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36 * Registers command-line modules for pre-5.0 binaries.
38 * \author Teemu Murtola <teemu.murtola@gmail.com>
42 #include "legacymodules.h"
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/report_methods.h"
64 #include "mdrun/mdrun_main.h"
65 #include "view/view.h"
71 * Command line module that provides information about obsolescence.
73 * Prints a message directing the user to a wiki page describing replacement
76 class ObsoleteToolModule
: public gmx::ICommandLineModule
79 //! Creates an obsolete tool module for a tool with the given name.
80 explicit ObsoleteToolModule(const char *name
)
85 const char *name() const override
89 const char *shortDescription() const override
94 void init(gmx::CommandLineModuleSettings
* /*settings*/) override
97 int run(int /*argc*/, char * /*argv*/[]) override
102 void writeHelp(const gmx::CommandLineHelpContext
& /*context*/) const override
108 void printMessage() const
111 "This tool is no longer present in GROMACS. Please see\n"
112 " http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/user-guide/cmdline.html#command-changes\n"
113 "for ideas how to perform the same tasks with the "
120 //! Initializer for a module that defaults to nice level zero.
121 void initSettingsNoNice(gmx::CommandLineModuleSettings
*settings
)
123 settings
->setDefaultNiceLevel(0);
127 * Convenience function for creating and registering a module.
129 * \param[in] manager Module manager to which to register the module.
130 * \param[in] mainFunction Main function to wrap.
131 * \param[in] name Name for the new module.
132 * \param[in] shortDescription One-line description for the new module.
134 void registerModule(gmx::CommandLineModuleManager
*manager
,
135 gmx::CommandLineModuleManager::CMainFunction mainFunction
,
136 const char *name
, const char *shortDescription
)
138 manager
->addModuleCMain(name
, shortDescription
, mainFunction
);
142 * Convenience function for creating and registering a module that defaults to
145 * \param[in] manager Module manager to which to register the module.
146 * \param[in] mainFunction Main function to wrap.
147 * \param[in] name Name for the new module.
148 * \param[in] shortDescription One-line description for the new module.
150 void registerModuleNoNice(gmx::CommandLineModuleManager
*manager
,
151 gmx::CommandLineModuleManager::CMainFunction mainFunction
,
152 const char *name
, const char *shortDescription
)
154 manager
->addModuleCMainWithSettings(name
, shortDescription
, mainFunction
,
155 &initSettingsNoNice
);
159 * Convenience function for registering a module for an obsolete tool.
161 * \param[in] manager Module manager to which to register the module.
162 * \param[in] name Name for the obsolete tool.
164 void registerObsoleteTool(gmx::CommandLineModuleManager
*manager
,
167 gmx::CommandLineModulePointer
module(new ObsoleteToolModule(name
));
168 manager
->addModule(std::move(module
));
173 void registerLegacyModules(gmx::CommandLineModuleManager
*manager
)
175 // Modules from this directory (were in src/kernel/).
176 registerModule(manager
, &gmx_check
, "check",
177 "Check and compare files");
178 registerModule(manager
, &gmx_dump
, "dump",
179 "Make binary files human readable");
180 registerModule(manager
, &gmx_grompp
, "grompp",
181 "Make a run input file");
182 registerModule(manager
, &gmx_convert_tpr
, "convert-tpr",
183 "Make a modifed run-input file");
184 registerObsoleteTool(manager
, "tpbconv");
185 registerModule(manager
, &gmx_x2top
, "x2top",
186 "Generate a primitive topology from coordinates");
188 registerModuleNoNice(manager
, &gmx::gmx_mdrun
, "mdrun",
189 "Perform a simulation, do a normal mode analysis or an energy minimization");
191 gmx::ICommandLineOptionsModule::registerModuleFactory(
192 manager
, gmx::InsertMoleculesInfo::name(),
193 gmx::InsertMoleculesInfo::shortDescription(),
194 &gmx::InsertMoleculesInfo::create
);
196 gmx::ICommandLineOptionsModule::registerModuleFactory(
197 manager
, gmx::ReportMethodsInfo::name
,
198 gmx::ReportMethodsInfo::shortDescription
,
199 &gmx::ReportMethodsInfo::create
);
201 gmx::ICommandLineOptionsModule::registerModuleFactory(
202 manager
, gmx::pdb2gmxInfo::name
,
203 gmx::pdb2gmxInfo::shortDescription
,
204 &gmx::pdb2gmxInfo::create
);
206 // Modules from gmx_ana.h.
