::registerModuleFactory(
 185             manager, gmx::DumpInfo::name,
 186             gmx::DumpInfo::shortDescription,
 187             &gmx::DumpInfo::create);
 188     registerModule(manager, &gmx_grompp, "grompp",
 189                    "Make a run input file");
 190     registerModule(manager, &gmx_convert_tpr, "convert-tpr",
 191                    "Make a modifed run-input file");
 192     registerObsoleteTool(manager, "tpbconv");
 193     registerModule(manager, &gmx_x2top, "x2top",
 194                    "Generate a primitive topology from coordinates");
 195
 196     registerModuleNoNice(manager, &gmx::gmx_mdrun, "mdrun",
 197                          "Perform a simulation, do a normal mode analysis or an energy minimization");
 198
 199     gmx::ICommandLineOptionsModule::registerModuleFactory(
 200             manager, gmx::InsertMoleculesInfo::name(),
 201             gmx::InsertMoleculesInfo::shortDescription(),
 202             &gmx::InsertMoleculesInfo::create);
 203
 204     gmx::ICommandLineOptionsModule::registerModuleFactory(
 205             manager, gmx::ReportMethodsInfo::name,
 206             gmx::ReportMethodsInfo::shortDescription,
 207             &gmx::ReportMethodsInfo::create);
 208
 209     gmx::ICommandLineOptionsModule::registerModuleFactory(
 210             manager, gmx::pdb2gmxInfo::name,
 211             gmx::pdb2gmxInfo::shortDescription,
 212             &gmx::pdb2gmxInfo::create);
 213
 214     // Modules from gmx_ana.h.
 215     registerModule(manager, &gmx_do_dssp, "do_dssp",
 216                    "Assign secondary structure and calculate solvent accessible surface area");
 217     registerModule(manager, &gmx_editconf, "editconf",
 218                    "Convert and manipulates structure files");
 219     registerModule(manager, &gmx_eneconv, "eneconv",
 220                    "Convert energy files");
 221     registerModule(manager, &gmx_solvate, "solvate",
 222                    "Solvate a system");
 223     registerObsoleteTool(manager, "genbox");
 224     registerModule(manager, &gmx_genconf, "genconf",
 225                    "Multiply a conformation in 'random' orientations");
 226     registerModule(manager, &gmx_genion, "genion",
 227                    "Generate monoatomic ions on energetically favorable positions");
 228     registerModule(manager, &gmx_genrestr, "genrestr",
 229                    "Generate position restraints or distance restraints for index groups");
 230     registerModule(manager, &gmx_make_edi, "make_edi",
 231                    "Generate input files for essential dynamics sampling");
 232     registerModule(manager, &gmx_make_ndx, "make_ndx",
 233                    "Make index files");
 234     registerModule(manager, &gmx_mk_angndx, "mk_angndx",
 235                    "Generate index files for 'gmx angle'");
 236     registerModule(manager, &gmx_trjcat, "trjcat",
 237                    "Concatenate trajectory files");
 238     registerModule(manager, &gmx_trjconv, "trjconv",
 239                    "Convert and manipulates trajectory files");
 240     registerModule(manager, &gmx_trjorder, "trjorder",
 241                    "Order molecules according to their distance to a group");
 242     registerModule(manager, &gmx_xpm2ps, "xpm2ps",
 243                    "Convert XPM (XPixelMap) matrices to postscript or XPM");
 244
 245     registerModule(manager, &gmx_anaeig, "anaeig",
 246                    "Analyze eigenvectors/normal modes");
 247     registerModule(manager, &gmx_analyze, "analyze",
 248                    "Analyze data sets");
 249     registerModule(manager, &gmx_g_angle, "angle",
 250                    "Calculate distributions and correlations for angles and dihedrals");
 251     registerModule(manager, &gmx_awh, "awh",
 252                    "Extract data from an accelerated weight histogram (AWH) run");
 253     registerModule(manager, &gmx_bar, "bar",
 254                    "Calculate free energy difference estimates through Bennett's acceptance ratio");
 255     registerObsoleteTool(manager, "bond");
 256     registerObsoleteTool(manager, "dist");
 257     registerObsoleteTool(manager, "sas");
 258     registerObsoleteTool(manager, "sgangle");
 259
 260     registerModule(manager, &gmx_bundle, "bundle",
 261                    "Analyze bundles of axes, e.g., helices");
 262     registerModule(manager, &gmx_chi, "chi",
 263                    "Calculate everything you want to know about chi and other dihedrals");
 264     registerModule(manager, &gmx_cluster, "cluster",
 265                    "Cluster structures");
 266     registerModule(manager, &gmx_clustsize, "clustsize",
 267                    "Calculate size distributions of atomic clusters");
