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
  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 NULL;
  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 // TODO: Consider removing duplication with CMainCommandLineModule from
 117 // cmdlinemodulemanager.cpp.
 118 class NoNiceModule : public gmx::ICommandLineModule
 119 {
 120     public:
 121         //! \copydoc gmx::CommandLineModuleManager::CMainFunction
 122         typedef gmx::CommandLineModuleManager::CMainFunction CMainFunction;
 123
 124         /*! \brief
 125          * Creates a wrapper module for the given main function.
 126          *
 127          * \param[in] name             Name for the module.
 128          * \param[in] shortDescription One-line description for the module.
 129          * \param[in] mainFunction     Main function to wrap.
 130          *
 131          * Does not throw.
 132          */
 133         NoNiceModule(const char *name, const char *shortDescription,
 134                      CMainFunction mainFunction)
 135             : name_(name), shortDescription_(shortDescription),
 136               mainFunction_(mainFunction)
 137         {
 138         }
 139
 140         virtual const char *name() const
 141         {
 142             return name_;
 143         }
 144         virtual const char *shortDescription() const
 145         {
 146             return shortDescription_;
 147         }
 148
 149         virtual void init(gmx::CommandLineModuleSettings *settings)
 150         {
 151             settings->setDefaultNiceLevel(0);
 152         }
 153         virtual int run(int argc, char *argv[])
 154         {
 155             return mainFunction_(argc, argv);
 156         }
 157         virtual void writeHelp(const gmx::CommandLineHelpContext &context) const
 158         {
 159             writeCommandLineHelpCMain(context, name_, mainFunction_);
 160         }
 161
 162     private:
 163         const char             *name_;
 164         const char             *shortDescription_;
 165         CMainFunction           mainFunction_;
 166 };
 167
 168 /*! \brief
 169  * Convenience function for creating and registering a module.
 170  *
 171  * \param[in] manager          Module manager to which to register the module.
 172  * \param[in] mainFunction     Main function to wrap.
 173  * \param[in] name             Name for the new module.
 174  * \param[in] shortDescription One-line description for the new module.
 175  */
 176 void registerModule(gmx::CommandLineModuleManager                *manager,
 177                     gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 178                     const char *name, const char *shortDescription)
 179 {
 180     manager->addModuleCMain(name, shortDescription, mainFunction);
 181 }
 182
 183 /*! \brief
 184  * Convenience function for creating and registering a module that defaults to
 185  * -nice 0.
 186  *
 187  * \param[in] manager          Module manager to which to register the module.
 188  * \param[in] mainFunction     Main function to wrap.
 189  * \param[in] name             Name for the new module.
 190  * \param[in] shortDescription One-line description for the new module.
 191  */
 192 void registerModuleNoNice(gmx::CommandLineModuleManager                *manager,
 193                           gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 194                           const char *name, const char *shortDescription)
 195 {
 196     gmx::CommandLineModulePointer module(
 197             new NoNiceModule(name, shortDescription, mainFunction));
 198     manager->addModule(std::move(module));
 199 }
 200
 201 /*! \brief
 202  * Convenience function for registering a module for an obsolete tool.
 203  *
 204  * \param[in] manager          Module manager to which to register the module.
 205  * \param[in] name             Name for the obsolete tool.
 206  */
 207 void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
 208                           const char                    *name)
 209 {
 210     gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
 211     manager->addModule(std::move(module));
 212 }
 213
 214 } // namespace
 215
 216 void registerLegacyModules(gmx::CommandLineModuleManager *manager)
 217 {
 218     // Modules from this directory (were in src/kernel/).