207 registerModule(manager
, &gmx_do_dssp
, "do_dssp",
208 "Assign secondary structure and calculate solvent accessible surface area");
209 registerModule(manager
, &gmx_editconf
, "editconf",
210 "Convert and manipulates structure files");
211 registerModule(manager
, &gmx_eneconv
, "eneconv",
212 "Convert energy files");
213 registerModule(manager
, &gmx_solvate
, "solvate",
215 registerObsoleteTool(manager
, "genbox");
216 registerModule(manager
, &gmx_genconf
, "genconf",
217 "Multiply a conformation in 'random' orientations");
218 registerModule(manager
, &gmx_genion
, "genion",
219 "Generate monoatomic ions on energetically favorable positions");
220 registerModule(manager
, &gmx_genrestr
, "genrestr",
221 "Generate position restraints or distance restraints for index groups");
222 registerModule(manager
, &gmx_make_edi
, "make_edi",
223 "Generate input files for essential dynamics sampling");
224 registerModule(manager
, &gmx_make_ndx
, "make_ndx",
226 registerModule(manager
, &gmx_mk_angndx
, "mk_angndx",
227 "Generate index files for 'gmx angle'");
228 registerModule(manager
, &gmx_trjcat
, "trjcat",
229 "Concatenate trajectory files");
230 registerModule(manager
, &gmx_trjconv
, "trjconv",
231 "Convert and manipulates trajectory files");
232 registerModule(manager
, &gmx_trjorder
, "trjorder",
233 "Order molecules according to their distance to a group");
234 registerModule(manager
, &gmx_xpm2ps
, "xpm2ps",
235 "Convert XPM (XPixelMap) matrices to postscript or XPM");
237 registerModule(manager
, &gmx_anaeig
, "anaeig",
238 "Analyze eigenvectors/normal modes");
239 registerModule(manager
, &gmx_analyze
, "analyze",
240 "Analyze data sets");
241 registerModule(manager
, &gmx_g_angle
, "angle",
242 "Calculate distributions and correlations for angles and dihedrals");
243 registerModule(manager
, &gmx_awh
, "awh",
244 "Extract data from an accelerated weight histogram (AWH) run");
245 registerModule(manager
, &gmx_bar
, "bar",
246 "Calculate free energy difference estimates through Bennett's acceptance ratio");
247 registerObsoleteTool(manager
, "bond");
248 registerObsoleteTool(manager
, "dist");
249 registerObsoleteTool(manager
, "sas");
250 registerObsoleteTool(manager
, "sgangle");
252 registerModule(manager
, &gmx_bundle
, "bundle",
253 "Analyze bundles of axes, e.g., helices");
254 registerModule(manager
, &gmx_chi
, "chi",
255 "Calculate everything you want to know about chi and other dihedrals");
256 registerModule(manager
, &gmx_cluster
, "cluster",
257 "Cluster structures");
258 registerModule(manager
, &gmx_clustsize
, "clustsize",
259 "Calculate size distributions of atomic clusters");
260 registerModule(manager
, &gmx_confrms
, "confrms",
261 "Fit two structures and calculates the RMSD");
262 registerModule(manager
, &gmx_covar
, "covar",
263 "Calculate and diagonalize the covariance matrix");
264 registerModule(manager
, &gmx_current
, "current",
265 "Calculate dielectric constants and current autocorrelation function");
266 registerModule(manager
, &gmx_density
, "density",
267 "Calculate the density of the system");
268 registerModule(manager
, &gmx_densmap
, "densmap",
269 "Calculate 2D planar or axial-radial density maps");
270 registerModule(manager
, &gmx_densorder
, "densorder",
271 "Calculate surface fluctuations");
272 registerModule(manager
, &gmx_dielectric
, "dielectric",
273 "Calculate frequency dependent dielectric constants");
274 registerModule(manager
, &gmx_dipoles
, "dipoles",
