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36 * Registers command-line modules for pre-5.0 binaries.
38 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 #include "legacymodules.h"
44 #include "gromacs/commandline/cmdlinemodule.h"
45 #include "gromacs/commandline/cmdlinemodulemanager.h"
47 #include "gromacs/gmxana/gmx_ana.h"
49 #include "../view/view.h"
50 #include "../mdrun/mdrun_main.h"
51 #include "gromacs/tools/check.h"
52 #include "gromacs/tools/dump.h"
53 #include "gromacs/tools/convert_tpr.h"
55 #include "legacycmainfunctions.h"
61 * Command line module that provides information about obsolescence.
63 * Prints a message directing the user to a wiki page describing replacement
66 class ObsoleteToolModule : public gmx::CommandLineModuleInterface
69 //! Creates an obsolete tool module for a tool with the given name.
70 explicit ObsoleteToolModule(const char *name)
75 virtual const char *name() const
79 virtual const char *shortDescription() const
84 virtual int run(int /*argc*/, char * /*argv*/[])
89 virtual void writeHelp(const gmx::CommandLineHelpContext & /*context*/) const
95 void printMessage() const
98 "This tool has been removed from Gromacs 5.0. Please see\n"
99 " http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0\n"
100 "for ideas how to perform the same tasks with the "
109 * Convenience function for creating and registering a module.
111 * \param[in] manager Module manager to which to register the module.
112 * \param[in] mainFunction Main function to wrap.
113 * \param[in] name Name for the new module.
114 * \param[in] shortDescription One-line description for the new module.
116 void registerModule(gmx::CommandLineModuleManager *manager,
117 gmx::CommandLineModuleManager::CMainFunction mainFunction,
118 const char *name, const char *shortDescription)
120 manager->addModuleCMain(name, shortDescription, mainFunction);
124 * Convenience function for registering a module for an obsolete tool.
126 * \param[in] manager Module manager to which to register the module.
127 * \param[in] name Name for the obsolete tool.
129 void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
132 gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
133 manager->addModule(move(module));
138 void registerLegacyModules(gmx::CommandLineModuleManager *manager)
140 // Modules from this directory (were in src/kernel/).
141 registerModule(manager, &gmx_check, "check",
142 "Check and compare files");
143 registerModule(manager, &gmx_dump, "dump",
144 "Make binary files human readable");
145 registerModule(manager, &gmx_grompp, "grompp",
146 "Make a run input file");
147 registerModule(manager, &gmx_pdb2gmx, "pdb2gmx",
148 "Convert coordinate files to topology and FF-compliant coordinate files");
149 registerModule(manager, &gmx_convert_tpr, "convert-tpr",
150 "Make a modifed run-input file");
152 registerModule(manager, &gmx_protonate, "protonate",
153 "Protonate structures");
154 registerModule(manager, &gmx_x2top, "x2top",
155 "Generate a primitive topology from coordinates");
157 registerModule(manager, &gmx_mdrun, "mdrun",
158 "Perform a simulation, do a normal mode analysis or an energy minimization");
160 // Modules from gmx_ana.h.
161 registerModule(manager, &gmx_do_dssp, "do_dssp",
162 "Assign secondary structure and calculate solvent accessible surface area");
163 registerModule(manager, &gmx_editconf, "editconf",
164 "Convert and manipulates structure files");
165 registerModule(manager, &gmx_eneconv, "eneconv",
166 "Convert energy files");
167 registerModule(manager, &gmx_genbox, "genbox",
169 registerModule(manager, &gmx_genconf, "genconf",
170 "Multiply a conformation in 'random' orientations");
171 registerModule(manager, &gmx_genion, "genion",
172 "Generate monoatomic ions on energetically favorable positions");
173 registerModule(manager, &gmx_genpr, "genrestr",
174 "Generate position restraints or distance restraints for index groups");
175 registerModule(manager, &gmx_make_edi, "make_edi",
176 "Generate input files for essential dynamics sampling");
177 registerModule(manager, &gmx_make_ndx, "make_ndx",
179 registerModule(manager, &gmx_mk_angndx, "mk_angndx",
180 "Generate index files for 'gmx angle'");
181 registerModule(manager, &gmx_trjcat, "trjcat",
182 "Concatenate trajectory files");
