src/gromacs/trajectoryanalysis/modules/convert_trj.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \internal \file
  36  * \brief
  37  * Implements gmx::analysismodules::ConvertTrj.
  38  *
  39  * \author Paul Bauer <paul.bauer.q@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42
  43 #include "gmxpre.h"
  44
  45 #include "convert_trj.h"
  46
  47 #include <algorithm>
  48
  49 #include "gromacs/coordinateio/coordinatefile.h"
  50 #include "gromacs/coordinateio/requirements.h"
  51 #include "gromacs/options/filenameoption.h"
  52 #include "gromacs/options/ioptionscontainer.h"
  53 #include "gromacs/selection/selectionoption.h"
  54 #include "gromacs/trajectoryanalysis/analysissettings.h"
  55 #include "gromacs/trajectoryanalysis/topologyinformation.h"
  56
  57 namespace gmx
  58 {
  59
  60 namespace analysismodules
  61 {
  62
  63 namespace
  64 {
  65
  66 /*
  67  * ConvertTrj
  68  */
  69
  70 class ConvertTrj : public TrajectoryAnalysisModule
  71 {
  72     public:
  73         ConvertTrj();
  74
  75         void initOptions(IOptionsContainer          *options,
  76                          TrajectoryAnalysisSettings *settings) override;
  77         void optionsFinished(TrajectoryAnalysisSettings *settings) override;
  78         void initAnalysis(const TrajectoryAnalysisSettings  &settings,
  79                           const TopologyInformation         &top) override;
  80         void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
  81                           TrajectoryAnalysisModuleData *pdata) override;
  82
  83         void finishAnalysis(int nframes) override;
  84         void writeOutput() override;
  85
  86     private:
  87         TrajectoryFrameWriterPointer        output_;
  88         Selection                           sel_;
  89         std::string                         name_;
  90         OutputRequirementOptionDirector     requirementsBuilder_;
  91 };
  92
  93 ConvertTrj::ConvertTrj()
  94 {
  95 }
  96
  97
  98 void
  99 ConvertTrj::initOptions(IOptionsContainer *options, TrajectoryAnalysisSettings *settings)
 100 {
 101     static const char *const desc[] = {
 102         "[THISMODULE] converts trajectory files between different formats.",
 103         "The module supports writing all GROMACS supported file formats from",
 104         "the supported input formats.",
 105         "",
 106         "Included is also a selection of possible options to modify individual",
 107         "trajectory frames, including options to produce slimmer",
 108         "output files. It is also possible to replace the particle information stored",
 109         "in the input trajectory with those from a structure file",
 110         "",
 111         "The module can also generate subsets of trajectories based on user supplied",
 112         "selections.",
 113     };
 114
 115     options->addOption(SelectionOption("select")
 116                            .store(&sel_)
 117                            .onlyAtoms()
 118                            .description("Selection of particles to write to the file"));
 119
 120     options->addOption(FileNameOption("o")
 121                            .filetype(eftTrajectory)
 122                            .outputFile()
 123                            .store(&name_).defaultBasename("trajout")
 124                            .required()
 125                            .description("Output trajectory"));
 126
 127     requirementsBuilder_.initOptions(options);
 128
 129     settings->setHelpText(desc);
 130 }
 131
 132 void
 133 ConvertTrj::optionsFinished(TrajectoryAnalysisSettings * settings)
 134 {
 135     int frameFlags = TRX_NEED_X;
 136
 137     frameFlags |= TRX_READ_V;
 138     frameFlags |= TRX_READ_F;
 139
 140     settings->setFrameFlags(frameFlags);
 141 }
 142
 143
 144 void
 145 ConvertTrj::initAnalysis(const TrajectoryAnalysisSettings    & /*settings*/,
 146                          const TopologyInformation          &top)
 147 {
 148     output_ = createTrajectoryFrameWriter(top.mtop(),
 149                                           sel_,
 150                                           name_,
 151                                           top.hasTopology() ? top.copyAtoms() : nullptr,
 152                                           requirementsBuilder_.process());
 153 }
 154
 155 void
 156 ConvertTrj::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc * /* pbc */,
 157                          TrajectoryAnalysisModuleData * /*pdata*/)
 158 {
 159     output_->prepareAndWriteFrame(frnr, fr);
 160 }
 161
 162 void
 163 ConvertTrj::finishAnalysis(int /*nframes*/)
 164 {
 165 }
 166
 167
 168
 169 void
 170 ConvertTrj::writeOutput()
 171 {
 172 }
 173
 174 }       // namespace
 175
 176 const char ConvertTrjInfo::name[]             = "convert-trj";
 177 const char ConvertTrjInfo::shortDescription[] =
 178     "Converts between different trajectory types";
 179
 180 TrajectoryAnalysisModulePointer ConvertTrjInfo::create()
 181 {
 182     return TrajectoryAnalysisModulePointer(new ConvertTrj);
 183 }
 184
 185 } // namespace analysismodules
 186
 187 } // namespace gmx