275 "Compute the total dipole plus fluctuations");
276 registerModule(manager
, &gmx_disre
, "disre",
277 "Analyze distance restraints");
278 registerModule(manager
, &gmx_dos
, "dos",
279 "Analyze density of states and properties based on that");
280 registerModule(manager
, &gmx_dyecoupl
, "dyecoupl",
281 "Extract dye dynamics from trajectories");
282 registerModule(manager
, &gmx_enemat
, "enemat",
283 "Extract an energy matrix from an energy file");
284 registerModule(manager
, &gmx_energy
, "energy",
285 "Writes energies to xvg files and display averages");
286 registerModule(manager
, &gmx_filter
, "filter",
287 "Frequency filter trajectories, useful for making smooth movies");
288 registerModule(manager
, &gmx_gyrate
, "gyrate",
289 "Calculate the radius of gyration");
290 registerModule(manager
, &gmx_h2order
, "h2order",
291 "Compute the orientation of water molecules");
292 registerModule(manager
, &gmx_hbond
, "hbond",
293 "Compute and analyze hydrogen bonds");
294 registerModule(manager
, &gmx_helix
, "helix",
295 "Calculate basic properties of alpha helices");
296 registerModule(manager
, &gmx_helixorient
, "helixorient",
297 "Calculate local pitch/bending/rotation/orientation inside helices");
298 registerModule(manager
, &gmx_hydorder
, "hydorder",
299 "Compute tetrahedrality parameters around a given atom");
300 registerModule(manager
, &gmx_lie
, "lie",
301 "Estimate free energy from linear combinations");
302 registerModule(manager
, &gmx_mdmat
, "mdmat",
303 "Calculate residue contact maps");
304 registerModule(manager
, &gmx_mindist
, "mindist",
305 "Calculate the minimum distance between two groups");
306 registerModule(manager
, &gmx_msd
, "msd",
307 "Calculates mean square displacements");
308 registerModule(manager
, &gmx_nmeig
, "nmeig",
309 "Diagonalize the Hessian for normal mode analysis");
310 registerModule(manager
, &gmx_nmens
, "nmens",
311 "Generate an ensemble of structures from the normal modes");
312 registerModule(manager
, &gmx_nmr
, "nmr",
313 "Analyze nuclear magnetic resonance properties from an energy file");
314 registerModule(manager
, &gmx_nmtraj
, "nmtraj",
315 "Generate a virtual oscillating trajectory from an eigenvector");
316 registerModule(manager
, &gmx_order
, "order",
317 "Compute the order parameter per atom for carbon tails");
318 registerModule(manager
, &gmx_pme_error
, "pme_error",
319 "Estimate the error of using PME with a given input file");
320 registerModule(manager
, &gmx_polystat
, "polystat",
321 "Calculate static properties of polymers");
322 registerModule(manager
, &gmx_potential
, "potential",
323 "Calculate the electrostatic potential across the box");
324 registerModule(manager
, &gmx_principal
, "principal",
325 "Calculate principal axes of inertia for a group of atoms");
326 registerModule(manager
, &gmx_rama
, "rama",
327 "Compute Ramachandran plots");
328 registerModule(manager
, &gmx_rms
, "rms",
329 "Calculate RMSDs with a reference structure and RMSD matrices");
330 registerModule(manager
, &gmx_rmsdist
, "rmsdist",
331 "Calculate atom pair distances averaged with power -2, -3 or -6");
332 registerModule(manager
, &gmx_rmsf
, "rmsf",
333 "Calculate atomic fluctuations");
334 registerModule(manager
, &gmx_rotacf
, "rotacf",
335 "Calculate the rotational correlation function for molecules");
336 registerModule(manager
, &gmx_rotmat
, "rotmat",
337 "Plot the rotation matrix for fitting to a reference structure");
338 registerModule(manager
, &gmx_saltbr
