include/io/formats.hpp

#ifndef GAIA_IO_FORMATS_HPP
#define GAIA_IO_FORMATS_HPP

#include <vector>
#include <string>
#include <fstream>
#include <map>
#include <iostream>

namespace gaia {
namespace io {

struct Molecule {
    std::string name;
    std::vector<double> coords;
    std::map<std::string, double> properties;
};

class FileIO {
public:
    static bool write_sdf(const std::string& filename, const Molecule& mol) {
        std::ofstream file(filename);
        if (!file.is_open()) return false;
        file << mol.name << "\n  GAIA generated\n\n";
        file << "  " << mol.coords.size()/3 << " 0 0 0 0 0 0 0 0 0 0 0\n";
        for (size_t i = 0; i < mol.coords.size(); i += 3) {
            file << "  " << mol.coords[i] << "  " << mol.coords[i+1] 
                 << "  " << mol.coords[i+2] << " 0 0 0 0 0 0\n";
        }
        file << "M END\n";
        file.close();
        return true;
    }
    
    static bool write_jsonld(const std::string& filename, 
                             const std::map<std::string, double>& scores) {
        std::ofstream file(filename);
        if (!file.is_open()) return false;
        file << "{\n  \"@context\": \"https://gaia.xyz/context.jsonld\",\n";
        file << "  \"@type\": \"BindingScores\",\n  \"scores\": {\n";
        int i = 0;
        for (const auto& pair : scores) {
            file << "    \"" << pair.first << "\": " << pair.second;
            if (i < (int)scores.size() - 1) file << ",";
            file << "\n";
            i++;
        }
        file << "  }\n}\n";
        file.close();
        return true;
    }
};

} // namespace io
} // namespace gaia

#endif