183 registerModule(manager, &gmx_trjconv, "trjconv",
184 "Convert and manipulates trajectory files");
185 registerModule(manager, &gmx_trjorder, "trjorder",
186 "Order molecules according to their distance to a group");
187 registerModule(manager, &gmx_xpm2ps, "xpm2ps",
188 "Convert XPM (XPixelMap) matrices to postscript or XPM");
190 registerModule(manager, &gmx_anadock, "anadock",
191 "Cluster structures from Autodock runs");
192 registerModule(manager, &gmx_anaeig, "anaeig",
193 "Analyze eigenvectors/normal modes");
194 registerModule(manager, &gmx_analyze, "analyze",
195 "Analyze data sets");
196 registerModule(manager, &gmx_g_angle, "angle",
197 "Calculate distributions and correlations for angles and dihedrals");
198 registerModule(manager, &gmx_bar, "bar",
199 "Calculate free energy difference estimates through Bennett's acceptance ratio");
200 registerObsoleteTool(manager, "bond");
201 registerObsoleteTool(manager, "dist");
202 registerObsoleteTool(manager, "sgangle");
204 registerModule(manager, &gmx_bundle, "bundle",
205 "Analyze bundles of axes, e.g., helices");
206 registerModule(manager, &gmx_chi, "chi",
207 "Calculate everything you want to know about chi and other dihedrals");
208 registerModule(manager, &gmx_cluster, "cluster",
209 "Cluster structures");
210 registerModule(manager, &gmx_clustsize, "clustsize",
211 "Calculate size distributions of atomic clusters");
212 registerModule(manager, &gmx_confrms, "confrms",
213 "Fit two structures and calculates the RMSD");
214 registerModule(manager, &gmx_covar, "covar",
215 "Calculate and diagonalize the covariance matrix");
216 registerModule(manager, &gmx_current, "current",
217 "Calculate dielectric constants and current autocorrelation function");
218 registerModule(manager, &gmx_density, "density",
219 "Calculate the density of the system");
220 registerModule(manager, &gmx_densmap, "densmap",
221 "Calculate 2D planar or axial-radial density maps");
222 registerModule(manager, &gmx_densorder, "densorder",
223 "Calculate surface fluctuations");
224 registerModule(manager, &gmx_dielectric, "dielectric",
225 "Calculate frequency dependent dielectric constants");
226 registerModule(manager, &gmx_dipoles, "dipoles",
227 "Compute the total dipole plus fluctuations");
228 registerModule(manager, &gmx_disre, "disre",
229 "Analyze distance restraints");
230 registerModule(manager, &gmx_dos, "dos",
231 "Analyze density of states and properties based on that");
232 registerModule(manager, &gmx_dyecoupl, "dyecoupl",
233 "Extract dye dynamics from trajectories");
234 registerModule(manager, &gmx_dyndom, "dyndom",
235 "Interpolate and extrapolate structure rotations");
236 registerModule(manager, &gmx_enemat, "enemat",
237 "Extract an energy matrix from an energy file");
238 registerModule(manager, &gmx_energy, "energy",
239 "Writes energies to xvg files and display averages");
240 registerModule(manager, &gmx_filter, "filter",
241 "Frequency filter trajectories, useful for making smooth movies");
242 registerModule(manager, &gmx_gyrate, "gyrate",
243 "Calculate the radius of gyration");
244 registerModule(manager, &gmx_h2order, "h2order",
245 "Compute the orientation of water molecules");
246 registerModule(manager, &gmx_hbond, "hbond",
247 "Compute and analyze hydrogen bonds");
248 registerModule(manager, &gmx_helix, "helix",
249 "Calculate basic properties of alpha helices");
250 registerModule(manager, &gmx_helixorient, "helixorient",
251 "Calculate local pitch/bending/rotation/orientation inside helices");
252 registerModule(manager, &gmx_hydorder, "hydorder",
253 "Compute tetrahedrality parameters around a given atom");
254 registerModule(manager, &gmx_kinetics, "kinetics",
255 "Analyze kinetic constants from properties based on the Eyring model");
256 registerModule(manager, &gmx_lie, "lie",
257 "Estimate free energy from linear combinations");
258 registerModule(manager, &gmx_mdmat, "mdmat",
259 "Calculate residue contact maps");
260 registerModule(manager, &gmx_mindist, "mindist",
261 "Calculate the minimum distance between two groups");
262 registerModule(manager, &gmx_morph, "morph",
263 "Interpolate linearly between conformations");
264 registerModule(manager, &gmx_msd, "msd",
265 "Calculates mean square displacements");
266 registerModule(manager, &gmx_nmeig, "nmeig",
