Class compound

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
inline std::string parent_id() const

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