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