StructurePreparationIO.h

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#ifndef SWOOSE_STRUCTUREPREPARATIONIO_H
#define SWOOSE_STRUCTUREPREPARATIONIO_H

#include <boost/filesystem.hpp>
#include <string>
#include <vector>

namespace bfs = boost::filesystem;

namespace Scine {
namespace Core {
struct Log;
}
namespace StructurePreparation {
struct StructurePreparationData;
struct StructurePreparationFiles;
struct TitrableSite;

namespace StructurePreparationIO {
void xyzToPdb(const std::string& xyzFile, const std::string& pdbFile);
void writeAtomicInfoFileForProtein(const StructurePreparationData& data, const std::string& atomicInfoFile);
void addAtomicInformationForNonRegContainer(StructurePreparationFiles& files, std::vector<std::vector<int>> subsystemMapping);
// determines the suffix of a file
std::string getSuffix(const bfs::path& filepath);
void writePdbFileWithResidueSpecifier(const StructurePreparationData& data, const std::string& proteinFile, Core::Log& log);

} // namespace StructurePreparationIO
} // namespace StructurePreparation
} // namespace Scine

#endif // SWOOSE_STRUCTUREPREPARATIONIO_H