# Class compound

- Defined in File compound.hpp

## Class Documentation

class compound

  a class that contains information about a chemical compound. This information is derived from the CDD by default.

  To create compounds, you use the factory method. You can add your own compound definitions by calling the push_dictionary function and pass it a valid CCD formatted file.

  Public Functions

  inline std::string id() const

    Return the alphanumeric code for the chemical component.

  inline std::string name() const

    Return the name of the chemical component.

  inline std::string type() const

    Return the type of monomer.

  inline std::string formula() const

    Return the chemical formula of the chemical component.

  inline float formula_weight() const

    Return the formula mass of the chemical component in Daltons.

  inline int formal_charge() const

    Return the formal charge on the chemical component.

  inline const std::vector<compound_atom> &atoms() const

    Return the list of atoms for this compound.

  inline const std::vector<compound_bond> &bonds() const

    Return the list of bonds for this compound.

  compound_atom get_atom_by_atom_id(const std::string &atom_id) const

    Return the atom with id atom_id.

  bool atoms_bonded(const std::string &atomId_1, const std::string &atomId_2) const

    Return true if atomId_1 is bonded to atomId_2.

  float bond_length(const std::string &atomId_1, const std::string &atomId_2) const

    Return the bond length between atomId_1 and atomId_2.

  inline bool is_water() const

    < Return if the compound is actually a water

  bool is_peptide() const

    Return whether this compound has a type of either ‘peptide linking’ or ‘L-peptide linking’.

  bool is_base() const

    Return whether this compound has a type of either ‘DNA linking’ or ‘RNA linking’.

  inline char one_letter_code() const

    Return the one letter code to use in a canonical sequence. If unknown the value ‘\0’ is returned.

  inline std::string parent_id() const

    Return the parent id code in case a parent is specified (e.g. MET for MSE).