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37 * Implements classes in analysissettings.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
44 #include "analysissettings.h"
46 #include "gromacs/commandline/cmdlineoptionsmodule.h"
47 #include "gromacs/fileio/trxio.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/topology/mtop_util.h"
50 #include "gromacs/topology/topology.h"
51 #include "gromacs/utility/arrayref.h"
52 #include "gromacs/utility/exceptions.h"
53 #include "gromacs/utility/gmxassert.h"
54 #include "gromacs/utility/smalloc.h"
56 #include "analysissettings-impl.h"
62 /********************************************************************
63 * TrajectoryAnalysisSettings
66 TrajectoryAnalysisSettings::TrajectoryAnalysisSettings()
69 impl_->frflags |= TRX_NEED_X;
73 TrajectoryAnalysisSettings::~TrajectoryAnalysisSettings()
78 void TrajectoryAnalysisSettings::setOptionsModuleSettings(
79 ICommandLineOptionsModuleSettings *settings)
81 impl_->optionsModuleSettings_ = settings;
86 TrajectoryAnalysisSettings::timeUnit() const
88 return impl_->timeUnit;
92 const AnalysisDataPlotSettings &
93 TrajectoryAnalysisSettings::plotSettings() const
95 return impl_->plotSettings;
100 TrajectoryAnalysisSettings::flags() const
107 TrajectoryAnalysisSettings::hasFlag(unsigned long flag) const
109 return impl_->flags & flag;
114 TrajectoryAnalysisSettings::hasPBC() const
121 TrajectoryAnalysisSettings::hasRmPBC() const
123 return impl_->bRmPBC;
128 TrajectoryAnalysisSettings::frflags() const
130 return impl_->frflags;
135 TrajectoryAnalysisSettings::setFlags(unsigned long flags)
137 impl_->flags = flags;
142 TrajectoryAnalysisSettings::setFlag(unsigned long flag, bool bSet)
146 impl_->flags |= flag;
150 impl_->flags &= ~flag;
156 TrajectoryAnalysisSettings::setPBC(bool bPBC)
163 TrajectoryAnalysisSettings::setRmPBC(bool bRmPBC)
165 impl_->bRmPBC = bRmPBC;
170 TrajectoryAnalysisSettings::setFrameFlags(int frflags)
172 impl_->frflags = frflags;
176 TrajectoryAnalysisSettings::setHelpText(const ConstArrayRef<const char *> &help)
178 GMX_RELEASE_ASSERT(impl_->optionsModuleSettings_ != nullptr,
179 "setHelpText() called in invalid context");
180 impl_->optionsModuleSettings_->setHelpText(help);
184 /********************************************************************
185 * TopologyInformation
188 TopologyInformation::TopologyInformation()
189 : mtop_(nullptr), top_(nullptr), bTop_(false), xtop_(nullptr), ePBC_(-1)
195 TopologyInformation::~TopologyInformation()
197 done_top_mtop(top_, mtop_);
204 t_topology *TopologyInformation::topology() const
206 if (top_ == nullptr && mtop_ != nullptr)
209 *top_ = gmx_mtop_t_to_t_topology(mtop_, false);
216 TopologyInformation::getTopologyConf(rvec **x, matrix box) const
220 copy_mat(const_cast<rvec *>(boxtop_), box);
227 GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));