if (context.outputFormat() != gmx::eHelpOutputFormat_Console)
{
GMX_THROW(gmx::NotImplementedError(
- "Command-line help is not implemented for this output format"));
+ "Command-line help is not implemented for this output format"));
}
char *argv[2];
// TODO: The constness should not be cast away.
void registerLegacyModules(gmx::CommandLineModuleManager *manager)
{
LegacyCmdLineWrapper::registerModule(manager, &gmx_do_dssp, "do_dssp",
- "Assign secondary structure and calculate solvent accessible surface area");
+ "Assign secondary structure and calculate solvent accessible surface area");
LegacyCmdLineWrapper::registerModule(manager, &gmx_editconf, "editconf",
- "Convert and manipulates structure files");
+ "Convert and manipulates structure files");
LegacyCmdLineWrapper::registerModule(manager, &gmx_eneconv, "eneconv",
- "Convert energy files");
+ "Convert energy files");
LegacyCmdLineWrapper::registerModule(manager, &gmx_genbox, "genbox",
- "Solvate a system");
+ "Solvate a system");
LegacyCmdLineWrapper::registerModule(manager, &gmx_genconf, "genconf",
- "Multiply a conformation in 'random' orientations");
+ "Multiply a conformation in 'random' orientations");
LegacyCmdLineWrapper::registerModule(manager, &gmx_genion, "genion",
- "Generate monoatomic ions on energetically favorable positions");
+ "Generate monoatomic ions on energetically favorable positions");
LegacyCmdLineWrapper::registerModule(manager, &gmx_genpr, "genrestr",
- "Generate position restraints or distance restraints for index groups");
+ "Generate position restraints or distance restraints for index groups");
LegacyCmdLineWrapper::registerModule(manager, &gmx_make_edi, "make_edi",
- "Generate input files for essential dynamics sampling");
+ "Generate input files for essential dynamics sampling");
LegacyCmdLineWrapper::registerModule(manager, &gmx_make_ndx, "make_ndx",
- "Make index files");
+ "Make index files");
LegacyCmdLineWrapper::registerModule(manager, &gmx_mk_angndx, "mk_angndx",
- "Generate index files for 'gmx angle'");
+ "Generate index files for 'gmx angle'");
LegacyCmdLineWrapper::registerModule(manager, &gmx_trjcat, "trjcat",
- "Concatenate trajectory files");
+ "Concatenate trajectory files");
LegacyCmdLineWrapper::registerModule(manager, &gmx_trjconv, "trjconv",
- "Convert and manipulates trajectory files");
+ "Convert and manipulates trajectory files");
LegacyCmdLineWrapper::registerModule(manager, &gmx_trjorder, "trjorder",
- "Order molecules according to their distance to a group");
+ "Order molecules according to their distance to a group");
LegacyCmdLineWrapper::registerModule(manager, &gmx_xpm2ps, "xpm2ps",
- "Convert XPM (XPixelMap) matrices to postscript or XPM");
+ "Convert XPM (XPixelMap) matrices to postscript or XPM");
// TODO: Include remaining binaries from src/tools/.
// These are commented out below, and have some issues to consider how to
// best handle them.
