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 addExtraComponents 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 std::string group() const

The group record is only available in CCP4 monomer library files. For CCD entries this value will always contain ‘non-polymer’

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