src/gromacs/trajectoryanalysis/analysissettings.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010-2018, The GROMACS development team.
   5  * Copyright (c) 2019, by the GROMACS development team, led by
   6  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   7  * and including many others, as listed in the AUTHORS file in the
   8  * top-level source directory and at http://www.gromacs.org.
   9  *
  10  * GROMACS is free software; you can redistribute it and/or
  11  * modify it under the terms of the GNU Lesser General Public License
  12  * as published by the Free Software Foundation; either version 2.1
  13  * of the License, or (at your option) any later version.
  14  *
  15  * GROMACS is distributed in the hope that it will be useful,
  16  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  17  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  18  * Lesser General Public License for more details.
  19  *
  20  * You should have received a copy of the GNU Lesser General Public
  21  * License along with GROMACS; if not, see
  22  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  23  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  24  *
  25  * If you want to redistribute modifications to GROMACS, please
  26  * consider that scientific software is very special. Version
  27  * control is crucial - bugs must be traceable. We will be happy to
  28  * consider code for inclusion in the official distribution, but
  29  * derived work must not be called official GROMACS. Details are found
  30  * in the README & COPYING files - if they are missing, get the
  31  * official version at http://www.gromacs.org.
  32  *
  33  * To help us fund GROMACS development, we humbly ask that you cite
  34  * the research papers on the package. Check out http://www.gromacs.org.
  35  */
  36 /*! \file
  37  * \brief
  38  * Declares gmx::TrajectoryAnalysisSettings.
  39  *
  40  * \author Teemu Murtola <teemu.murtola@gmail.com>
  41  * \inpublicapi
  42  * \ingroup module_trajectoryanalysis
  43  */
  44 #ifndef GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
  45 #define GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
  46
  47 #include <string>
  48
  49 #include "gromacs/options/timeunitmanager.h"
  50 #include "gromacs/utility/classhelpers.h"
  51
  52 namespace gmx
  53 {
  54
  55 template<typename T>
  56 class ArrayRef;
  57
  58 class AnalysisDataPlotSettings;
  59 class ICommandLineOptionsModuleSettings;
  60 class Options;
  61 class TrajectoryAnalysisRunnerCommon;
  62
  63 /*! \brief
  64  * Trajectory analysis module configuration object.
  65  *
  66  * This class is used by trajectory analysis modules to inform the caller
  67  * about the requirements they have on the input (e.g., whether a topology is
  68  * required, or whether PBC removal makes sense).  It is also used to pass
  69  * similar information back to the analysis module after parsing user input.
  70  *
  71  * Having this functionality as a separate class makes the
  72  * TrajectoryAnalysisModule interface much cleaner, and also reduces the need to
  73  * change existing code when new options are added.
  74  *
  75  * Methods in this class do not throw, except for the constructor, which may
  76  * throw an std::bad_alloc.
  77  *
  78  * \todo
  79  * Remove plain flags from the public interface.
  80  *
  81  * \inpublicapi
  82  * \ingroup module_trajectoryanalysis
  83  */
  84 class TrajectoryAnalysisSettings
  85 {
  86 public:
  87     //! Recognized flags.
  88     enum
  89     {
  90         /*! \brief
  91          * Forces loading of a topology file.
  92          *
  93          * If this flag is not specified, the topology file is loaded only
  94          * if it is provided on the command line explicitly.
  95          */
  96         efRequireTop = 1 << 0,
  97         /*! \brief
  98          * Requests topology coordinates.
  99          *
 100          * If this flag is specified, the position coordinates loaded from the
 101          * topology can be accessed, otherwise they are not loaded.
 102          *
 103          * \see TopologyInformation
 104          */
 105         efUseTopX = 1 << 1,
 106         /*! \brief
 107          * Requests topology coordinates.
 108          *
 109          * If this flag is specified, the velocity coordinates loaded from the
 110          * topology can be accessed, otherwise they are not loaded.
 111          *
 112          * \see TopologyInformation
 113          */
 114         efUseTopV = 1 << 2,
 115         /*! \brief
 116          * Disallows the user from changing PBC handling.
 117          *
 118          * If this option is not specified, the analysis module (see
 119          * TrajectoryAnalysisModule::analyzeFrame()) may be passed a NULL
 120          * PBC structure, and it should be able to handle such a situation.
 121          *
 122          * \see setPBC()
 123          */
 124         efNoUserPBC = 1 << 4,
 125         /*! \brief
 126          * Disallows the user from changing PBC removal.
 127          *
 128          * \see setRmPBC()
 129          */
 130         efNoUserRmPBC = 1 << 5,
 131     };
 132
 133     //! Initializes default settings.
 134     TrajectoryAnalysisSettings();
 135     ~TrajectoryAnalysisSettings();
 136
 137     //! Injects command line options module settings for some methods to use.
 138     void setOptionsModuleSettings(ICommandLineOptionsModuleSettings* settings);
 139
 140     //! Returns the time unit the user has requested.
 141     TimeUnit timeUnit() const;
 142     //! Returns common settings for analysis data plot modules.
 143     const AnalysisDataPlotSettings& plotSettings() const;
 144
 145     //! Returns the currently set flags.
 146     unsigned long flags() const;
 147     //! Tests whether a flag has been set.
 148     bool hasFlag(unsigned long flag) const;
 149     /*! \brief
 150      * Returns whether PBC should be used.
 151      *
 152      * Returns the value set with setPBC() and/or overridden by the user.
 153      * The user-provided value can be accessed in
 154      * TrajectoryAnalysisModule::optionsFinished(), and can be overridden
 155      * with a call to setPBC().
 156      */
 157     bool hasPBC() const;
 158     /*! \brief
 159      * Returns whether molecules should be made whole.
 160      *
 161      * See hasPBC() for information on accessing or overriding the
 162      * user-provided value.
 163      */
 164     bool hasRmPBC() const;
 165     //! Returns the currently set frame flags.
 166     int frflags() const;
 167
 168     /*! \brief
 169      * Sets flags.
 170      *
 171      * Overrides any earlier set flags.
 172      * By default, no flags are set.
 173      */
 174     void setFlags(unsigned long flags);
 175     //! Sets or clears an individual flag.
 176     void setFlag(unsigned long flag, bool bSet = true);
 177     /*! \brief
 178      * Sets whether PBC are used.
 179      *
 180      * \param[in]  bPBC   true if PBC should be used.
 181      *
 182      * If called in TrajectoryAnalysisModule::initOptions(), this function
 183      * sets the default for whether PBC are used in the analysis.
 184      * If \ref efNoUserPBC is not set, a command-line option is provided
 185      * for the user to override the default value.
 186      * If called later, it overrides the setting provided by the user or an
 187      * earlier call.
 188      *
 189      * If this function is not called, the default is to use PBC.
 190      *
 191      * If PBC are not used, the \p pbc pointer passed to
 192      * TrajectoryAnalysisModule::analyzeFrame() is NULL.
 193      * The value of the flag can also be accessed with hasPBC().
 194      *
 195      * \see efNoUserPBC
 196      */
 197     void setPBC(bool bPBC);
 198     /*! \brief
 199      * Sets whether molecules are made whole.
 200      *
 201      * \param[in]     bRmPBC true if molecules should be made whole.
 202      *
 203      * If called in TrajectoryAnalysisModule::initOptions(), this function
 204      * sets the default for whether molecules are made whole.
 205      * If \ref efNoUserRmPBC is not set, a command-line option is provided
 206      * for the user to override the default value.
 207      * If called later, it overrides the setting provided by the user or an
 208      * earlier call.
 209      *
 210      * If this function is not called, the default is to make molecules
 211      * whole.
 212      *
 213      * The main use of this function is to call it with \c false if your
 214      * analysis program does not require whole molecules as this can
 215      * increase the performance.
 216      * In such a case, you can also specify \ref efNoUserRmPBC to not to
 217      * confuse the user with an option that would only slow the program
 218      * down.
 219      *
 220      * \see efNoUserRmPBC
 221      */
 222     void setRmPBC(bool bRmPBC);
 223     /*! \brief
 224      * Sets flags that determine what to read from the trajectory.
 225      *
 226      * \param[in]     frflags Flags for what to read from the trajectory file.
 227      *
 228      * If this function is not called, the flags default to TRX_NEED_X.
 229      * If the analysis module needs some other information (velocities,
 230      * forces), it can call this function to load additional information
 231      * from the trajectory.
 232      */
 233     void setFrameFlags(int frflags);
 234
 235     //! \copydoc ICommandLineOptionsModuleSettings::setHelpText()
 236     void setHelpText(const ArrayRef<const char* const>& help);
 237
 238 private:
 239     class Impl;
 240
 241     PrivateImplPointer<Impl> impl_;
 242
 243     friend class TrajectoryAnalysisRunnerCommon;
 244 };
 245
 246 } // namespace gmx
 247
 248 #endif