17 #include <yaml-cpp/yaml.h>
22 namespace StructurePreparation {
23 class StructureProcessor;
27 class MolecularDynamics;
28 class XyzStreamHandler;
35 void runPDBPreparationTask(StructurePreparation::StructureProcessor processor,
const std::string& structureFile,
36 const std::string& mode, Core::Log& log);
39 void runMMCalculationTask(Core::Calculator& calculator,
const std::string& structureFile,
40 Utils::PropertyList properties, Core::Log& log);
43 void runQmmmCalculationTask(Core::Calculator& calculator,
const std::string& structureFile,
44 Utils::PropertyList properties, Core::Log& log,
const YAML::Node& yamlNode);
47 void runSFAMParametrizationTask(Core::MMParametrizer& parametrizer,
const std::string& structureFile, Core::Log& log);
50 void runMDSimulationTask(Utils::MolecularDynamics& md,
const std::string& structureFile, Core::Log& log);
53 void runMMOptimizationTask(Core::Calculator& calculator, Utils::GeometryOptimizerBase& optimizer,
54 const std::string& structureFile, Core::Log& log,
const YAML::Node& yamlNode);
57 template<
class OptimizerType>
58 void runQmmmOptimizationTask(Core::Calculator& calculator, Utils::QmmmGeometryOptimizer<OptimizerType>& optimizer,
59 const std::string& structureFile, Core::Log& log,
const YAML::Node& yamlNode);
62 void runQmRegionSelectionTask(
const std::string& structureFile, Core::Log& log, YAML::Node& yamlNode,
63 std::string yamlSettingsPath);
69 #endif // SWOOSE_TASKS_H