 219     registerModule(manager, &gmx_check, "check",
 220                    "Check and compare files");
 221     registerModule(manager, &gmx_dump, "dump",
 222                    "Make binary files human readable");
 223     registerModule(manager, &gmx_grompp, "grompp",
 224                    "Make a run input file");
 225     registerModule(manager, &gmx_pdb2gmx, "pdb2gmx",
 226                    "Convert coordinate files to topology and FF-compliant coordinate files");
 227     registerModule(manager, &gmx_convert_tpr, "convert-tpr",
 228                    "Make a modifed run-input file");
 229     registerObsoleteTool(manager, "tpbconv");
 230     registerModule(manager, &gmx_x2top, "x2top",
 231                    "Generate a primitive topology from coordinates");
 232
 233     registerModuleNoNice(manager, &gmx_mdrun, "mdrun",
 234                          "Perform a simulation, do a normal mode analysis or an energy minimization");
 235
 236     gmx::ICommandLineOptionsModule::registerModuleFactory(
 237             manager, gmx::InsertMoleculesInfo::name,
 238             gmx::InsertMoleculesInfo::shortDescription,
 239             &gmx::InsertMoleculesInfo::create);
 240
 241     // Modules from gmx_ana.h.
 242     registerModule(manager, &gmx_do_dssp, "do_dssp",
 243                    "Assign secondary structure and calculate solvent accessible surface area");
 244     registerModule(manager, &gmx_editconf, "editconf",
 245                    "Convert and manipulates structure files");
 246     registerModule(manager, &gmx_eneconv, "eneconv",
 247                    "Convert energy files");
 248     registerModule(manager, &gmx_solvate, "solvate",
 249                    "Solvate a system");
 250     registerObsoleteTool(manager, "genbox");
 251     registerModule(manager, &gmx_genconf, "genconf",
 252                    "Multiply a conformation in 'random' orientations");
 253     registerModule(manager, &gmx_genion, "genion",
 254                    "Generate monoatomic ions on energetically favorable positions");
 255     registerModule(manager, &gmx_genpr, "genrestr",
 256                    "Generate position restraints or distance restraints for index groups");
 257     registerModule(manager, &gmx_make_edi, "make_edi",
 258                    "Generate input files for essential dynamics sampling");
 259     registerModule(manager, &gmx_make_ndx, "make_ndx",
 260                    "Make index files");
 261     registerModule(manager, &gmx_mk_angndx, "mk_angndx",
 262                    "Generate index files for 'gmx angle'");
 263     registerModule(manager, &gmx_trjcat, "trjcat",
 264                    "Concatenate trajectory files");
 265     registerModule(manager, &gmx_trjconv, "trjconv",
 266                    "Convert and manipulates trajectory files");
 267     registerModule(manager, &gmx_trjorder, "trjorder",
 268                    "Order molecules according to their distance to a group");
 269     registerModule(manager, &gmx_xpm2ps, "xpm2ps",
 270                    "Convert XPM (XPixelMap) matrices to postscript or XPM");
 271
 272     registerModule(manager, &gmx_anadock, "anadock",
 273                    "Cluster structures from Autodock runs");
 274     registerModule(manager, &gmx_anaeig, "anaeig",
 275                    "Analyze eigenvectors/normal modes");
 276     registerModule(manager, &gmx_analyze, "analyze",
 277                    "Analyze data sets");
 278     registerModule(manager, &gmx_g_angle, "angle",
 279                    "Calculate distributions and correlations for angles and dihedrals");
 280     registerModule(manager, &gmx_bar, "bar",
 281                    "Calculate free energy difference estimates through Bennett's acceptance ratio");
 282     registerObsoleteTool(manager, "bond");
 283     registerObsoleteTool(manager, "dist");
 284     registerObsoleteTool(manager, "sas");
 285     registerObsoleteTool(manager, "sgangle");
 286
 287     registerModule(manager, &gmx_bundle, "bundle",
 288                    "Analyze bundles of axes, e.g., helices");
 289     registerModule(manager, &gmx_chi, "chi",
 290                    "Calculate everything you want to know about chi and other dihedrals");
 291     registerModule(manager, &gmx_cluster, "cluster",
 292                    "Cluster structures");
 293     registerModule(manager, &gmx_clustsize, "clustsize",
 294                    "Calculate size distributions of atomic clusters");
 295     registerModule(manager, &gmx_confrms, "confrms",
 296                    "Fit two structures and calculates the RMSD");
 297     registerModule(manager, &gmx_covar, "covar",