267 "Diagonalize the Hessian for normal mode analysis");
268 registerModule(manager, &gmx_nmens, "nmens",
269 "Generate an ensemble of structures from the normal modes");
270 registerModule(manager, &gmx_nmtraj, "nmtraj",
271 "Generate a virtual oscillating trajectory from an eigenvector");
272 registerModule(manager, &gmx_options, "options", NULL);
273 registerModule(manager, &gmx_order, "order",
274 "Compute the order parameter per atom for carbon tails");
275 registerModule(manager, &gmx_pme_error, "pme_error",
276 "Estimate the error of using PME with a given input file");
277 registerModule(manager, &gmx_polystat, "polystat",
278 "Calculate static properties of polymers");
279 registerModule(manager, &gmx_potential, "potential",
280 "Calculate the electrostatic potential across the box");
281 registerModule(manager, &gmx_principal, "principal",
282 "Calculate principal axes of inertia for a group of atoms");
283 registerModule(manager, &gmx_rama, "rama",
284 "Compute Ramachandran plots");
285 registerModule(manager, &gmx_rdf, "rdf",
286 "Calculate radial distribution functions");
287 registerModule(manager, &gmx_rms, "rms",
288 "Calculate RMSDs with a reference structure and RMSD matrices");
289 registerModule(manager, &gmx_rmsdist, "rmsdist",
290 "Calculate atom pair distances averaged with power -2, -3 or -6");
291 registerModule(manager, &gmx_rmsf, "rmsf",
292 "Calculate atomic fluctuations");
293 registerModule(manager, &gmx_rotacf, "rotacf",
294 "Calculate the rotational correlation function for molecules");
295 registerModule(manager, &gmx_rotmat, "rotmat",
296 "Plot the rotation matrix for fitting to a reference structure");
297 registerModule(manager, &gmx_saltbr, "saltbr",
298 "Compute salt bridges");
299 registerModule(manager, &gmx_sans, "sans",
300 "Compute small angle neutron scattering spectra");
301 registerModule(manager, &gmx_sas, "sas",
302 "Compute solvent accessible surface area");
303 registerModule(manager, &gmx_saxs, "saxs",
304 "Compute small angle X-ray scattering spectra");
305 registerModule(manager, &gmx_sham, "sham",
306 "Compute free energies or other histograms from histograms");
307 registerModule(manager, &gmx_sigeps, "sigeps",
308 "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
309 registerModule(manager, &gmx_sorient, "sorient",
310 "Analyze solvent orientation around solutes");
311 registerModule(manager, &gmx_spatial, "spatial",
312 "Calculate the spatial distribution function");
313 registerModule(manager, &gmx_spol, "spol",
314 "Analyze solvent dipole orientation and polarization around solutes");
315 registerModule(manager, &gmx_tcaf, "tcaf",
316 "Calculate viscosities of liquids");
317 registerModule(manager, &gmx_traj, "traj",
318 "Plot x, v, f, box, temperature and rotational energy from trajectories");
319 registerModule(manager, &gmx_tune_pme, "tune_pme",
320 "Time mdrun as a function of PME nodes to optimize settings");
321 registerModule(manager, &gmx_vanhove, "vanhove",
322 "Compute Van Hove displacement and correlation functions");
323 registerModule(manager, &gmx_velacc, "velacc",
324 "Calculate velocity autocorrelation functions");
325 registerModule(manager, &gmx_wham, "wham",
326 "Perform weighted histogram analysis after umbrella sampling");
327 registerModule(manager, &gmx_wheel, "wheel",
328 "Plot helical wheels");
329 registerModule(manager, &gmx_view, "view",
330 "View a trajectory on an X-Windows terminal");
333 gmx::CommandLineModuleGroup group =
334 manager->addModuleGroup("Generating topologies and coordinates");
335 group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
336 group.addModule("protonate");
337 group.addModule("x2top");
338 group.addModule("genbox");
339 group.addModule("genconf");
340 group.addModule("genion");
341 group.addModule("genrestr");
342 group.addModule("pdb2gmx");
345 gmx::CommandLineModuleGroup group =
346 manager->addModuleGroup("Running a simulation");
347 group.addModule("grompp");
348 group.addModule("mdrun");
349 group.addModule("convert-tpr");
352 gmx::CommandLineModuleGroup group =
353 manager->addModuleGroup("Viewing trajectories");
354 group.addModule("nmtraj");
355 group.addModule("view");
358 gmx::CommandLineModuleGroup group =
359 manager->addModuleGroup("Processing energies");
360 group.addModule("enemat");
361 group.addModule("energy");
