atom.hpp

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#ifndef INDIGOX_CLASSES_ATOM_HPP
#define INDIGOX_CLASSES_ATOM_HPP

#include "../utils/fwd_declares.hpp"

#include <Eigen/Dense>
#include <memory>
#include <vector>

namespace indigox {
  class Atom {
    friend class indigox::Molecule;
    friend class cereal::access;

  public:
    using AtomBonds = std::vector<Bond>;
    using AtomAngles = std::vector<Angle>;
    using AtomDihedrals = std::vector<Dihedral>;

  public:
    enum class Stereo {
      UNDEFINED, 
      ACHIRAL,   
      R,         
      S,         
    };

  private:
    template <typename Archive>
    void serialise(Archive &archive, const uint32_t version);

  public:
    INDIGOX_GENERIC_PIMPL_CLASS_DEFAULTS(Atom);
    INDIGOX_GENERIC_PIMPL_CLASS_OPERATORS(Atom, atm);

  private:
    Atom(const Molecule &molecule, const Element &element, double x, double y,
         double z, std::string name);

  public:
    int64_t NumBonds() const;

    int64_t NumAngles() const;

    int64_t NumDihedrals() const;

    bool HasType() const;

    const Element &GetElement() const;

    int32_t GetFormalCharge() const;

    double GetPartialCharge() const;

    int64_t GetTag() const;

    int64_t GetID() const;

    int32_t GetResidueID();

    std::string GetResidueName();

    int32_t GetChargeGroupID() const;

    int32_t GetImplicitCount() const;

    int32_t NumHydrogenBonds() const;
    int32_t NumHeavyAtomBonds() const;

    const Molecule &GetMolecule() const;

    const std::string &GetName() const;

    double GetX() const;

    double GetY() const;

    double GetZ() const;

    Stereo GetStereochemistry() const;

    const Eigen::Vector3d &GetPosition() const;

    int32_t AddImplicitHydrogen();

    int32_t RemoveImplicitHydrogen();

    void SetElement(const Element &e);

    void SetElement(std::string e);

    void SetElement(int32_t e);

    void SetFormalCharge(int32_t q);

    void SetChargeGroupID(int32_t id);

    void SetPartialCharge(double q);

    void SetImplicitCount(int32_t h);

    void SetTag(int32_t i);

    void SetName(std::string n);

    void SetPosition(double x, double y, double z);

    void SetStereochemistry(Stereo s);

  private:
    void AddBond(const Bond &b);

    void AddAngle(const Angle &a);

    void AddDihedral(const Dihedral &d);

    void RemoveBond(const Bond &b);

    void RemoveAngle(const Angle &a);

    void RemoveDihedral(const Dihedral &d);

  public:
    const AtomBonds &GetBonds() const;
    const AtomAngles &GetAngles() const;
    const AtomDihedrals &GetDihedrals() const;

    int64_t GetIndex() const;

    const FFAtom &GetType() const;

    void SetType(const FFAtom &type);

  private:
    void Reset();

  private:
    struct Impl;
    std::shared_ptr<Impl> m_data;
  };

  using AtomStereo = indigox::Atom::Stereo;
} // namespace indigox

#endif /* INDIGOX_CLASSES_ATOM_HPP */