*/
class DensityFittingOptions final : public IMdpOptionProvider
{
- public:
- //! From IMdpOptionProvider
- void initMdpTransform(IKeyValueTreeTransformRules * rules) override;
+public:
+ //! From IMdpOptionProvider
+ void initMdpTransform(IKeyValueTreeTransformRules* rules) override;
- /*! \brief
- * Build mdp parameters for density fitting to be output after pre-processing.
- * \param[in, out] builder the builder for the mdp options output KV-tree.
- * \note This should be symmetrical to option initialization without
- * employing manual prefixing with the section name string once
- * the legacy code blocking this design is removed.
- */
- void buildMdpOutput(KeyValueTreeObjectBuilder *builder) const override;
+ /*! \brief
+ * Build mdp parameters for density fitting to be output after pre-processing.
+ * \param[in, out] builder the builder for the mdp options output KV-tree.
+ * \note This should be symmetrical to option initialization without
+ * employing manual prefixing with the section name string once
+ * the legacy code blocking this design is removed.
+ */
+ void buildMdpOutput(KeyValueTreeObjectBuilder* builder) const override;
- /*! \brief
- * Connect option name and data.
- */
- void initMdpOptions(IOptionsContainerWithSections *options) override;
+ /*! \brief
+ * Connect option name and data.
+ */
+ void initMdpOptions(IOptionsContainerWithSections* options) override;
- //! Report if this set of options is active
- bool active() const;
+ //! Report if this set of options is active
+ bool active() const;
- //! Process input options to parameters, including input file reading.
- const DensityFittingParameters &buildParameters();
+ //! Process input options to parameters, including input file reading.
+ const DensityFittingParameters& buildParameters();
- /*! \brief Evaluate and store atom indices.
- *
- * During pre-processing, use the group string from the options to
- * evaluate the indices of the atoms to be subject to forces from this
- * module.
- */
- void setFitGroupIndices(const IndexGroupsAndNames &indexGroupsAndNames);
+ /*! \brief Evaluate and store atom indices.
+ *
+ * During pre-processing, use the group string from the options to
+ * evaluate the indices of the atoms to be subject to forces from this
+ * module.
+ */
+ void setFitGroupIndices(const IndexGroupsAndNames& indexGroupsAndNames);
- //! Store the paramers that are not mdp options in the tpr file
- void writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder);
+ //! Store the paramers that are not mdp options in the tpr file
+ void writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder);
- //! Set the internal parameters that are stored in the tpr file
- void readInternalParametersFromKvt(const KeyValueTreeObject &tree);
+ //! Set the internal parameters that are stored in the tpr file
+ void readInternalParametersFromKvt(const KeyValueTreeObject& tree);
- //! Return the file name of the reference density
- const std::string &referenceDensityFileName() const;
+ //! Return the file name of the reference density
+ const std::string& referenceDensityFileName() const;
- //! Check if input parameters are consistent with other simulation parameters
- void checkEnergyCaluclationFrequency(EnergyCalculationFrequencyErrors * energyCalculationFrequencyErrors) const;
+ //! Check if input parameters are consistent with other simulation parameters
+ void checkEnergyCaluclationFrequency(EnergyCalculationFrequencyErrors* energyCalculationFrequencyErrors) const;
- private:
- const std::string c_activeTag_ = "active";
+private:
+ const std::string c_activeTag_ = "active";
- /*! \brief Denote the .mdp option that defines the group of fit atoms.
- * \note Changing this string will break .tpr backwards compability
- */
- const std::string c_groupTag_ = "group";
- std::string groupString_ = "protein";
+ /*! \brief Denote the .mdp option that defines the group of fit atoms.
+ * \note Changing this string will break .tpr backwards compability
+ */
+ const std::string c_groupTag_ = "group";
+ std::string groupString_ = "protein";
- const std::string c_similarityMeasureTag_ = "similarity-measure";
+ const std::string c_similarityMeasureTag_ = "similarity-measure";
- const std::string c_amplitudeMethodTag_ = "atom-spreading-weight";
+ const std::string c_amplitudeMethodTag_ = "atom-spreading-weight";
- const std::string c_forceConstantTag_ = "force-constant";
+ const std::string c_forceConstantTag_ = "force-constant";
- const std::string c_gaussianTransformSpreadingWidthTag_ = "gaussian-transform-spreading-width";
- const std::string c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_
- = "gaussian-transform-spreading-range-in-multiples-of-width";
+ const std::string c_gaussianTransformSpreadingWidthTag_ = "gaussian-transform-spreading-width";
+ const std::string c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_ =
+ "gaussian-transform-spreading-range-in-multiples-of-width";
- const std::string c_referenceDensityFileNameTag_ = "reference-density-filename";
- std::string referenceDensityFileName_ = "reference.mrc";
+ const std::string c_referenceDensityFileNameTag_ = "reference-density-filename";
+ std::string referenceDensityFileName_ = "reference.mrc";
- const std::string c_everyNStepsTag_ = "nst";
+ const std::string c_everyNStepsTag_ = "nst";
- const std::string c_normalizeDensitiesTag_ = "normalize-densities";
+ const std::string c_normalizeDensitiesTag_ = "normalize-densities";
- const std::string c_adaptiveForceScalingTag_ = "adaptive-force-scaling";
+ const std::string c_adaptiveForceScalingTag_ = "adaptive-force-scaling";
- const std::string c_adaptiveForceScalingTimeConstantTag_ = "adaptive-force-scaling-time-constant";
+ const std::string c_adaptiveForceScalingTimeConstantTag_ =
+ "adaptive-force-scaling-time-constant";
- DensityFittingParameters parameters_;
+ DensityFittingParameters parameters_;
};
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff