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