 298                    "Calculate and diagonalize the covariance matrix");
 299     registerModule(manager, &gmx_current, "current",
 300                    "Calculate dielectric constants and current autocorrelation function");
 301     registerModule(manager, &gmx_density, "density",
 302                    "Calculate the density of the system");
 303     registerModule(manager, &gmx_densmap, "densmap",
 304                    "Calculate 2D planar or axial-radial density maps");
 305     registerModule(manager, &gmx_densorder, "densorder",
 306                    "Calculate surface fluctuations");
 307     registerModule(manager, &gmx_dielectric, "dielectric",
 308                    "Calculate frequency dependent dielectric constants");
 309     registerModule(manager, &gmx_dipoles, "dipoles",
 310                    "Compute the total dipole plus fluctuations");
 311     registerModule(manager, &gmx_disre, "disre",
 312                    "Analyze distance restraints");
 313     registerModule(manager, &gmx_dos, "dos",
 314                    "Analyze density of states and properties based on that");
 315     registerModule(manager, &gmx_dyecoupl, "dyecoupl",
 316                    "Extract dye dynamics from trajectories");
 317     registerModule(manager, &gmx_dyndom, "dyndom",
 318                    "Interpolate and extrapolate structure rotations");
 319     registerModule(manager, &gmx_enemat, "enemat",
 320                    "Extract an energy matrix from an energy file");
 321     registerModule(manager, &gmx_energy, "energy",
 322                    "Writes energies to xvg files and display averages");
 323     registerModule(manager, &gmx_filter, "filter",
 324                    "Frequency filter trajectories, useful for making smooth movies");
 325     registerModule(manager, &gmx_gyrate, "gyrate",
 326                    "Calculate the radius of gyration");
 327     registerModule(manager, &gmx_h2order, "h2order",
 328                    "Compute the orientation of water molecules");
 329     registerModule(manager, &gmx_hbond, "hbond",
 330                    "Compute and analyze hydrogen bonds");
 331     registerModule(manager, &gmx_helix, "helix",
 332                    "Calculate basic properties of alpha helices");
 333     registerModule(manager, &gmx_helixorient, "helixorient",
 334                    "Calculate local pitch/bending/rotation/orientation inside helices");
 335     registerModule(manager, &gmx_hydorder, "hydorder",
 336                    "Compute tetrahedrality parameters around a given atom");
 337     registerModule(manager, &gmx_lie, "lie",
 338                    "Estimate free energy from linear combinations");
 339     registerModule(manager, &gmx_mdmat, "mdmat",
 340                    "Calculate residue contact maps");
 341     registerModule(manager, &gmx_mindist, "mindist",
 342                    "Calculate the minimum distance between two groups");
 343     registerModule(manager, &gmx_morph, "morph",
 344                    "Interpolate linearly between conformations");
 345     registerModule(manager, &gmx_msd, "msd",
 346                    "Calculates mean square displacements");
 347     registerModule(manager, &gmx_nmeig, "nmeig",
 348                    "Diagonalize the Hessian for normal mode analysis");
 349     registerModule(manager, &gmx_nmens, "nmens",
 350                    "Generate an ensemble of structures from the normal modes");
 351     registerModule(manager, &gmx_nmtraj, "nmtraj",
 352                    "Generate a virtual oscillating trajectory from an eigenvector");
 353     registerModule(manager, &gmx_order, "order",
 354                    "Compute the order parameter per atom for carbon tails");
 355     registerModule(manager, &gmx_pme_error, "pme_error",
 356                    "Estimate the error of using PME with a given input file");
 357     registerModule(manager, &gmx_polystat, "polystat",
 358                    "Calculate static properties of polymers");
 359     registerModule(manager, &gmx_potential, "potential",
 360                    "Calculate the electrostatic potential across the box");
 361     registerModule(manager, &gmx_principal, "principal",
 362                    "Calculate principal axes of inertia for a group of atoms");
 363     registerModule(manager, &gmx_rama, "rama",
 364                    "Compute Ramachandran plots");
 365     registerModule(manager, &gmx_rms, "rms",
 366                    "Calculate RMSDs with a reference structure and RMSD matrices");
 367     registerModule(manager, &gmx_rmsdist, "rmsdist",
 368                    "Calculate atom pair distances averaged with power -2, -3 or -6");
