*/
class ObsoleteToolModule : public gmx::ICommandLineModule
{
- public:
- //! Creates an obsolete tool module for a tool with the given name.
- explicit ObsoleteToolModule(const char *name)
- : name_(name)
- {
- }
+public:
+ //! Creates an obsolete tool module for a tool with the given name.
+ explicit ObsoleteToolModule(const char* name) : name_(name) {}
- const char *name() const override
- {
- return name_;
- }
- const char *shortDescription() const override
- {
- return nullptr;
- }
+ const char* name() const override { return name_; }
+ const char* shortDescription() const override { return nullptr; }
- void init(gmx::CommandLineModuleSettings * /*settings*/) override
- {
- }
- int run(int /*argc*/, char * /*argv*/[]) override
- {
- printMessage();
- return 0;
- }
- void writeHelp(const gmx::CommandLineHelpContext & /*context*/) const override
- {
- printMessage();
- }
+ void init(gmx::CommandLineModuleSettings* /*settings*/) override {}
+ int run(int /*argc*/, char* /*argv*/[]) override
+ {
+ printMessage();
+ return 0;
+ }
+ void writeHelp(const gmx::CommandLineHelpContext& /*context*/) const override
+ {
+ printMessage();
+ }
- private:
- void printMessage() const
- {
- std::fprintf(stderr,
- "This tool is no longer present in GROMACS. Please see\n"
- " http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/user-guide/cmdline.html#command-changes\n"
- "for ideas how to perform the same tasks with the "
- "new tools.\n");
- }
+private:
+ void printMessage() const
+ {
+ std::fprintf(stderr,
+ "This tool is no longer present in GROMACS. Please see\n"
+ " "
+ "http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/"
+ "user-guide/cmdline.html#command-changes\n"
+ "for ideas how to perform the same tasks with the "
+ "new tools.\n");
+ }
- const char *name_;
+ const char* name_;
};
//! Initializer for a module that defaults to nice level zero.
-void initSettingsNoNice(gmx::CommandLineModuleSettings *settings)
+void initSettingsNoNice(gmx::CommandLineModuleSettings* settings)
{
settings->setDefaultNiceLevel(0);
}
* \param[in] name Name for the new module.
* \param[in] shortDescription One-line description for the new module.
*/
-void registerModule(gmx::CommandLineModuleManager *manager,
- gmx::CommandLineModuleManager::CMainFunction mainFunction,
- const char *name, const char *shortDescription)
+void registerModule(gmx::CommandLineModuleManager* manager,
+ gmx::CommandLineModuleManager::CMainFunction mainFunction,
+ const char* name,
+ const char* shortDescription)
{
manager->addModuleCMain(name, shortDescription, mainFunction);
}
* \param[in] name Name for the new module.
* \param[in] shortDescription One-line description for the new module.
*/
-void registerModuleNoNice(gmx::CommandLineModuleManager *manager,
- gmx::CommandLineModuleManager::CMainFunction mainFunction,
- const char *name, const char *shortDescription)
+void registerModuleNoNice(gmx::CommandLineModuleManager* manager,
+ gmx::CommandLineModuleManager::CMainFunction mainFunction,
+ const char* name,
+ const char* shortDescription)
{
- manager->addModuleCMainWithSettings(name, shortDescription, mainFunction,
- &initSettingsNoNice);
+ manager->addModuleCMainWithSettings(name, shortDescription, mainFunction, &initSettingsNoNice);
}
/*! \brief
* \param[in] manager Module manager to which to register the module.
* \param[in] name Name for the obsolete tool.