, "saltbr",
339 "Compute salt bridges");
340 registerModule(manager
, &gmx_sans
, "sans",
341 "Compute small angle neutron scattering spectra");
342 registerModule(manager
, &gmx_saxs
, "saxs",
343 "Compute small angle X-ray scattering spectra");
344 registerModule(manager
, &gmx_sham
, "sham",
345 "Compute free energies or other histograms from histograms");
346 registerModule(manager
, &gmx_sigeps
, "sigeps",
347 "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
348 registerModule(manager
, &gmx_sorient
, "sorient",
349 "Analyze solvent orientation around solutes");
350 registerModule(manager
, &gmx_spatial
, "spatial",
351 "Calculate the spatial distribution function");
352 registerModule(manager
, &gmx_spol
, "spol",
353 "Analyze solvent dipole orientation and polarization around solutes");
354 registerModule(manager
, &gmx_tcaf
, "tcaf",
355 "Calculate viscosities of liquids");
356 registerModule(manager
, &gmx_traj
, "traj",
357 "Plot x, v, f, box, temperature and rotational energy from trajectories");
358 registerModule(manager
, &gmx_tune_pme
, "tune_pme",
359 "Time mdrun as a function of PME ranks to optimize settings");
360 registerModule(manager
, &gmx_vanhove
, "vanhove",
361 "Compute Van Hove displacement and correlation functions");
362 registerModule(manager
, &gmx_velacc
, "velacc",
363 "Calculate velocity autocorrelation functions");
364 registerModule(manager
, &gmx_wham
, "wham",
365 "Perform weighted histogram analysis after umbrella sampling");
366 registerModule(manager
, &gmx_wheel
, "wheel",
367 "Plot helical wheels");
368 registerModuleNoNice(manager
, &gmx_view
, "view",
369 "View a trajectory on an X-Windows terminal");
372 gmx::CommandLineModuleGroup group
=
373 manager
->addModuleGroup("Generating topologies and coordinates");
374 group
.addModuleWithDescription("editconf", "Edit the box and write subgroups");
375 group
.addModule("x2top");
376 group
.addModule("solvate");
377 group
.addModule("insert-molecules");
378 group
.addModule("genconf");
379 group
.addModule("genion");
380 group
.addModule("genrestr");
381 group
.addModule("pdb2gmx");
384 gmx::CommandLineModuleGroup group
=
385 manager
->addModuleGroup("Running a simulation");
386 group
.addModule("grompp");
387 group
.addModule("mdrun");
388 group
.addModule("convert-tpr");
391 gmx::CommandLineModuleGroup group
=
392 manager
->addModuleGroup("Viewing trajectories");
393 group
.addModule("nmtraj");
394 group
.addModule("view");
397 gmx::CommandLineModuleGroup group
=
398 manager
->addModuleGroup("Processing energies");
399 group
.addModule("enemat");
400 group
.addModule("energy");
401 group
.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
404 gmx::CommandLineModuleGroup group
=
405 manager
->addModuleGroup("Converting files");
406 group
.addModule("editconf");
407 group
.addModule("eneconv");
408 group
.addModule("sigeps");
409 group
.addModule("trjcat");
410 group
.addModule("trjconv");
411 group
.addModule("xpm2ps");
414 gmx::CommandLineModuleGroup group
=
415 manager
->addModuleGroup("Tools");
416 group
.addModule("analyze");
417 group
.addModule("awh");
418 group
.addModule("filter");
419 group
.addModule("lie");
420 group
.addModule("pme_error");
421 group
.addModule("sham");
422 group
.addModule("spatial");
423 group
.addModule("traj");
424 group
.addModule("tune_pme");
425 group
.addModule("wham");
426 group
.addModule("check");
427 group
.addModule("dump");
428 group
.addModule("make_ndx");
429 group