 369     registerModule(manager, &gmx_rmsf, "rmsf",
 370                    "Calculate atomic fluctuations");
 371     registerModule(manager, &gmx_rotacf, "rotacf",
 372                    "Calculate the rotational correlation function for molecules");
 373     registerModule(manager, &gmx_rotmat, "rotmat",
 374                    "Plot the rotation matrix for fitting to a reference structure");
 375     registerModule(manager, &gmx_saltbr, "saltbr",
 376                    "Compute salt bridges");
 377     registerModule(manager, &gmx_sans, "sans",
 378                    "Compute small angle neutron scattering spectra");
 379     registerModule(manager, &gmx_saxs, "saxs",
 380                    "Compute small angle X-ray scattering spectra");
 381     registerModule(manager, &gmx_sham, "sham",
 382                    "Compute free energies or other histograms from histograms");
 383     registerModule(manager, &gmx_sigeps, "sigeps",
 384                    "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
 385     registerModule(manager, &gmx_sorient, "sorient",
 386                    "Analyze solvent orientation around solutes");
 387     registerModule(manager, &gmx_spatial, "spatial",
 388                    "Calculate the spatial distribution function");
 389     registerModule(manager, &gmx_spol, "spol",
 390                    "Analyze solvent dipole orientation and polarization around solutes");
 391     registerModule(manager, &gmx_tcaf, "tcaf",
 392                    "Calculate viscosities of liquids");
 393     registerModule(manager, &gmx_traj, "traj",
 394                    "Plot x, v, f, box, temperature and rotational energy from trajectories");
 395     registerModule(manager, &gmx_tune_pme, "tune_pme",
 396                    "Time mdrun as a function of PME ranks to optimize settings");
 397     registerModule(manager, &gmx_vanhove, "vanhove",
 398                    "Compute Van Hove displacement and correlation functions");
 399     registerModule(manager, &gmx_velacc, "velacc",
 400                    "Calculate velocity autocorrelation functions");
 401     registerModule(manager, &gmx_wham, "wham",
 402                    "Perform weighted histogram analysis after umbrella sampling");
 403     registerModule(manager, &gmx_wheel, "wheel",
 404                    "Plot helical wheels");
 405     registerModuleNoNice(manager, &gmx_view, "view",
 406                          "View a trajectory on an X-Windows terminal");
 407
 408     {
 409         gmx::CommandLineModuleGroup group =
 410             manager->addModuleGroup("Generating topologies and coordinates");
 411         group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
 412         group.addModule("x2top");
 413         group.addModule("solvate");
 414         group.addModule("insert-molecules");
 415         group.addModule("genconf");
 416         group.addModule("genion");
 417         group.addModule("genrestr");
 418         group.addModule("pdb2gmx");
 419     }
 420     {
 421         gmx::CommandLineModuleGroup group =
 422             manager->addModuleGroup("Running a simulation");
 423         group.addModule("grompp");
 424         group.addModule("mdrun");
 425         group.addModule("convert-tpr");
 426     }
 427     {
 428         gmx::CommandLineModuleGroup group =
 429             manager->addModuleGroup("Viewing trajectories");
 430         group.addModule("nmtraj");
 431         group.addModule("view");
 432     }
 433     {
 434         gmx::CommandLineModuleGroup group =
 435             manager->addModuleGroup("Processing energies");
 436         group.addModule("enemat");
 437         group.addModule("energy");
 438         group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
 439     }
 440     {
 441         gmx::CommandLineModuleGroup group =
 442             manager->addModuleGroup("Converting files");
 443         group.addModule("editconf");
 444         group.addModule("eneconv");
 445         group.addModule("sigeps");
 446         group.addModule("trjcat");
 447         group.addModule("trjconv");
 448         group.addModule("xpm2ps");
 449     }
 450     {
 451         gmx::CommandLineModuleGroup group =
 452             manager->addModuleGroup("Tools");
 453         group.addModule("analyze");
 454         group.addModule("dyndom");
 455         group.addModule("filter");
 456         group.addModule("lie");
 457         group.addModule("morph");
 458         group.addModule("pme_error");
 459         group.addModule("sham");
 460         group.addModule("spatial");
 461         group.addModule("traj");
 462         group.addModule("tune_pme");
 463         group.addModule("wham");