*/
-void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
- const char *name)
+void registerObsoleteTool(gmx::CommandLineModuleManager* manager, const char* name)
{
gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
manager->addModule(std::move(module));
} // namespace
-void registerLegacyModules(gmx::CommandLineModuleManager *manager)
+void registerLegacyModules(gmx::CommandLineModuleManager* manager)
{
- registerModule(manager, &gmx_check, "check",
- "Check and compare files");
+ registerModule(manager, &gmx_check, "check", "Check and compare files");
gmx::ICommandLineOptionsModule::registerModuleFactory(
- manager, gmx::DumpInfo::name,
- gmx::DumpInfo::shortDescription,
- &gmx::DumpInfo::create);
- registerModule(manager, &gmx_grompp, "grompp",
- "Make a run input file");
- registerModule(manager, &gmx_convert_tpr, "convert-tpr",
- "Make a modifed run-input file");
+ manager, gmx::DumpInfo::name, gmx::DumpInfo::shortDescription, &gmx::DumpInfo::create);
+ registerModule(manager, &gmx_grompp, "grompp", "Make a run input file");
+ registerModule(manager, &gmx_convert_tpr, "convert-tpr", "Make a modifed run-input file");
registerObsoleteTool(manager, "tpbconv");
- registerModule(manager, &gmx_x2top, "x2top",
- "Generate a primitive topology from coordinates");
+ registerModule(manager, &gmx_x2top, "x2top", "Generate a primitive topology from coordinates");
- registerModuleNoNice(manager, &gmx::gmx_mdrun, "mdrun",
- "Perform a simulation, do a normal mode analysis or an energy minimization");
+ registerModuleNoNice(
+ manager, &gmx::gmx_mdrun, "mdrun",
+ "Perform a simulation, do a normal mode analysis or an energy minimization");
gmx::ICommandLineOptionsModule::registerModuleFactory(
manager, gmx::NonbondedBenchmarkInfo::name,
- gmx::NonbondedBenchmarkInfo::shortDescription,
- &gmx::NonbondedBenchmarkInfo::create);
+ gmx::NonbondedBenchmarkInfo::shortDescription, &gmx::NonbondedBenchmarkInfo::create);
- gmx::ICommandLineOptionsModule::registerModuleFactory(
- manager, gmx::InsertMoleculesInfo::name(),
- gmx::InsertMoleculesInfo::shortDescription(),
- &gmx::InsertMoleculesInfo::create);
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::InsertMoleculesInfo::name(),
+ gmx::InsertMoleculesInfo::shortDescription(),
+ &gmx::InsertMoleculesInfo::create);
- gmx::ICommandLineOptionsModule::registerModuleFactory(
- manager, gmx::ReportMethodsInfo::name,
- gmx::ReportMethodsInfo::shortDescription,
- &gmx::ReportMethodsInfo::create);
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::ReportMethodsInfo::name,
+ gmx::ReportMethodsInfo::shortDescription,
+ &gmx::ReportMethodsInfo::create);
- gmx::ICommandLineOptionsModule::registerModuleFactory(
- manager, gmx::pdb2gmxInfo::name,
- gmx::pdb2gmxInfo::shortDescription,
- &gmx::pdb2gmxInfo::create);
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::pdb2gmxInfo::name,
+ gmx::pdb2gmxInfo::shortDescription,
+ &gmx::pdb2gmxInfo::create);
// Modules from gmx_ana.h.
registerModule(manager, &gmx_do_dssp, "do_dssp",
"Assign secondary structure and calculate solvent accessible surface area");
- registerModule(manager, &gmx_editconf, "editconf",
- "Convert and manipulates structure files");
- registerModule(manager, &gmx_eneconv, "eneconv",
- "Convert energy files");
- registerModule(manager, &gmx_solvate, "solvate",
- "Solvate a system");
+ registerModule(manager, &gmx_editconf, "editconf", "Convert and manipulates structure files");
+ registerModule(manager, &gmx_eneconv, "eneconv", "Convert energy files");
+ registerModule(manager, &gmx_solvate, "solvate", "Solvate a system");
registerObsoleteTool(manager, "genbox");
registerModule(manager, &gmx_genconf, "genconf",
"Multiply a conformation in 'random' orientations");
"Generate position restraints or distance restraints for index groups");
registerModule(manager, &gmx_make_edi, "make_edi",
"Generate input files for essential dynamics sampling");
- registerModule(manager, &gmx_make_ndx, "make_ndx",
- "Make index files");
- registerModule(manager, &gmx_mk_angndx, "mk_angndx",
- "Generate index files for 'gmx angle'");
- registerModule(manager, &gmx_trjcat, "trjcat",
- "Concatenate trajectory files");
- registerModule(manager, &gmx_trjconv, "trjconv",
- "Convert and manipulates trajectory files");
+ registerModule(manager, &gmx_make_ndx, "make_ndx", "Make index files");
+ registerModule(manager, &gmx_mk_angndx, "mk_angndx", "Generate index files for 'gmx angle'");
+ registerModule(manager, &gmx_trjcat, "trjcat", "Concatenate trajectory files");
+ registerModule(manager, &gmx_trjconv, "trjconv", "Convert and manipulates trajectory files");