LegacyCmdLineWrapper::registerModule(manager, &gmx_anadock, "anadock",
- "Cluster structures from Autodock runs");
+ "Cluster structures from Autodock runs");
LegacyCmdLineWrapper::registerModule(manager, &gmx_anaeig, "anaeig",
- "Analyze eigenvectors/normal modes");
+ "Analyze eigenvectors/normal modes");
LegacyCmdLineWrapper::registerModule(manager, &gmx_analyze, "analyze",
- "Analyze data sets");
+ "Analyze data sets");
LegacyCmdLineWrapper::registerModule(manager, &gmx_g_angle, "angle",
- "Calculate distributions and correlations for angles and dihedrals");
+ "Calculate distributions and correlations for angles and dihedrals");
LegacyCmdLineWrapper::registerModule(manager, &gmx_bar, "bar",
- "Calculate free energy difference estimates through Bennett's acceptance ratio");
+ "Calculate free energy difference estimates through Bennett's acceptance ratio");
LegacyCmdLineWrapper::registerModule(manager, &gmx_bond, "bond",
- "Calculate distances between atoms and bond length distributions");
+ "Calculate distances between atoms and bond length distributions");
LegacyCmdLineWrapper::registerModule(manager, &gmx_bundle, "bundle",
- "Analyze bundles of axes, e.g., helices");
+ "Analyze bundles of axes, e.g., helices");
LegacyCmdLineWrapper::registerModule(manager, &gmx_chi, "chi",
- "Calculate everything you want to know about chi and other dihedrals");
+ "Calculate everything you want to know about chi and other dihedrals");
LegacyCmdLineWrapper::registerModule(manager, &gmx_cluster, "cluster",
- "Cluster structures");
+ "Cluster structures");
LegacyCmdLineWrapper::registerModule(manager, &gmx_clustsize, "clustsize",
- "Calculate size distributions of atomic clusters");
+ "Calculate size distributions of atomic clusters");
LegacyCmdLineWrapper::registerModule(manager, &gmx_confrms, "confrms",
- "Fit two structures and calculates the RMSD");
+ "Fit two structures and calculates the RMSD");
LegacyCmdLineWrapper::registerModule(manager, &gmx_covar, "covar",
- "Calculate and diagonalize the covariance matrix");
+ "Calculate and diagonalize the covariance matrix");
LegacyCmdLineWrapper::registerModule(manager, &gmx_current, "current",
- "Calculate dielectric constants and charge autocorrelation function");
+ "Calculate dielectric constants and charge autocorrelation function");
LegacyCmdLineWrapper::registerModule(manager, &gmx_density, "density",
- "Calculate the density of the system");
+ "Calculate the density of the system");
LegacyCmdLineWrapper::registerModule(manager, &gmx_densmap, "densmap",
- "Calculate 2D planar or axial-radial density maps");
+ "Calculate 2D planar or axial-radial density maps");
LegacyCmdLineWrapper::registerModule(manager, &gmx_densorder, "densorder",
- "Calculate surface fluctuations");
+ "Calculate surface fluctuations");
LegacyCmdLineWrapper::registerModule(manager, &gmx_dielectric, "dielectric",
- "Calculate frequency dependent dielectric constants");
+ "Calculate frequency dependent dielectric constants");
LegacyCmdLineWrapper::registerModule(manager, &gmx_dipoles, "dipoles",
- "Compute the total dipole plus fluctuations");
+ "Compute the total dipole plus fluctuations");
LegacyCmdLineWrapper::registerModule(manager, &gmx_disre, "disre",
- "Analyze distance restraints");
+ "Analyze distance restraints");
LegacyCmdLineWrapper::registerModule(manager, &gmx_dist, "dist",
- "Calculate distances between centers of mass of two groups");
+ "Calculate distances between centers of mass of two groups");
LegacyCmdLineWrapper::registerModule(manager, &gmx_dos, "dos",
- "Analyze density of states and properties based on that");
+ "Analyze density of states and properties based on that");
LegacyCmdLineWrapper::registerModule(manager, &gmx_dyecoupl, "dyecoupl",
- "Extract dye dynamics from trajectories");
+ "Extract dye dynamics from trajectories");
LegacyCmdLineWrapper::registerModule(manager, &gmx_dyndom, "dyndom",
- "Interpolate and extrapolate structure rotations");
+ "Interpolate and extrapolate structure rotations");
LegacyCmdLineWrapper::registerModule(manager, &gmx_enemat, "enemat",
- "Extract an energy matrix from an energy file");
+ "Extract an energy matrix from an energy file");