 464         group.addModule("check");
 465         group.addModule("dump");
 466         group.addModule("make_ndx");
 467         group.addModule("mk_angndx");
 468         group.addModule("trjorder");
 469         group.addModule("xpm2ps");
 470     }
 471     {
 472         gmx::CommandLineModuleGroup group =
 473             manager->addModuleGroup("Distances between structures");
 474         group.addModule("cluster");
 475         group.addModule("confrms");
 476         group.addModule("rms");
 477         group.addModule("rmsf");
 478     }
 479     {
 480         gmx::CommandLineModuleGroup group =
 481             manager->addModuleGroup("Distances in structures over time");
 482         group.addModule("mindist");
 483         group.addModule("mdmat");
 484         group.addModule("polystat");
 485         group.addModule("rmsdist");
 486     }
 487     {
 488         gmx::CommandLineModuleGroup group =
 489             manager->addModuleGroup("Mass distribution properties over time");
 490         group.addModule("gyrate");
 491         group.addModule("msd");
 492         group.addModule("polystat");
 493         group.addModule("rdf");
 494         group.addModule("rotacf");
 495         group.addModule("rotmat");
 496         group.addModule("sans");
 497         group.addModule("saxs");
 498         group.addModule("traj");
 499         group.addModule("vanhove");
 500     }
 501     {
 502         gmx::CommandLineModuleGroup group =
 503             manager->addModuleGroup("Analyzing bonded interactions");
 504         group.addModule("angle");
 505         group.addModule("mk_angndx");
 506     }
 507     {
 508         gmx::CommandLineModuleGroup group =
 509             manager->addModuleGroup("Structural properties");
 510         group.addModule("anadock");
 511         group.addModule("bundle");
 512         group.addModule("clustsize");
 513         group.addModule("disre");
 514         group.addModule("hbond");
 515         group.addModule("order");
 516         group.addModule("principal");
 517         group.addModule("rdf");
 518         group.addModule("saltbr");
 519         group.addModule("sorient");
 520         group.addModule("spol");
 521     }
 522     {
 523         gmx::CommandLineModuleGroup group =
 524             manager->addModuleGroup("Kinetic properties");
 525         group.addModule("bar");
 526         group.addModule("current");
 527         group.addModule("dos");
 528         group.addModule("dyecoupl");
 529         group.addModule("principal");
 530         group.addModule("tcaf");
 531         group.addModule("traj");
 532         group.addModule("vanhove");
 533         group.addModule("velacc");
 534     }
 535     {
 536         gmx::CommandLineModuleGroup group =
 537             manager->addModuleGroup("Electrostatic properties");
 538         group.addModule("current");
 539         group.addModule("dielectric");
 540         group.addModule("dipoles");
 541         group.addModule("potential");
 542         group.addModule("spol");
 543         group.addModule("genion");
 544     }
 545     {
 546         gmx::CommandLineModuleGroup group =
 547             manager->addModuleGroup("Protein-specific analysis");
 548         group.addModule("do_dssp");
 549         group.addModule("chi");
 550         group.addModule("helix");
 551         group.addModule("helixorient");
 552         group.addModule("rama");
 553         group.addModule("wheel");
 554     }
 555     {
 556         gmx::CommandLineModuleGroup group =
 557             manager->addModuleGroup("Interfaces");
 558         group.addModule("bundle");
 559         group.addModule("density");
 560         group.addModule("densmap");
 561         group.addModule("densorder");
 562         group.addModule("h2order");
 563         group.addModule("hydorder");
 564         group.addModule("order");
 565         group.addModule("potential");
 566     }
 567     {
 568         gmx::CommandLineModuleGroup group =
 569             manager->addModuleGroup("Covariance analysis");
 570         group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
 571         group.addModule("covar");
 572         group.addModule("make_edi");
 573     }
 574     {
 575         gmx::CommandLineModuleGroup group =
 576             manager->addModuleGroup("Normal modes");
 577         group.addModuleWithDescription("anaeig", "Analyze the normal modes");
 578         group.addModule("nmeig");
 579         group.addModule("nmtraj");
 580         group.addModule("nmens");
 581         group.addModule("grompp");
 582         group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");
 583     }
 584 }