IO.h

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#ifndef INCLUDE_MOLASSEMBLER_IO_H
#define INCLUDE_MOLASSEMBLER_IO_H

#include "Molassembler/Types.h"
#include "Utils/Typenames.h"

#include <string>
#include <vector>

namespace Scine {
namespace Utils {

// Forward declarations
class AtomCollection;
class BondOrderCollection;
} // namespace Utils

namespace Molassembler {

// More forward declarations
class Molecule;
class AngstromPositions;

namespace IO {

class MASM_EXPORT LineNotation {
public:
  static const bool& enabled();
  static Molecule fromCanonicalSMILES(const std::string& can);
  static Molecule fromIsomericSMILES(const std::string& smi);
  static Molecule fromInChI(const std::string& inchi);

private:
  static Molecule fromFormat(const std::string& lineNotation, const std::string& format);
};

MASM_EXPORT std::pair<Utils::AtomCollection, Utils::BondOrderCollection> exchangeFormat(
  const Molecule& molecule,
  const AngstromPositions& angstromWrapper
);

MASM_EXPORT std::pair<Utils::AtomCollection, Utils::BondOrderCollection> exchangeFormat(
  const Molecule& molecule,
  const Utils::PositionCollection& positions
);

MASM_EXPORT std::tuple<Utils::AtomCollection, Utils::BondOrderCollection, std::vector<AtomIndex>> shuffle(
  const Utils::AtomCollection& ac,
  const Utils::BondOrderCollection& bos
);

MASM_EXPORT Molecule read(const std::string& filename);

MASM_EXPORT std::vector<Molecule> split(const std::string& filename);

MASM_EXPORT void write(
  const std::string& filename,
  const Molecule& molecule,
  const AngstromPositions& angstromWrapper
);

MASM_EXPORT void write(
  const std::string& filename,
  const Molecule& molecule,
  const Utils::PositionCollection& positions
);

MASM_EXPORT void write(const std::string& filename, const Molecule& molecule);

} // namespace IO
} // namespace Molassembler
} // namespace Scine

#endif