src/gromacs/selection/selectionoptionbehavior.h

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  35 /*! \file
  36  * \brief
  37  * Declares gmx::SelectionOptionBehavior.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \inpublicapi
  41  * \ingroup module_selection
  42  */
  43 #ifndef GMX_SELECTION_SELECTIONOPTIONBEHAVIOR_H
  44 #define GMX_SELECTION_SELECTIONOPTIONBEHAVIOR_H
  45
  46 #include <string>
  47
  48 #include "gromacs/options/ioptionsbehavior.h"
  49 #include "gromacs/utility/classhelpers.h"
  50
  51 struct gmx_mtop_t;
  52
  53 namespace gmx
  54 {
  55
  56 class IOptionsContainer;
  57 class Options;
  58 class SelectionCollection;
  59
  60 /*! \brief
  61  * Provides topology information to SelectionOptionBehavior.
  62  *
  63  * Modules that use SelectionOptionBehavior need to implement this interface
  64  * to provide functionality to load topology information for use with the
  65  * selections.
  66  *
  67  * If future need arises to use similar information elsewhere, this can be
  68  * moved to, e.g., the topology module, but for now it is here for simplicity.
  69  * Also, if/when there will be more modules that use this, we can identify
  70  * common code from those users and possibly provide a shared implementation
  71  * (e.g., in the form of another IOptionsBehavior), but currently there are too
  72  * few users to identify any useful reusable functionality from the callers.
  73  *
  74  * \see SelectionCollection::setTopology().
  75  *
  76  * \inpublicapi
  77  * \ingroup module_selection
  78  */
  79 class ITopologyProvider
  80 {
  81     public:
  82         /*! \brief
  83          * Returns the topology to use.
  84          *
  85          * \param[in] required  Whether the topology is required by the caller.
  86          *
  87          * Can return NULL if \p required is `false` and the topology is not
  88          * provided by the user.
  89          * If \p required is `true`, should throw an error if the topology
  90          * cannot be loaded.
  91          *
  92          * This method may get called multiple times, potentially with
  93          * different values of \p required.  Subsequent calls should just
  94          * return the same topology that was loaded in the first call.
  95          */
  96         virtual gmx_mtop_t *getTopology(bool required) = 0;
  97         /*! \brief
  98          * Returns the number of atoms.
  99          *
 100          * This method is only called if getTopology() returns NULL.
 101          * It should return the number of atoms that at most need to be
 102          * selected by the selections.
 103          */
 104         virtual int getAtomCount()                     = 0;
 105
 106     protected:
 107         virtual ~ITopologyProvider();
 108 };
 109
 110 /*! \brief
 111  * Options behavior to allow using SelectionOptions.
 112  *
 113  * This behavior wraps SelectionOptionManager, as well as all calls to
 114  * SelectionCollection up to and including selection compilation.
 115  *
 116  * To use selections through SelectionOption options in a
 117  * ICommandLineOptionsModule, you need to
 118  *  * create a SelectionCollection object,
 119  *  * implement ITopologyProvider to return the topology or number of atoms
 120  *    to be used with the selections,
 121  *  * create and add a SelectionOptionBehavior, and call initOptions() to add
 122  *    common options for selection control,
 123  *  * use SelectionOption options to specify the selections used, and
 124  *  * evaluate the selections when running the module for the desired sets of
 125  *    coordinates (see SelectionCollection::evaluate()).
 126  *
 127  * The SelectionOptionBehavior provides the following functionalities to the
 128  * module:
 129  *  * Creates SelectionOptionManager and manages all calls to it.
 130  *  * Creates an option to provide an `ndx` file, and loads it when necessary.
 131  *  * Creates options to control general aspects of selections (see
 132  *    SelectionCollection::initOptions()), as well as a generic option to
 133  *    provide selections from a file.
 134  *  * After all options have been processed, provides an interactive
 135  *    command-line prompt for any missing selections.
 136  *  * Compiles the selections.
 137  *
 138  * The behavior needs to be added before any options are created.
 139  *
 140  * \inpublicapi
 141  * \ingroup module_selection
 142  */
 143 class SelectionOptionBehavior : public IOptionsBehavior
 144 {
 145     public:
 146         /*! \brief
 147          * Creates a behavior to use selections.
 148          *
 149          * \param[in,out] selections  Selection collection to use.
 150          * \param[in]     topologyProvider  Callback to load/provide topology
 151          *     information to selections when required.
 152          *
 153          * The methods in \p topologyProvider are called after all options have
 154          * been parsed and finished, so the caller can, e.g., load the topology
 155          * from a file specified by a file option.
 156          */
 157         SelectionOptionBehavior(SelectionCollection *selections,
 158                                 ITopologyProvider   *topologyProvider);
 159         ~SelectionOptionBehavior() override;
 160
 161         /*! \brief
 162          * Add common options for controlling selections.
 163          *
 164          * This method is separate from the constructor so that the caller can
 165          * control the order of options better.
 166          */
 167         void initOptions(IOptionsContainer *options);
 168
 169         // From IOptionsBehavior
 170         void initBehavior(Options *options) override;
 171         void optionsFinishing(Options * /*options*/) override {}
 172         void optionsFinished() override;
 173
 174     private:
 175         class Impl;
 176
 177         PrivateImplPointer<Impl> impl_;
 178 };
 179
 180
 181 } // namespace gmx
 182
 183 #endif