LegacyCmdLineWrapper::registerModule(manager, &gmx_energy, "energy",
- "Writes energies to xvg files and display averages");
+ "Writes energies to xvg files and display averages");
LegacyCmdLineWrapper::registerModule(manager, &gmx_filter, "filter",
- "Frequency filter trajectories, useful for making smooth movies");
+ "Frequency filter trajectories, useful for making smooth movies");
LegacyCmdLineWrapper::registerModule(manager, &gmx_gyrate, "gyrate",
- "Calculate the radius of gyration");
+ "Calculate the radius of gyration");
LegacyCmdLineWrapper::registerModule(manager, &gmx_h2order, "h2order",
- "Compute the orientation of water molecules");
+ "Compute the orientation of water molecules");
LegacyCmdLineWrapper::registerModule(manager, &gmx_hbond, "hbond",
- "Compute and analyze hydrogen bonds");
+ "Compute and analyze hydrogen bonds");
LegacyCmdLineWrapper::registerModule(manager, &gmx_helix, "helix",
- "Calculate basic properties of alpha helices");
+ "Calculate basic properties of alpha helices");
LegacyCmdLineWrapper::registerModule(manager, &gmx_helixorient, "helixorient",
- "Calculate local pitch/bending/rotation/orientation inside helices");
+ "Calculate local pitch/bending/rotation/orientation inside helices");
LegacyCmdLineWrapper::registerModule(manager, &gmx_hydorder, "hydorder",
- "Compute tetrahedrality parameters around a given atom");
+ "Compute tetrahedrality parameters around a given atom");
LegacyCmdLineWrapper::registerModule(manager, &gmx_kinetics, "kinetics",
- "Analyze kinetic constants from properties based on the Eyring model");
+ "Analyze kinetic constants from properties based on the Eyring model");
LegacyCmdLineWrapper::registerModule(manager, &gmx_lie, "lie",
- "Estimate free energy from linear combinations");
+ "Estimate free energy from linear combinations");
LegacyCmdLineWrapper::registerModule(manager, &gmx_mdmat, "mdmat",
- "Calculate residue contact maps");
+ "Calculate residue contact maps");
LegacyCmdLineWrapper::registerModule(manager, &gmx_mindist, "mindist",
- "Calculate the minimum distance between two groups");
+ "Calculate the minimum distance between two groups");
LegacyCmdLineWrapper::registerModule(manager, &gmx_morph, "morph",
- "Interpolate linearly between conformations");
+ "Interpolate linearly between conformations");
LegacyCmdLineWrapper::registerModule(manager, &gmx_msd, "msd",
- "Calculates mean square displacements");
+ "Calculates mean square displacements");
LegacyCmdLineWrapper::registerModule(manager, &gmx_nmeig, "nmeig",
- "Diagonalize the Hessian for normal mode analysis");
+ "Diagonalize the Hessian for normal mode analysis");
LegacyCmdLineWrapper::registerModule(manager, &gmx_nmens, "nmens",
- "Generate an ensemble of structures from the normal modes");
+ "Generate an ensemble of structures from the normal modes");
LegacyCmdLineWrapper::registerModule(manager, &gmx_nmtraj, "nmtraj",
- "Generate a virtual oscillating trajectory from an eigenvector");
+ "Generate a virtual oscillating trajectory from an eigenvector");
LegacyCmdLineWrapper::registerModule(manager, &gmx_options, "options",
- NULL);
+ NULL);
LegacyCmdLineWrapper::registerModule(manager, &gmx_order, "order",
- "Compute the order parameter per atom for carbon tails");
+ "Compute the order parameter per atom for carbon tails");
//LegacyCmdLineWrapper::registerModule(manager, &gmx_pme_error, "pme_error",
// "Estimate the error of using PME with a given input file");
LegacyCmdLineWrapper::registerModule(manager, &gmx_polystat, "polystat",
- "Calculate static properties of polymers");
+ "Calculate static properties of polymers");
LegacyCmdLineWrapper::registerModule(manager, &gmx_potential, "potential",
- "Calculate the electrostatic potential across the box");
+ "Calculate the electrostatic potential across the box");
LegacyCmdLineWrapper::registerModule(manager, &gmx_principal, "principal",
- "Calculate principal axes of inertia for a group of atoms");
+ "Calculate principal axes of inertia for a group of atoms");
LegacyCmdLineWrapper::registerModule(manager, &gmx_rama, "rama",
- "Compute Ramachandran plots");
+ "Compute Ramachandran plots");