362 group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
365 gmx::CommandLineModuleGroup group =
366 manager->addModuleGroup("Converting files");
367 group.addModule("editconf");
368 group.addModule("eneconv");
369 group.addModule("sigeps");
370 group.addModule("trjcat");
371 group.addModule("trjconv");
372 group.addModule("xpm2ps");
375 gmx::CommandLineModuleGroup group =
376 manager->addModuleGroup("Tools");
377 group.addModule("analyze");
378 group.addModule("dyndom");
379 group.addModule("filter");
380 group.addModule("lie");
381 group.addModule("morph");
382 group.addModule("pme_error");
383 group.addModule("sham");
384 group.addModule("spatial");
385 group.addModule("traj");
386 group.addModule("tune_pme");
387 group.addModule("wham");
388 group.addModule("check");
389 group.addModule("dump");
390 group.addModule("make_ndx");
391 group.addModule("mk_angndx");
392 group.addModule("trjorder");
393 group.addModule("xpm2ps");
396 gmx::CommandLineModuleGroup group =
397 manager->addModuleGroup("Distances between structures");
398 group.addModule("cluster");
399 group.addModule("confrms");
400 group.addModule("rms");
401 group.addModule("rmsf");
404 gmx::CommandLineModuleGroup group =
405 manager->addModuleGroup("Distances in structures over time");
406 group.addModule("mindist");
407 group.addModule("mdmat");
408 group.addModule("polystat");
409 group.addModule("rmsdist");
412 gmx::CommandLineModuleGroup group =
413 manager->addModuleGroup("Mass distribution properties over time");
414 group.addModule("gyrate");
415 group.addModule("msd");
416 group.addModule("polystat");
417 group.addModule("rdf");
418 group.addModule("rotacf");
419 group.addModule("rotmat");
420 group.addModule("sans");
421 group.addModule("saxs");
422 group.addModule("traj");
423 group.addModule("vanhove");
426 gmx::CommandLineModuleGroup group =
427 manager->addModuleGroup("Analyzing bonded interactions");
428 group.addModule("angle");
429 group.addModule("mk_angndx");
432 gmx::CommandLineModuleGroup group =
433 manager->addModuleGroup("Structural properties");
434 group.addModule("anadock");
435 group.addModule("bundle");
436 group.addModule("clustsize");
437 group.addModule("disre");
438 group.addModule("hbond");
439 group.addModule("order");
440 group.addModule("principal");
441 group.addModule("rdf");
442 group.addModule("saltbr");
443 group.addModule("sas");
444 group.addModule("sorient");
445 group.addModule("spol");
448 gmx::CommandLineModuleGroup group =
449 manager->addModuleGroup("Kinetic properties");
450 group.addModule("bar");
451 group.addModule("current");
452 group.addModule("dos");
453 group.addModule("dyecoupl");
454 group.addModule("kinetics");
455 group.addModule("principal");
456 group.addModule("tcaf");
457 group.addModule("traj");
458 group.addModule("vanhove");
459 group.addModule("velacc");
462 gmx::CommandLineModuleGroup group =
463 manager->addModuleGroup("Electrostatic properties");
464 group.addModule("current");
465 group.addModule("dielectric");
466 group.addModule("dipoles");
467 group.addModule("potential");
468 group.addModule("spol");
469 group.addModule("genion");
472 gmx::CommandLineModuleGroup group =
473 manager->addModuleGroup("Protein-specific analysis");
474 group.addModule("do_dssp");
475 group.addModule("chi");
476 group.addModule("helix");
477 group.addModule("helixorient");
478 group.addModule("rama");
479 group.addModule("wheel");
482 gmx::CommandLineModuleGroup group =
483 manager->addModuleGroup("Interfaces");
484 group.addModule("bundle");
485 group.addModule("density");
486 group.addModule("densmap");
487 group.addModule("densorder");
488 group.addModule("h2order");
489 group.addModule("hydorder");
490 group.addModule("order");
491 group.addModule("potential");
494 gmx::CommandLineModuleGroup group =
495 manager->addModuleGroup("Covariance analysis");
496 group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
497 group.addModule("covar");
498 group.addModule("make_edi");
501 gmx::CommandLineModuleGroup group =
502 manager->addModuleGroup("Normal modes");
503 group.addModuleWithDescription("anaeig", "Analyze the normal modes");
504 group.addModule("nmeig");
505 group.addModule("nmtraj");
506 group.addModule("nmens");
507 group.addModule("grompp");
508 group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");