 268     registerModule(manager, &gmx_confrms, "confrms",
 269                    "Fit two structures and calculates the RMSD");
 270     registerModule(manager, &gmx_covar, "covar",
 271                    "Calculate and diagonalize the covariance matrix");
 272     registerModule(manager, &gmx_current, "current",
 273                    "Calculate dielectric constants and current autocorrelation function");
 274     registerModule(manager, &gmx_density, "density",
 275                    "Calculate the density of the system");
 276     registerModule(manager, &gmx_densmap, "densmap",
 277                    "Calculate 2D planar or axial-radial density maps");
 278     registerModule(manager, &gmx_densorder, "densorder",
 279                    "Calculate surface fluctuations");
 280     registerModule(manager, &gmx_dielectric, "dielectric",
 281                    "Calculate frequency dependent dielectric constants");
 282     registerModule(manager, &gmx_dipoles, "dipoles",
 283                    "Compute the total dipole plus fluctuations");
 284     registerModule(manager, &gmx_disre, "disre",
 285                    "Analyze distance restraints");
 286     registerModule(manager, &gmx_dos, "dos",
 287                    "Analyze density of states and properties based on that");
 288     registerModule(manager, &gmx_dyecoupl, "dyecoupl",
 289                    "Extract dye dynamics from trajectories");
 290     registerModule(manager, &gmx_enemat, "enemat",
 291                    "Extract an energy matrix from an energy file");
 292     registerModule(manager, &gmx_energy, "energy",
 293                    "Writes energies to xvg files and display averages");
 294     registerModule(manager, &gmx_filter, "filter",
 295                    "Frequency filter trajectories, useful for making smooth movies");
 296     registerModule(manager, &gmx_gyrate, "gyrate",
 297                    "Calculate the radius of gyration");
 298     registerModule(manager, &gmx_h2order, "h2order",
 299                    "Compute the orientation of water molecules");
 300     registerModule(manager, &gmx_hbond, "hbond",
 301                    "Compute and analyze hydrogen bonds");
 302     registerModule(manager, &gmx_helix, "helix",
 303                    "Calculate basic properties of alpha helices");
 304     registerModule(manager, &gmx_helixorient, "helixorient",
 305                    "Calculate local pitch/bending/rotation/orientation inside helices");
 306     registerModule(manager, &gmx_hydorder, "hydorder",
 307                    "Compute tetrahedrality parameters around a given atom");
 308     registerModule(manager, &gmx_lie, "lie",
 309                    "Estimate free energy from linear combinations");
 310     registerModule(manager, &gmx_mdmat, "mdmat",
 311                    "Calculate residue contact maps");
 312     registerModule(manager, &gmx_mindist, "mindist",
 313                    "Calculate the minimum distance between two groups");
 314     registerModule(manager, &gmx_msd, "msd",
 315                    "Calculates mean square displacements");
 316     registerModule(manager, &gmx_nmeig, "nmeig",
 317                    "Diagonalize the Hessian for normal mode analysis");
 318     registerModule(manager, &gmx_nmens, "nmens",
 319                    "Generate an ensemble of structures from the normal modes");
 320     registerModule(manager, &gmx_nmr, "nmr",
 321                    "Analyze nuclear magnetic resonance properties from an energy file");
 322     registerModule(manager, &gmx_nmtraj, "nmtraj",
 323                    "Generate a virtual oscillating trajectory from an eigenvector");
 324     registerModule(manager, &gmx_order, "order",
 325                    "Compute the order parameter per atom for carbon tails");
 326     registerModule(manager, &gmx_pme_error, "pme_error",
 327                    "Estimate the error of using PME with a given input file");
 328     registerModule(manager, &gmx_polystat, "polystat",
 329                    "Calculate static properties of polymers");
 330     registerModule(manager, &gmx_potential, "potential",
 331                    "Calculate the electrostatic potential across the box");
 332     registerModule(manager, &gmx_principal, "principal",
 333                    "Calculate principal axes of inertia for a group of atoms");
 334     registerModule(manager, &gmx_rama, "rama",
 335                    "Compute Ramachandran plots");
 336     registerModule(manager, &gmx_rms, "rms",
 337                    "Calculate RMSDs with a reference structure and RMSD matrices");
 338     registerModule(manager, &gmx_rmsdist, "rmsdist",