LegacyCmdLineWrapper::registerModule(manager, &gmx_rdf, "rdf",
- "Calculate radial distribution functions");
+ "Calculate radial distribution functions");
LegacyCmdLineWrapper::registerModule(manager, &gmx_rms, "rms",
- "Calculate RMSDs with a reference structure and RMSD matrices");
+ "Calculate RMSDs with a reference structure and RMSD matrices");
LegacyCmdLineWrapper::registerModule(manager, &gmx_rmsdist, "rmsdist",
- "Calculate atom pair distances averaged with power -2, -3 or -6");
+ "Calculate atom pair distances averaged with power -2, -3 or -6");
LegacyCmdLineWrapper::registerModule(manager, &gmx_rmsf, "rmsf",
- "Calculate atomic fluctuations");
+ "Calculate atomic fluctuations");
LegacyCmdLineWrapper::registerModule(manager, &gmx_rotacf, "rotacf",
- "Calculate the rotational correlation function for molecules");
+ "Calculate the rotational correlation function for molecules");
LegacyCmdLineWrapper::registerModule(manager, &gmx_rotmat, "rotmat",
- "Plot the rotation matrix for fitting to a reference structure");
+ "Plot the rotation matrix for fitting to a reference structure");
LegacyCmdLineWrapper::registerModule(manager, &gmx_saltbr, "saltbr",
- "Compute salt bridges");
+ "Compute salt bridges");
LegacyCmdLineWrapper::registerModule(manager, &gmx_sans, "sans",
- "Compute the small angle neutron scattering spectra");
+ "Compute the small angle neutron scattering spectra");
LegacyCmdLineWrapper::registerModule(manager, &gmx_sas, "sas",
- "Compute solvent accessible surface area");
+ "Compute solvent accessible surface area");
LegacyCmdLineWrapper::registerModule(manager, &gmx_saxs, "saxs",
- "Calculates SAXS structure factors based on Cromer's method");
+ "Calculates SAXS structure factors based on Cromer's method");
LegacyCmdLineWrapper::registerModule(manager, &gmx_sgangle, "sgangle",
- "Compute the angle and distance between two groups");
+ "Compute the angle and distance between two groups");
LegacyCmdLineWrapper::registerModule(manager, &gmx_sham, "sham",
- "Compute free energies or other histograms from histograms");
+ "Compute free energies or other histograms from histograms");
LegacyCmdLineWrapper::registerModule(manager, &gmx_sigeps, "sigeps",
- "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
+ "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
LegacyCmdLineWrapper::registerModule(manager, &gmx_sorient, "sorient",
- "Analyze solvent orientation around solutes");
+ "Analyze solvent orientation around solutes");
LegacyCmdLineWrapper::registerModule(manager, &gmx_spatial, "spatial",
- "Calculate the spatial distribution function");
+ "Calculate the spatial distribution function");
LegacyCmdLineWrapper::registerModule(manager, &gmx_spol, "spol",
- "Analyze solvent dipole orientation and polarization around solutes");
+ "Analyze solvent dipole orientation and polarization around solutes");
LegacyCmdLineWrapper::registerModule(manager, &gmx_tcaf, "tcaf",
- "Calculate viscosities of liquids");
+ "Calculate viscosities of liquids");
LegacyCmdLineWrapper::registerModule(manager, &gmx_traj, "traj",
- "Plot x, v, f, box, temperature and rotational energy from trajectories");
+ "Plot x, v, f, box, temperature and rotational energy from trajectories");
//LegacyCmdLineWrapper::registerModule(manager, &gmx_tune_pme, "tune_pme",
// "Time mdrun as a function of PME nodes to optimize settings");
LegacyCmdLineWrapper::registerModule(manager, &gmx_vanhove, "vanhove",
- "Compute Van Hove correlation functions");
+ "Compute Van Hove correlation functions");
LegacyCmdLineWrapper::registerModule(manager, &gmx_velacc, "velacc",
- "Calculate velocity autocorrelation functions");
+ "Calculate velocity autocorrelation functions");
LegacyCmdLineWrapper::registerModule(manager, &gmx_wham, "wham",
- "Perform weighted histogram analysis after umbrella sampling");
+ "Perform weighted histogram analysis after umbrella sampling");
LegacyCmdLineWrapper::registerModule(manager, &gmx_wheel, "wheel",
- "Plot helical wheels");
+ "Plot helical wheels");
// TODO: Also include binaries from other directories than src/tools/:
// "g_protonate|Protonate structures");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff