2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
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/genconf.h"
49 #include "gromacs/gmxpreprocess/grompp.h"
50 #include "gromacs/gmxpreprocess/insert-molecules.h"
51 #include "gromacs/gmxpreprocess/pdb2gmx.h"
52 #include "gromacs/gmxpreprocess/protonate.h"
53 #include "gromacs/gmxpreprocess/solvate.h"
54 #include "gromacs/gmxpreprocess/x2top.h"
55 #include "gromacs/tools/check.h"
56 #include "gromacs/tools/convert_tpr.h"
57 #include "gromacs/tools/dump.h"
59 #include "mdrun/mdrun_main.h"
60 #include "view/view.h"
66 * Command line module that provides information about obsolescence.
68 * Prints a message directing the user to a wiki page describing replacement
71 class ObsoleteToolModule : public gmx::CommandLineModuleInterface
74 //! Creates an obsolete tool module for a tool with the given name.
75 explicit ObsoleteToolModule(const char *name)
80 virtual const char *name() const
84 virtual const char *shortDescription() const
89 virtual int run(int /*argc*/, char * /*argv*/[])
94 virtual void writeHelp(const gmx::CommandLineHelpContext & /*context*/) const
100 void printMessage() const
103 "This tool has been removed from Gromacs 5.0. Please see\n"
104 " http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0\n"
105 "for ideas how to perform the same tasks with the "
114 * Convenience function for creating and registering a module.
116 * \param[in] manager Module manager to which to register the module.
117 * \param[in] mainFunction Main function to wrap.
118 * \param[in] name Name for the new module.
119 * \param[in] shortDescription One-line description for the new module.
121 void registerModule(gmx::CommandLineModuleManager *manager,
122 gmx::CommandLineModuleManager::CMainFunction mainFunction,
123 const char *name, const char *shortDescription)
125 manager->addModuleCMain(name, shortDescription, mainFunction);
129 * Convenience function for registering a module for an obsolete tool.
131 * \param[in] manager Module manager to which to register the module.
132 * \param[in] name Name for the obsolete tool.
134 void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
137 gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
138 manager->addModule(move(module));
143 void registerLegacyModules(gmx::CommandLineModuleManager *manager)
145 // Modules from this directory (were in src/kernel/).
146 registerModule(manager, &gmx_check, "check",
147 "Check and compare files");
148 registerModule(manager, &gmx_dump, "dump",
149 "Make binary files human readable");
150 registerModule(manager, &gmx_grompp, "grompp",
151 "Make a run input file");
152 registerModule(manager, &gmx_pdb2gmx, "pdb2gmx",
153 "Convert coordinate files to topology and FF-compliant coordinate files");
154 registerModule(manager, &gmx_convert_tpr, "convert-tpr",
155 "Make a modifed run-input file");
156 registerObsoleteTool(manager, "tpbconv");
158 registerModule(manager, &gmx_protonate, "protonate",
159 "Protonate structures");
160 registerModule(manager, &gmx_x2top, "x2top",
161 "Generate a primitive topology from coordinates");
163 registerModule(manager, &gmx_mdrun, "mdrun",
164 "Perform a simulation, do a normal mode analysis or an energy minimization");
166 // Modules from gmx_ana.h.