 339                    "Calculate atom pair distances averaged with power -2, -3 or -6");
 340     registerModule(manager, &gmx_rmsf, "rmsf",
 341                    "Calculate atomic fluctuations");
 342     registerModule(manager, &gmx_rotacf, "rotacf",
 343                    "Calculate the rotational correlation function for molecules");
 344     registerModule(manager, &gmx_rotmat, "rotmat",
 345                    "Plot the rotation matrix for fitting to a reference structure");
 346     registerModule(manager, &gmx_saltbr, "saltbr",
 347                    "Compute salt bridges");
 348     registerModule(manager, &gmx_sans, "sans",
 349                    "Compute small angle neutron scattering spectra");
 350     registerModule(manager, &gmx_saxs, "saxs",
 351                    "Compute small angle X-ray scattering spectra");
 352     registerModule(manager, &gmx_sham, "sham",
 353                    "Compute free energies or other histograms from histograms");
 354     registerModule(manager, &gmx_sigeps, "sigeps",
 355                    "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
 356     registerModule(manager, &gmx_sorient, "sorient",
 357                    "Analyze solvent orientation around solutes");
 358     registerModule(manager, &gmx_spatial, "spatial",
 359                    "Calculate the spatial distribution function");
 360     registerModule(manager, &gmx_spol, "spol",
 361                    "Analyze solvent dipole orientation and polarization around solutes");
 362     registerModule(manager, &gmx_tcaf, "tcaf",
 363                    "Calculate viscosities of liquids");
 364     registerModule(manager, &gmx_traj, "traj",
 365                    "Plot x, v, f, box, temperature and rotational energy from trajectories");
 366     registerModule(manager, &gmx_tune_pme, "tune_pme",
 367                    "Time mdrun as a function of PME ranks to optimize settings");
 368     registerModule(manager, &gmx_vanhove, "vanhove",
 369                    "Compute Van Hove displacement and correlation functions");
 370     registerModule(manager, &gmx_velacc, "velacc",
 371                    "Calculate velocity autocorrelation functions");
 372     registerModule(manager, &gmx_wham, "wham",
 373                    "Perform weighted histogram analysis after umbrella sampling");
 374     registerModule(manager, &gmx_wheel, "wheel",
 375                    "Plot helical wheels");
 376     registerModuleNoNice(manager, &gmx_view, "view",
 377                          "View a trajectory on an X-Windows terminal");
 378
 379     {
 380         gmx::CommandLineModuleGroup group =
 381             manager->addModuleGroup("Generating topologies and coordinates");
 382         group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
 383         group.addModule("x2top");
 384         group.addModule("solvate");
 385         group.addModule("insert-molecules");
 386         group.addModule("genconf");
 387         group.addModule("genion");
 388         group.addModule("genrestr");
 389         group.addModule("pdb2gmx");
 390     }
 391     {
 392         gmx::CommandLineModuleGroup group =
 393             manager->addModuleGroup("Running a simulation");
 394         group.addModule("grompp");
 395         group.addModule("mdrun");
 396         group.addModule("convert-tpr");
 397     }
 398     {
 399         gmx::CommandLineModuleGroup group =
 400             manager->addModuleGroup("Viewing trajectories");
 401         group.addModule("nmtraj");
 402         group.addModule("view");
 403     }
 404     {
 405         gmx::CommandLineModuleGroup group =
 406             manager->addModuleGroup("Processing energies");
 407         group.addModule("enemat");
 408         group.addModule("energy");
 409         group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
 410     }
 411     {
 412         gmx::CommandLineModuleGroup group =
 413             manager->addModuleGroup("Converting files");
 414         group.addModule("editconf");
 415         group.addModule("eneconv");
 416         group.addModule("sigeps");
 417         group.addModule("trjcat");
 418         group.addModule("trjconv");
 419         group.addModule("xpm2ps");
 420     }
 421     {
 422         gmx::CommandLineModuleGroup group =
 423             manager->addModuleGroup("Tools");
 424         group.addModule("analyze");
 425         group.addModule("awh");
 426         group.addModule("filter");
 427         group.addModule("lie");
 428         group.addModule("pme_error");
 429         group.addModule("sham");
 430         group.addModule("spatial");
 431         group.addModule("traj");
 432         group.addModule("tune_pme");
