/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h is in libgromacs-dev 2016.1-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 | /*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* GROMACS is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with GROMACS; if not, see
* http://www.gnu.org/licenses, or write to the Free Software Foundation,
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
* If you want to redistribute modifications to GROMACS, please
* consider that scientific software is very special. Version
* control is crucial - bugs must be traceable. We will be happy to
* consider code for inclusion in the official distribution, but
* derived work must not be called official GROMACS. Details are found
* in the README & COPYING files - if they are missing, get the
* official version at http://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \file
* \brief
* Declares gmx::TrajectoryAnalysisCommandLineRunner.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
* \ingroup module_trajectoryanalysis
*/
#ifndef GMX_TRAJECTORYANALYSIS_CMDLINERUNNER_H
#define GMX_TRAJECTORYANALYSIS_CMDLINERUNNER_H
#include <functional>
#include <memory>
#include "gromacs/trajectoryanalysis/analysismodule.h"
namespace gmx
{
class CommandLineModuleManager;
class ICommandLineOptionsModule;
/*! \brief
* Runner for command-line trajectory analysis tools.
*
* This class provides static methods to implement a command-line analysis
* program, given a TrajectoryAnalysisModule object (or a factory of such).
* It takes care of common command-line parameters, initializing and evaluating
* selections, and looping over trajectory frames.
*
* \inpublicapi
* \ingroup module_trajectoryanalysis
*/
class TrajectoryAnalysisCommandLineRunner
{
public:
/*! \brief
* Factory method type for creating a trajectory analysis module.
*
* This method allows the module creation to be postponed to the point
* where the module is needed, reducing initialization costs in, e.g.,
* the `gmx` binary, and simplifying exception handling.
*/
typedef std::function<TrajectoryAnalysisModulePointer()>
ModuleFactoryMethod;
/*! \brief
* Implements a main() method that runs a given module.
*
* \tparam ModuleType Trajectory analysis module.
* \param argc \c argc passed to main().
* \param argv \c argv passed to main().
*
* This method abstracts away all the logic required to implement a
* main() method in user tools, allowing that to be changed without
* requiring changes to the tools themselves.
*
* \p ModuleType should be default-constructible and derive from
* TrajectoryAnalysisModule.
*
* Does not throw. All exceptions are caught and handled internally.
*/
template <class ModuleType>
static int runAsMain(int argc, char *argv[])
{
return runAsMain(argc, argv, &createModule<ModuleType>);
}
/*! \brief
* Implements a main() method that runs a given module.
*
* \param argc \c argc passed to main().
* \param argv \c argv passed to main().
* \param factory Function that creates the module on demand.
*
* Implements the template runAsMain(), but can also be used
* independently.
*
* Does not throw. All exceptions are caught and handled internally.
*/
static int runAsMain(int argc, char *argv[],
ModuleFactoryMethod factory);
/*! \brief
* Registers a command-line module that runs a given module.
*
* \param manager Manager to register the module to.
* \param name Name of the module to register.
* \param description One-line description for the module to register.
* \param factory Function that creates the module on demand.
*
* \p name and \p descriptions must be string constants or otherwise
* stay valid for the duration of the program execution.
*/
static void registerModule(CommandLineModuleManager *manager,
const char *name, const char *description,
ModuleFactoryMethod factory);
/*! \brief
* Create a command-line module that runs the provided analysis module.
*
* \param[in] module Module to run.
* \returns Command-line module that runs the provided analysis
* module.
* \throws std::bad_alloc if out of memory.
*
* This is mainly provided for testing purposes that want to bypass
* CommandLineModuleManager.
*/
static std::unique_ptr<ICommandLineOptionsModule>
createModule(TrajectoryAnalysisModulePointer module);
private:
// Prevent instantiation.
TrajectoryAnalysisCommandLineRunner() {}
/*! \brief
* Creates a trajectory analysis module of a given type.
*
* \tparam ModuleType Module to create.
*/
template <class ModuleType>
static TrajectoryAnalysisModulePointer createModule()
{
return TrajectoryAnalysisModulePointer(new ModuleType());
}
};
} // namespace gmx
#endif
|