167 registerModule(manager, &gmx_do_dssp, "do_dssp",
168 "Assign secondary structure and calculate solvent accessible surface area");
169 registerModule(manager, &gmx_editconf, "editconf",
170 "Convert and manipulates structure files");
171 registerModule(manager, &gmx_eneconv, "eneconv",
172 "Convert energy files");
173 registerModule(manager, &gmx_solvate, "solvate",
175 registerModule(manager, &gmx_insert_molecules, "insert-molecules",
176 "Insert molecules into existing vacancies");
177 registerObsoleteTool(manager, "genbox");
178 registerModule(manager, &gmx_genconf, "genconf",
179 "Multiply a conformation in 'random' orientations");
180 registerModule(manager, &gmx_genion, "genion",
181 "Generate monoatomic ions on energetically favorable positions");
182 registerModule(manager, &gmx_genpr, "genrestr",
183 "Generate position restraints or distance restraints for index groups");
184 registerModule(manager, &gmx_make_edi, "make_edi",
185 "Generate input files for essential dynamics sampling");
186 registerModule(manager, &gmx_make_ndx, "make_ndx",
188 registerModule(manager, &gmx_mk_angndx, "mk_angndx",
189 "Generate index files for 'gmx angle'");
190 registerModule(manager, &gmx_trjcat, "trjcat",
191 "Concatenate trajectory files");
192 registerModule(manager, &gmx_trjconv, "trjconv",
193 "Convert and manipulates trajectory files");
194 registerModule(manager, &gmx_trjorder, "trjorder",
195 "Order molecules according to their distance to a group");
196 registerModule(manager, &gmx_xpm2ps, "xpm2ps",
197 "Convert XPM (XPixelMap) matrices to postscript or XPM");
199 registerModule(manager, &gmx_anadock, "anadock",
200 "Cluster structures from Autodock runs");
201 registerModule(manager, &gmx_anaeig, "anaeig",
202 "Analyze eigenvectors/normal modes");
203 registerModule(manager, &gmx_analyze, "analyze",
204 "Analyze data sets");
205 registerModule(manager, &gmx_g_angle, "angle",
206 "Calculate distributions and correlations for angles and dihedrals");
207 registerModule(manager, &gmx_bar, "bar",
208 "Calculate free energy difference estimates through Bennett's acceptance ratio");
209 registerObsoleteTool(manager, "bond");
210 registerObsoleteTool(manager, "dist");
211 registerObsoleteTool(manager, "sas");
212 registerObsoleteTool(manager, "sgangle");
214 registerModule(manager, &gmx_bundle, "bundle",
215 "Analyze bundles of axes, e.g., helices");
216 registerModule(manager, &gmx_chi, "chi",
217 "Calculate everything you want to know about chi and other dihedrals");
218 registerModule(manager, &gmx_cluster, "cluster",
219 "Cluster structures");
220 registerModule(manager, &gmx_clustsize, "clustsize",
221 "Calculate size distributions of atomic clusters");
222 registerModule(manager, &gmx_confrms, "confrms",
223 "Fit two structures and calculates the RMSD");
224 registerModule(manager, &gmx_covar, "covar",
225 "Calculate and diagonalize the covariance matrix");
226 registerModule(manager, &gmx_current, "current",
227 "Calculate dielectric constants and current autocorrelation function");
228 registerModule(manager, &gmx_density, "density",
229 "Calculate the density of the system");
230 registerModule(manager, &gmx_densmap, "densmap",
231 "Calculate 2D planar or axial-radial density maps");
232 registerModule(manager, &gmx_densorder, "densorder",
233 "Calculate surface fluctuations");
234 registerModule(manager, &gmx_dielectric, "dielectric",
235 "Calculate frequency dependent dielectric constants");
236 registerModule(manager, &gmx_dipoles, "dipoles",
237 "Compute the total dipole plus fluctuations");
238 registerModule(manager, &gmx_disre, "disre",
239 "Analyze distance restraints");
240 registerModule(manager, &gmx_dos, "dos",
241 "Analyze density of states and properties based on that");
242 registerModule(manager, &gmx_dyecoupl, "dyecoupl",
243 "Extract dye dynamics from trajectories");
244 registerModule(manager, &gmx_dyndom, "dyndom",
245 "Interpolate and extrapolate structure rotations");
246 registerModule(manager, &gmx_enemat, "enemat",
247 "Extract an energy matrix from an energy file");
248 registerModule(manager, &gmx_energy, "energy",
249 "Writes energies to xvg files and display averages");
250 registerModule(manager, &gmx_filter, "filter",
251 "Frequency filter trajectories, useful for making smooth movies");
252 registerModule(manager, &gmx_gyrate, "gyrate",
253 "Calculate the radius of gyration");
254 registerModule(manager, &gmx_h2order, "h2order",
255 "Compute the orientation of water molecules");
256 registerModule(manager, &gmx_hbond, "hbond",
257 "Compute and analyze hydrogen bonds");
258 registerModule(manager, &gmx_helix, "helix",
259 "Calculate basic properties of alpha helices");
260 registerModule(manager, &gmx_helixorient, "helixorient",
261 "Calculate local pitch/bending/rotation/orientation inside helices");
262 registerModule(manager, &gmx_hydorder, "hydorder",
263 "Compute tetrahedrality parameters around a given atom");
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_saxs, "saxs",
310 "Compute small angle X-ray scattering spectra");
311 registerModule(manager, &gmx_sham, "sham",
312 "Compute free energies or other histograms from histograms");
313 registerModule(manager, &gmx_sigeps, "sigeps",
314 "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
315 registerModule(manager, &gmx_sorient, "sorient",
316 "Analyze solvent orientation around solutes");
317 registerModule(manager, &gmx_spatial, "spatial",
318 "Calculate the spatial distribution function");
319 registerModule(manager, &gmx_spol, "spol",
320 "Analyze solvent dipole orientation and polarization around solutes");
321 registerModule(manager, &gmx_tcaf, "tcaf",
322 "Calculate viscosities of liquids");
323 registerModule(manager, &gmx_traj, "traj",
324 "Plot x, v, f, box, temperature and rotational energy from trajectories");
325 registerModule(manager, &gmx_tune_pme, "tune_pme",
326 "Time mdrun as a function of PME ranks to optimize settings");
327 registerModule(manager, &gmx_vanhove, "vanhove",
328 "Compute Van Hove displacement and correlation functions");
329 registerModule(manager, &gmx_velacc, "velacc",
330 "Calculate velocity autocorrelation functions");
331 registerModule(manager, &gmx_wham, "wham",
332 "Perform weighted histogram analysis after umbrella sampling");
333 registerModule(manager, &gmx_wheel, "wheel",
334 "Plot helical wheels");
335 registerModule(manager, &gmx_view, "view",
336 "View a trajectory on an X-Windows terminal");
339 gmx::CommandLineModuleGroup group =
340 manager->addModuleGroup("Generating topologies and coordinates");
341 group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
342 group.addModule("protonate");
343 group.addModule("x2top");
344 group.addModule("solvate");
345 group.addModule("insert-molecules");
346 group.addModule("genconf");
347 group.addModule("genion");
348 group.addModule("genrestr");
349 group.addModule("pdb2gmx");
352 gmx::CommandLineModuleGroup group =
353 manager->addModuleGroup("Running a simulation");
354 group.addModule("grompp");
355 group.addModule("mdrun");
356 group.addModule("convert-tpr");
359 gmx::CommandLineModuleGroup group =
360 manager->addModuleGroup("Viewing trajectories");
361 group.addModule("nmtraj");
362 group.addModule("view");
365 gmx::CommandLineModuleGroup group =
366 manager->addModuleGroup("Processing energies");
367 group.addModule("enemat");
368 group.addModule("energy");
369 group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
372 gmx::CommandLineModuleGroup group =
373 manager->addModuleGroup("Converting files");
374 group.addModule("editconf");
375 group.addModule("eneconv");
376 group.addModule("sigeps");
377 group.addModule("trjcat");
378 group.addModule("trjconv");
379 group.addModule("xpm2ps");
382 gmx::CommandLineModuleGroup group =
