}
/*! \brief Helper to declare mdp output.
*
- * Enforces uniform mdp options output sting that are always prepended with the
- * correct string for the densityfitting mdp options and is consistent with the
- * options name and transformation.
+ * Enforces uniform mdp options output strings that are always prepended with the
+ * correct string for the densityfitting mdp options and are consistent with the
+ * options name and transformation type.
*
* \tparam OptionType the type of the mdp option
* \param[in] builder the KVT builder to generate the output
option);
}
+/*! \brief Helper to declare mdp output comments.
+ *
+ * Enforces uniform mdp options comment output strings that are always prepended
+ * with the correct string for the densityfitting mdp options and are consistent
+ * with the options name and transformation type.
+ *
+ * \param[in] builder the KVT builder to generate the output
+ * \param[in] comment on the mdp option
+ * \param[in] optionTag string tag that describes the mdp option
+ */
+void addDensityFittingMdpOutputValueComment(KeyValueTreeObjectBuilder *builder,
+ const std::string &comment,
+ const std::string &optionTag)
+{
+ builder->addValue<std::string>("comment-" + DensityFittingModuleInfo::name_ + "-" + optionTag, comment);
+}
+
} // namespace
void DensityFittingOptions::initMdpTransform(IKeyValueTreeTransformRules * rules)
void DensityFittingOptions::buildMdpOutput(KeyValueTreeObjectBuilder *builder) const
{
+
+ addDensityFittingMdpOutputValueComment(builder, "", "empty-line");
+ addDensityFittingMdpOutputValueComment(builder, "; Density guided simulation", "module");
+
addDensityFittingMdpOutputValue(builder, parameters_.active_, c_activeTag_);
if (parameters_.active_)
{
addDensityFittingMdpOutputValue(builder, groupString_, c_groupTag_);
+
+ addDensityFittingMdpOutputValueComment(builder, "; Similarity measure between densities: inner-product, or relative-entropy", c_similarityMeasureTag_);
addDensityFittingMdpOutputValue<std::string>(builder,
c_densitySimilarityMeasureMethodNames[parameters_.similarityMeasureMethod_],
c_similarityMeasureTag_);
+ addDensityFittingMdpOutputValueComment(builder, "; Atom amplitude for spreading onto grid: unity, mass, or charges", c_amplitudeMethodTag_);
addDensityFittingMdpOutputValue<std::string>(builder,
c_densityFittingAmplitudeMethodNames[parameters_.amplitudeLookupMethod_],
c_amplitudeMethodTag_);
addDensityFittingMdpOutputValue(builder, parameters_.forceConstant_, c_forceConstantTag_);
addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingWidth_, c_gaussianTransformSpreadingWidthTag_);
addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_, c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
+ addDensityFittingMdpOutputValueComment(builder, "; Reference density file location as absolute path or relative to the gmx mdrun calling location", c_referenceDensityFileNameTag_);
addDensityFittingMdpOutputValue(builder, referenceDensityFileName_, c_referenceDensityFileNameTag_);
addDensityFittingMdpOutputValue(builder, parameters_.calculationIntervalInSteps_, c_everyNStepsTag_);
+ addDensityFittingMdpOutputValueComment(builder, "; Normalize the sum of density voxel values to one", c_normalizeDensitiesTag_);
addDensityFittingMdpOutputValue(builder, parameters_.normalizeDensities_, c_normalizeDensitiesTag_);
}
}
}
stream.close();
- EXPECT_EQ(stream.toString(), std::string("density-guided-simulation-active = false\n"));
+ EXPECT_EQ(stream.toString(),
+ std::string(
+ "\n; Density guided simulation\ndensity-guided-simulation-active = false\n"));
}
TEST_F(DensityFittingOptionsTest, OutputDefaultValuesWhenActive)
stream.close();
std::string expected
= {
+ "\n"
+ "; Density guided simulation\n"
"density-guided-simulation-active = true\n"
"density-guided-simulation-group = protein\n"
+ "; Similarity measure between densities: inner-product, or relative-entropy\n"
"density-guided-simulation-similarity-measure = inner-product\n"
+ "; Atom amplitude for spreading onto grid: unity, mass, or charges\n"
"density-guided-simulation-amplitude-method = unity\n"
"density-guided-simulation-force-constant = 1e+09\n"
"density-guided-simulation-gaussian-transform-spreading-width = 0.2\n"
"density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width = 4\n"
+ "; Reference density file location as absolute path or relative to the gmx mdrun calling location\n"
"density-guided-simulation-reference-density-filename = reference.mrc\n"
"density-guided-simulation-nst = 1\n"
+ "; Normalize the sum of density voxel values to one\n"
"density-guided-simulation-normalize-densities = true\n"
};
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff