/usr/include/gromacs/selection/selectionoptionbehavior.h is in libgromacs-dev 2018.1-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 | /*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2015,2016, 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::SelectionOptionBehavior.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_SELECTIONOPTIONBEHAVIOR_H
#define GMX_SELECTION_SELECTIONOPTIONBEHAVIOR_H
#include <string>
#include "gromacs/options/ioptionsbehavior.h"
#include "gromacs/utility/classhelpers.h"
struct gmx_mtop_t;
namespace gmx
{
class IOptionsContainer;
class Options;
class SelectionCollection;
/*! \brief
* Provides topology information to SelectionOptionBehavior.
*
* Modules that use SelectionOptionBehavior need to implement this interface
* to provide functionality to load topology information for use with the
* selections.
*
* If future need arises to use similar information elsewhere, this can be
* moved to, e.g., the topology module, but for now it is here for simplicity.
* Also, if/when there will be more modules that use this, we can identify
* common code from those users and possibly provide a shared implementation
* (e.g., in the form of another IOptionsBehavior), but currently there are too
* few users to identify any useful reusable functionality from the callers.
*
* \see SelectionCollection::setTopology().
*
* \inpublicapi
* \ingroup module_selection
*/
class ITopologyProvider
{
public:
/*! \brief
* Returns the topology to use.
*
* \param[in] required Whether the topology is required by the caller.
*
* Can return NULL if \p required is `false` and the topology is not
* provided by the user.
* If \p required is `true`, should throw an error if the topology
* cannot be loaded.
*
* This method may get called multiple times, potentially with
* different values of \p required. Subsequent calls should just
* return the same topology that was loaded in the first call.
*/
virtual gmx_mtop_t *getTopology(bool required) = 0;
/*! \brief
* Returns the number of atoms.
*
* This method is only called if getTopology() returns NULL.
* It should return the number of atoms that at most need to be
* selected by the selections.
*/
virtual int getAtomCount() = 0;
protected:
virtual ~ITopologyProvider();
};
/*! \brief
* Options behavior to allow using SelectionOptions.
*
* This behavior wraps SelectionOptionManager, as well as all calls to
* SelectionCollection up to and including selection compilation.
*
* To use selections through SelectionOption options in a
* ICommandLineOptionsModule, you need to
* * create a SelectionCollection object,
* * implement ITopologyProvider to return the topology or number of atoms
* to be used with the selections,
* * create and add a SelectionOptionBehavior, and call initOptions() to add
* common options for selection control,
* * use SelectionOption options to specify the selections used, and
* * evaluate the selections when running the module for the desired sets of
* coordinates (see SelectionCollection::evaluate()).
*
* The SelectionOptionBehavior provides the following functionalities to the
* module:
* * Creates SelectionOptionManager and manages all calls to it.
* * Creates an option to provide an `ndx` file, and loads it when necessary.
* * Creates options to control general aspects of selections (see
* SelectionCollection::initOptions()), as well as a generic option to
* provide selections from a file.
* * After all options have been processed, provides an interactive
* command-line prompt for any missing selections.
* * Compiles the selections.
*
* The behavior needs to be added before any options are created.
*
* \inpublicapi
* \ingroup module_selection
*/
class SelectionOptionBehavior : public IOptionsBehavior
{
public:
/*! \brief
* Creates a behavior to use selections.
*
* \param[in,out] selections Selection collection to use.
* \param[in] topologyProvider Callback to load/provide topology
* information to selections when required.
*
* The methods in \p topologyProvider are called after all options have
* been parsed and finished, so the caller can, e.g., load the topology
* from a file specified by a file option.
*/
SelectionOptionBehavior(SelectionCollection *selections,
ITopologyProvider *topologyProvider);
~SelectionOptionBehavior();
/*! \brief
* Add common options for controlling selections.
*
* This method is separate from the constructor so that the caller can
* control the order of options better.
*/
void initOptions(IOptionsContainer *options);
// From IOptionsBehavior
virtual void initBehavior(Options *options);
virtual void optionsFinishing(Options * /*options*/) {}
virtual void optionsFinished();
private:
class Impl;
PrivateImplPointer<Impl> impl_;
};
} // namespace gmx
#endif
|