registerModule(manager, &gmx_trjorder, "trjorder",
"Order molecules according to their distance to a group");
registerModule(manager, &gmx_xpm2ps, "xpm2ps",
"Convert XPM (XPixelMap) matrices to postscript or XPM");
- registerModule(manager, &gmx_anaeig, "anaeig",
- "Analyze eigenvectors/normal modes");
- registerModule(manager, &gmx_analyze, "analyze",
- "Analyze data sets");
+ registerModule(manager, &gmx_anaeig, "anaeig", "Analyze eigenvectors/normal modes");
+ registerModule(manager, &gmx_analyze, "analyze", "Analyze data sets");
registerModule(manager, &gmx_g_angle, "angle",
"Calculate distributions and correlations for angles and dihedrals");
registerModule(manager, &gmx_awh, "awh",
registerObsoleteTool(manager, "sas");
registerObsoleteTool(manager, "sgangle");
- registerModule(manager, &gmx_bundle, "bundle",
- "Analyze bundles of axes, e.g., helices");
+ registerModule(manager, &gmx_bundle, "bundle", "Analyze bundles of axes, e.g., helices");
registerModule(manager, &gmx_chi, "chi",
"Calculate everything you want to know about chi and other dihedrals");
- registerModule(manager, &gmx_cluster, "cluster",
- "Cluster structures");
+ registerModule(manager, &gmx_cluster, "cluster", "Cluster structures");
registerModule(manager, &gmx_clustsize, "clustsize",
"Calculate size distributions of atomic clusters");
- registerModule(manager, &gmx_confrms, "confrms",
- "Fit two structures and calculates the RMSD");
- registerModule(manager, &gmx_covar, "covar",
- "Calculate and diagonalize the covariance matrix");
+ registerModule(manager, &gmx_confrms, "confrms", "Fit two structures and calculates the RMSD");
+ registerModule(manager, &gmx_covar, "covar", "Calculate and diagonalize the covariance matrix");
registerModule(manager, &gmx_current, "current",
"Calculate dielectric constants and current autocorrelation function");
- registerModule(manager, &gmx_density, "density",
- "Calculate the density of the system");
+ registerModule(manager, &gmx_density, "density", "Calculate the density of the system");
registerModule(manager, &gmx_densmap, "densmap",
"Calculate 2D planar or axial-radial density maps");
- registerModule(manager, &gmx_densorder, "densorder",
- "Calculate surface fluctuations");
+ registerModule(manager, &gmx_densorder, "densorder", "Calculate surface fluctuations");
registerModule(manager, &gmx_dielectric, "dielectric",
"Calculate frequency dependent dielectric constants");
- registerModule(manager, &gmx_dipoles, "dipoles",
- "Compute the total dipole plus fluctuations");
- registerModule(manager, &gmx_disre, "disre",
- "Analyze distance restraints");
+ registerModule(manager, &gmx_dipoles, "dipoles", "Compute the total dipole plus fluctuations");
+ registerModule(manager, &gmx_disre, "disre", "Analyze distance restraints");
registerModule(manager, &gmx_dos, "dos",
"Analyze density of states and properties based on that");
- registerModule(manager, &gmx_dyecoupl, "dyecoupl",
- "Extract dye dynamics from trajectories");
- registerModule(manager, &gmx_enemat, "enemat",
- "Extract an energy matrix from an energy file");
+ registerModule(manager, &gmx_dyecoupl, "dyecoupl", "Extract dye dynamics from trajectories");
+ registerModule(manager, &gmx_enemat, "enemat", "Extract an energy matrix from an energy file");
registerModule(manager, &gmx_energy, "energy",
"Writes energies to xvg files and display averages");
registerModule(manager, &gmx_filter, "filter",
"Frequency filter trajectories, useful for making smooth movies");
- registerModule(manager, &gmx_gyrate, "gyrate",
- "Calculate the radius of gyration");
- registerModule(manager, &gmx_h2order, "h2order",
- "Compute the orientation of water molecules");
- registerModule(manager, &gmx_hbond, "hbond",
- "Compute and analyze hydrogen bonds");
- registerModule(manager, &gmx_helix, "helix",
- "Calculate basic properties of alpha helices");
+ registerModule(manager, &gmx_gyrate, "gyrate", "Calculate the radius of gyration");
+ registerModule(manager, &gmx_h2order, "h2order", "Compute the orientation of water molecules");
+ registerModule(manager, &gmx_hbond, "hbond", "Compute and analyze hydrogen bonds");
+ registerModule(manager, &gmx_helix, "helix", "Calculate basic properties of alpha helices");
registerModule(manager, &gmx_helixorient, "helixorient",
"Calculate local pitch/bending/rotation/orientation inside helices");
registerModule(manager, &gmx_hydorder, "hydorder",
"Compute tetrahedrality parameters around a given atom");
- registerModule(manager, &gmx_lie, "lie",
- "Estimate free energy from linear combinations");
- registerModule(manager, &gmx_mdmat, "mdmat",
- "Calculate residue contact maps");
+ registerModule(manager, &gmx_lie, "lie", "Estimate free energy from linear combinations");
+ registerModule(manager, &gmx_mdmat, "mdmat", "Calculate residue contact maps");
registerModule(manager, &gmx_mindist, "mindist",
"Calculate the minimum distance between two groups");
- registerModule(manager, &gmx_msd, "msd",
- "Calculates mean square displacements");
- registerModule(manager, &gmx_nmeig, "nmeig",
- "Diagonalize the Hessian for normal mode analysis");
+ registerModule(manager, &gmx_msd, "msd", "Calculates mean square displacements");
+ registerModule(manager, &gmx_nmeig, "nmeig", "Diagonalize the Hessian for normal mode analysis");
registerModule(manager, &gmx_nmens, "nmens",
"Generate an ensemble of structures from the normal modes");
registerModule(manager, &gmx_nmr, "nmr",
"Compute the order parameter per atom for carbon tails");
registerModule(manager, &gmx_pme_error, "pme_error",
"Estimate the error of using PME with a given input file");
- registerModule(manager, &gmx_polystat, "polystat",
- "Calculate static properties of polymers");
+ registerModule(manager, &gmx_polystat, "polystat", "Calculate static properties of polymers");
registerModule(manager, &gmx_potential, "potential",
"Calculate the electrostatic potential across the box");
registerModule(manager, &gmx_principal, "principal",
"Calculate principal axes of inertia for a group of atoms");
- registerModule(manager, &gmx_rama, "rama",
- "Compute Ramachandran plots");
+ registerModule(manager, &gmx_rama, "rama", "Compute Ramachandran plots");
registerModule(manager, &gmx_rms, "rms",
"Calculate RMSDs with a reference structure and RMSD matrices");
registerModule(manager, &gmx_rmsdist, "rmsdist",
"Calculate atom pair distances averaged with power -2, -3 or -6");
- registerModule(manager, &gmx_rmsf, "rmsf",
- "Calculate atomic fluctuations");
+ registerModule(manager, &gmx_rmsf, "rmsf", "Calculate atomic fluctuations");
registerModule(manager, &gmx_rotacf, "rotacf",
"Calculate the rotational correlation function for molecules");
registerModule(manager, &gmx_rotmat, "rotmat",
"Plot the rotation matrix for fitting to a reference structure");
- registerModule(manager, &gmx_saltbr, "saltbr",
- "Compute salt bridges");
- registerModule(manager, &gmx_sans, "sans",
- "Compute small angle neutron scattering spectra");
- registerModule(manager, &gmx_saxs, "saxs",
- "Compute small angle X-ray scattering spectra");
+ registerModule(manager, &gmx_saltbr, "saltbr", "Compute salt bridges");
+ registerModule(manager, &gmx_sans, "sans", "Compute small angle neutron scattering spectra");
+ registerModule(manager, &gmx_saxs, "saxs", "Compute small angle X-ray scattering spectra");
registerModule(manager, &gmx_sham, "sham",
"Compute free energies or other histograms from histograms");
registerModule(manager, &gmx_sigeps, "sigeps",
"Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
- registerModule(manager, &gmx_sorient, "sorient",
- "Analyze solvent orientation around solutes");
- registerModule(manager, &gmx_spatial, "spatial",
- "Calculate the spatial distribution function");
+ registerModule(manager, &gmx_sorient, "sorient", "Analyze solvent orientation around solutes");
+ registerModule(manager, &gmx_spatial, "spatial", "Calculate the spatial distribution function");
registerModule(manager, &gmx_spol, "spol",
"Analyze solvent dipole orientation and polarization around solutes");
- registerModule(manager, &gmx_tcaf, "tcaf",
- "Calculate viscosities of liquids");
+ registerModule(manager, &gmx_tcaf, "tcaf", "Calculate viscosities of liquids");
registerModule(manager, &gmx_traj, "traj",
"Plot x, v, f, box, temperature and rotational energy from trajectories");
registerModule(manager, &gmx_tune_pme, "tune_pme",
"Time mdrun as a function of PME ranks to optimize settings");
registerModule(manager, &gmx_vanhove, "vanhove",
"Compute Van Hove displacement and correlation functions");
- registerModule(manager, &gmx_velacc, "velacc",
- "Calculate velocity autocorrelation functions");
+ registerModule(manager, &gmx_velacc, "velacc", "Calculate velocity autocorrelation functions");
registerModule(manager, &gmx_wham, "wham",
"Perform weighted histogram analysis after umbrella sampling");
- registerModule(manager, &gmx_wheel, "wheel",
- "Plot helical wheels");
- registerModuleNoNice(manager, &gmx_view, "view",
- "View a trajectory on an X-Windows terminal");
+ registerModule(manager, &gmx_wheel, "wheel", "Plot helical wheels");
+ registerModuleNoNice(manager, &gmx_view, "view", "View a trajectory on an X-Windows terminal");
{
gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Generating topologies and coordinates");
+ manager->addModuleGroup("Generating topologies and coordinates");
group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
group.addModule("x2top");
group.addModule("solvate");
group.addModule("pdb2gmx");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Running a simulation");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Running a simulation");
group.addModule("grompp");
group.addModule("mdrun");
group.addModule("convert-tpr");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Viewing trajectories");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Viewing trajectories");
group.addModule("nmtraj");
group.addModule("view");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Processing energies");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Processing energies");
group.addModule("enemat");
group.addModule("energy");
- group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
+ group.addModuleWithDescription("mdrun",
+ "(Re)calculate energies for trajectory frames with -rerun");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Converting files");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Converting files");
group.addModule("editconf");
group.addModule("eneconv");
group.addModule("sigeps");
group.addModule("xpm2ps");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Tools");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Tools");
group.addModule("analyze");
group.addModule("awh");
group.addModule("filter");
group.addModule("report-methods");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Distances between structures");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Distances between structures");
group.addModule("cluster");
group.addModule("confrms");
group.addModule("rms");
}
{
gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Distances in structures over time");
+ manager->addModuleGroup("Distances in structures over time");
group.addModule("mindist");
group.addModule("mdmat");
group.addModule("polystat");
}
{
gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Mass distribution properties over time");
+ manager->addModuleGroup("Mass distribution properties over time");
group.addModule("gyrate");
group.addModule("msd");
group.addModule("polystat");
}
{
gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Analyzing bonded interactions");
+ manager->addModuleGroup("Analyzing bonded interactions");
group.addModule("angle");
group.addModule("mk_angndx");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Structural properties");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Structural properties");
group.addModule("bundle");
group.addModule("clustsize");
group.addModule("disre");
group.addModule("spol");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Kinetic properties");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Kinetic properties");
group.addModule("bar");
group.addModule("current");
group.addModule("dos");
group.addModule("velacc");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Electrostatic properties");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Electrostatic properties");
group.addModule("current");
group.addModule("dielectric");
group.addModule("dipoles");
group.addModule("genion");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Protein-specific analysis");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Protein-specific analysis");
group.addModule("do_dssp");
group.addModule("chi");
group.addModule("helix");
group.addModule("wheel");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Interfaces");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Interfaces");
group.addModule("bundle");
group.addModule("density");
group.addModule("densmap");
group.addModule("potential");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Covariance analysis");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Covariance analysis");
group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
group.addModule("covar");
group.addModule("make_edi");
}
{
- gmx::CommandLineModuleGroup group =
- manager->addModuleGroup("Normal modes");
+ gmx::CommandLineModuleGroup group = manager->addModuleGroup("Normal modes");
group.addModuleWithDescription("anaeig", "Analyze the normal modes");
group.addModule("nmeig");
group.addModule("nmtraj");
group.addModule("nmens");
group.addModule("grompp");
- group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");
+ group.addModuleWithDescription("mdrun",
+ "Find a potential energy minimum and calculate the Hessian");
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff