src/gromacs/coordinateio/outputadapters/setatoms.cpp

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  35 /*!\internal
  36  * \file
  37  * \brief
  38  * Implements setatoms class.
  39  *
  40  * \author Paul Bauer <paul.bauer.q@gmail.com>
  41  * \ingroup module_coordinateio
  42  */
  43
  44 #include "gmxpre.h"
  45
  46 #include "setatoms.h"
  47
  48 #include <algorithm>
  49
  50 #include "gromacs/trajectory/trajectoryframe.h"
  51 #include "gromacs/utility/exceptions.h"
  52
  53 namespace gmx
  54 {
  55
  56 void SetAtoms::checkAbilityDependencies(unsigned long abilities) const
  57 {
  58     if ((abilities & convertFlag(moduleRequirements_)) == 0U)
  59     {
  60         std::string errorMessage =
  61                 "Output file type does not support writing atom information. "
  62                 "You need to use PDB, GRO or TNG as the file type for this.";
  63         GMX_THROW(InconsistentInputError(errorMessage.c_str()));
  64     }
  65 }
  66
  67 void SetAtoms::processFrame(const int /*framenumber*/, t_trxframe* input)
  68 {
  69     switch (atomFlag_)
  70     {
  71         case (ChangeAtomsType::Never):
  72             input->bAtoms = false;
  73             input->atoms  = nullptr;
  74             break;
  75         case (ChangeAtomsType::Always):
  76             if (!haveAtoms(*input))
  77             {
  78                 GMX_THROW(
  79                         InconsistentInputError("Atoms needed by output but not "
  80                                                "available in input frame or topology"));
  81             }
  82             input->bAtoms = true;
  83             if (haveStructureFileAtoms())
  84             {
  85                 input->atoms = atoms();
  86             }
  87             break;
  88         case (ChangeAtomsType::PreservedIfPresent): break;
  89         case (ChangeAtomsType::AlwaysFromStructure):
  90             if (!haveStructureFileAtoms())
  91             {
  92                 GMX_THROW(
  93                         InconsistentInputError("Requested to add atoms information "
  94                                                "to coordinate frame when it was not available"));
  95             }
  96             input->bAtoms = true;
  97             input->atoms  = atoms();
  98             break;
  99         default: GMX_THROW(InconsistentInputError("Value for atom flag not understood"));
 100     }
 101 }
 102
 103 bool SetAtoms::haveFrameAtoms(const t_trxframe& input)
 104 {
 105     return input.bAtoms;
 106 }
 107
 108 } // namespace gmx