Class branch

Defined in File model.hpp

Inheritance Relationships

Base Type

public std::vector< sugar >

Class Documentation

class branch : public std::vector<sugar>

A branch is a list of sugars.

A list is how it is stored, but a branch is like a branch in a tree, with potentially lots of sub branches. Each sugar is linked to a sugar up in the branch with its (almost always) C1 atom.

Public Functions

branch(structure &structure, const std::string &asym_id, const std::string &entity_id): constructor

branch(const branch&) = delete

branch &operator=(const branch&) = delete

void link_atoms(): Update the link atoms in all sugars in this branch.

std::string name() const: Return the name of the branch.

float weight() const: Return the weight of the branch based on the formulae of the sugars.

inline std::string get_asym_id() const: Return the asym_id.

inline std::string get_entity_id() const: Return the entity_id.

inline structure &get_structure(): Return the structure.

inline structure &get_structure() const: Return the structure.

sugar &get_sugar_by_num(int nr): Return a reference to the sugar with number num.

inline const sugar &get_sugar_by_num(int nr) const: Return a const reference to the sugar with number num.

sugar &construct_sugar(const std::string &compound_id): Construct a new sugar with compound ID compound_id in this branch and return a reference to the newly created sugar. Use this to create a first sugar in a branch.

sugar &construct_sugar(const std::string &compound_id, const std::string &atom_id, int linked_sugar_nr, const std::string &linked_atom_id): Construct a new sugar with compound ID compound_id in this branch and return a reference to the newly created sugar. The newly created sugar will be connected to an already created sugar in the branch using the information in atom_id, linked_sugar_nr and linked_atom_id.