 433         group.addModule("wham");
 434         group.addModule("check");
 435         group.addModule("dump");
 436         group.addModule("make_ndx");
 437         group.addModule("mk_angndx");
 438         group.addModule("trjorder");
 439         group.addModule("xpm2ps");
 440         group.addModule("report-methods");
 441     }
 442     {
 443         gmx::CommandLineModuleGroup group =
 444             manager->addModuleGroup("Distances between structures");
 445         group.addModule("cluster");
 446         group.addModule("confrms");
 447         group.addModule("rms");
 448         group.addModule("rmsf");
 449     }
 450     {
 451         gmx::CommandLineModuleGroup group =
 452             manager->addModuleGroup("Distances in structures over time");
 453         group.addModule("mindist");
 454         group.addModule("mdmat");
 455         group.addModule("polystat");
 456         group.addModule("rmsdist");
 457     }
 458     {
 459         gmx::CommandLineModuleGroup group =
 460             manager->addModuleGroup("Mass distribution properties over time");
 461         group.addModule("gyrate");
 462         group.addModule("msd");
 463         group.addModule("polystat");
 464         group.addModule("rdf");
 465         group.addModule("rotacf");
 466         group.addModule("rotmat");
 467         group.addModule("sans");
 468         group.addModule("saxs");
 469         group.addModule("traj");
 470         group.addModule("vanhove");
 471     }
 472     {
 473         gmx::CommandLineModuleGroup group =
 474             manager->addModuleGroup("Analyzing bonded interactions");
 475         group.addModule("angle");
 476         group.addModule("mk_angndx");
 477     }
 478     {
 479         gmx::CommandLineModuleGroup group =
 480             manager->addModuleGroup("Structural properties");
 481         group.addModule("bundle");
 482         group.addModule("clustsize");
 483         group.addModule("disre");
 484         group.addModule("hbond");
 485         group.addModule("order");
 486         group.addModule("principal");
 487         group.addModule("rdf");
 488         group.addModule("saltbr");
 489         group.addModule("sorient");
 490         group.addModule("spol");
 491     }
 492     {
 493         gmx::CommandLineModuleGroup group =
 494             manager->addModuleGroup("Kinetic properties");
 495         group.addModule("bar");
 496         group.addModule("current");
 497         group.addModule("dos");
 498         group.addModule("dyecoupl");
 499         group.addModule("principal");
 500         group.addModule("tcaf");
 501         group.addModule("traj");
 502         group.addModule("vanhove");
 503         group.addModule("velacc");
 504     }
 505     {
 506         gmx::CommandLineModuleGroup group =
 507             manager->addModuleGroup("Electrostatic properties");
 508         group.addModule("current");
 509         group.addModule("dielectric");
 510         group.addModule("dipoles");
 511         group.addModule("potential");
 512         group.addModule("spol");
 513         group.addModule("genion");
 514     }
 515     {
 516         gmx::CommandLineModuleGroup group =
 517             manager->addModuleGroup("Protein-specific analysis");
 518         group.addModule("do_dssp");
 519         group.addModule("chi");
 520         group.addModule("helix");
 521         group.addModule("helixorient");
 522         group.addModule("rama");
 523         group.addModule("wheel");
 524     }
 525     {
 526         gmx::CommandLineModuleGroup group =
 527             manager->addModuleGroup("Interfaces");
 528         group.addModule("bundle");
 529         group.addModule("density");
 530         group.addModule("densmap");
 531         group.addModule("densorder");
 532         group.addModule("h2order");
 533         group.addModule("hydorder");
 534         group.addModule("order");
 535         group.addModule("potential");
 536     }
 537     {
 538         gmx::CommandLineModuleGroup group =
 539             manager->addModuleGroup("Covariance analysis");
 540         group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
 541         group.addModule("covar");
 542         group.addModule("make_edi");
 543     }
 544     {
 545         gmx::CommandLineModuleGroup group =
 546             manager->addModuleGroup("Normal modes");
 547         group.addModuleWithDescription("anaeig", "Analyze the normal modes");
 548         group.addModule("nmeig");
 549         group.addModule("nmtraj");
 550         group.addModule("nmens");
 551         group.addModule("grompp");
 552         group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");
 553     }
 554 }