.addModule("mk_angndx");
430 group
.addModule("trjorder");
431 group
.addModule("xpm2ps");
432 group
.addModule("report-methods");
435 gmx::CommandLineModuleGroup group
=
436 manager
->addModuleGroup("Distances between structures");
437 group
.addModule("cluster");
438 group
.addModule("confrms");
439 group
.addModule("rms");
440 group
.addModule("rmsf");
443 gmx::CommandLineModuleGroup group
=
444 manager
->addModuleGroup("Distances in structures over time");
445 group
.addModule("mindist");
446 group
.addModule("mdmat");
447 group
.addModule("polystat");
448 group
.addModule("rmsdist");
451 gmx::CommandLineModuleGroup group
=
452 manager
->addModuleGroup("Mass distribution properties over time");
453 group
.addModule("gyrate");
454 group
.addModule("msd");
455 group
.addModule("polystat");
456 group
.addModule("rdf");
457 group
.addModule("rotacf");
458 group
.addModule("rotmat");
459 group
.addModule("sans");
460 group
.addModule("saxs");
461 group
.addModule("traj");
462 group
.addModule("vanhove");
465 gmx::CommandLineModuleGroup group
=
466 manager
->addModuleGroup("Analyzing bonded interactions");
467 group
.addModule("angle");
468 group
.addModule("mk_angndx");
471 gmx::CommandLineModuleGroup group
=
472 manager
->addModuleGroup("Structural properties");
473 group
.addModule("bundle");
474 group
.addModule("clustsize");
475 group
.addModule("disre");
476 group
.addModule("hbond");
477 group
.addModule("order");
478 group
.addModule("principal");
479 group
.addModule("rdf");
480 group
.addModule("saltbr");
481 group
.addModule("sorient");
482 group
.addModule("spol");
485 gmx::CommandLineModuleGroup group
=
486 manager
->addModuleGroup("Kinetic properties");
487 group
.addModule("bar");
488 group
.addModule("current");
489 group
.addModule("dos");
490 group
.addModule("dyecoupl");
491 group
.addModule("principal");
492 group
.addModule("tcaf");
493 group
.addModule("traj");
494 group
.addModule("vanhove");
495 group
.addModule("velacc");
498 gmx::CommandLineModuleGroup group
=
499 manager
->addModuleGroup("Electrostatic properties");
500 group
.addModule("current");
501 group
.addModule("dielectric");
502 group
.addModule("dipoles");
503 group
.addModule("potential");
504 group
.addModule("spol");
505 group
.addModule("genion");
508 gmx::CommandLineModuleGroup group
=
509 manager
->addModuleGroup("Protein-specific analysis");
510 group
.addModule("do_dssp");
511 group
.addModule("chi");
512 group
.addModule("helix");
513 group
.addModule("helixorient");
514 group
.addModule("rama");
515 group
.addModule("wheel");
518 gmx::CommandLineModuleGroup group
=
519 manager
->addModuleGroup("Interfaces");
520 group
.addModule("bundle");
521 group
.addModule("density");
522 group
.addModule("densmap");
523 group
.addModule("densorder");
524 group
.addModule("h2order");
525 group
.addModule("hydorder");
526 group
.addModule("order");
527 group
.addModule("potential");
530 gmx::CommandLineModuleGroup group
=
531 manager
->addModuleGroup("Covariance analysis");
532 group
.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
533 group
.addModule("covar");
534 group
.addModule("make_edi");
537 gmx::CommandLineModuleGroup group
=
538 manager
->addModuleGroup("Normal modes");
539 group
.addModuleWithDescription("anaeig", "Analyze the normal modes");
540 group
.addModule("nmeig");
541 group
.addModule("nmtraj");
542 group
.addModule("nmens");
543 group
.addModule("grompp");
544 group
.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");