383 manager->addModuleGroup("Tools");
384 group.addModule("analyze");
385 group.addModule("dyndom");
386 group.addModule("filter");
387 group.addModule("lie");
388 group.addModule("morph");
389 group.addModule("pme_error");
390 group.addModule("sham");
391 group.addModule("spatial");
392 group.addModule("traj");
393 group.addModule("tune_pme");
394 group.addModule("wham");
395 group.addModule("check");
396 group.addModule("dump");
397 group.addModule("make_ndx");
398 group.addModule("mk_angndx");
399 group.addModule("trjorder");
400 group.addModule("xpm2ps");
403 gmx::CommandLineModuleGroup group =
404 manager->addModuleGroup("Distances between structures");
405 group.addModule("cluster");
406 group.addModule("confrms");
407 group.addModule("rms");
408 group.addModule("rmsf");
411 gmx::CommandLineModuleGroup group =
412 manager->addModuleGroup("Distances in structures over time");
413 group.addModule("mindist");
414 group.addModule("mdmat");
415 group.addModule("polystat");
416 group.addModule("rmsdist");
419 gmx::CommandLineModuleGroup group =
420 manager->addModuleGroup("Mass distribution properties over time");
421 group.addModule("gyrate");
422 group.addModule("msd");
423 group.addModule("polystat");
424 group.addModule("rdf");
425 group.addModule("rotacf");
426 group.addModule("rotmat");
427 group.addModule("sans");
428 group.addModule("saxs");
429 group.addModule("traj");
430 group.addModule("vanhove");
433 gmx::CommandLineModuleGroup group =
434 manager->addModuleGroup("Analyzing bonded interactions");
435 group.addModule("angle");
436 group.addModule("mk_angndx");
439 gmx::CommandLineModuleGroup group =
440 manager->addModuleGroup("Structural properties");
441 group.addModule("anadock");
442 group.addModule("bundle");
443 group.addModule("clustsize");
444 group.addModule("disre");
445 group.addModule("hbond");
446 group.addModule("order");
447 group.addModule("principal");
448 group.addModule("rdf");
449 group.addModule("saltbr");
450 group.addModule("sorient");
451 group.addModule("spol");
454 gmx::CommandLineModuleGroup group =
455 manager->addModuleGroup("Kinetic properties");
456 group.addModule("bar");
457 group.addModule("current");
458 group.addModule("dos");
459 group.addModule("dyecoupl");
460 group.addModule("principal");
461 group.addModule("tcaf");
462 group.addModule("traj");
463 group.addModule("vanhove");
464 group.addModule("velacc");
467 gmx::CommandLineModuleGroup group =
468 manager->addModuleGroup("Electrostatic properties");
469 group.addModule("current");
470 group.addModule("dielectric");
471 group.addModule("dipoles");
472 group.addModule("potential");
473 group.addModule("spol");
474 group.addModule("genion");
477 gmx::CommandLineModuleGroup group =
478 manager->addModuleGroup("Protein-specific analysis");
479 group.addModule("do_dssp");
480 group.addModule("chi");
481 group.addModule("helix");
482 group.addModule("helixorient");
483 group.addModule("rama");
484 group.addModule("wheel");
487 gmx::CommandLineModuleGroup group =
488 manager->addModuleGroup("Interfaces");
489 group.addModule("bundle");
490 group.addModule("density");
491 group.addModule("densmap");
492 group.addModule("densorder");
493 group.addModule("h2order");
494 group.addModule("hydorder");
495 group.addModule("order");
496 group.addModule("potential");
499 gmx::CommandLineModuleGroup group =
500 manager->addModuleGroup("Covariance analysis");
501 group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
502 group.addModule("covar");
503 group.addModule("make_edi");
506 gmx::CommandLineModuleGroup group =
507 manager->addModuleGroup("Normal modes");
508 group.addModuleWithDescription("anaeig", "Analyze the normal modes");
509 group.addModule("nmeig");
510 group.addModule("nmtraj");
511 group.addModule("nmens");
512 group.addModule("grompp");
513 group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");