Class residue

Inheritance Relationships

Derived Types

Class Documentation

class residue

The class residue is a collection of atoms forming a molecule.

This class is used to store ligand e.g. Derived classes are monomer and sugar.

Subclassed by cif::mm::monomer, cif::mm::sugar

Public Functions

inline residue(structure &structure, const std::string &compoundID, const std::string &asymID, int seqID, const std::string &authAsymID, const std::string &authSeqID, const std::string &pdbInsCode)

Construct a new residue object based on key items.

residue(structure &structure, const std::vector<atom> &atoms)

Construct a new residue in structure with the atoms in atoms

std::string get_entity_id() const

Return the entity_id of this residue

EntityType entity_type() const

Return the entity type of this residue

inline const std::string &get_asym_id() const

Return the asym_id.

inline int get_seq_id() const

Return the seq_id.

inline const std::string get_auth_asym_id() const

Return the auth_asym_id.

inline const std::string get_auth_seq_id() const

Return the auth_seq_id.

inline std::string get_pdb_ins_code() const

Return the pdb_ins_code.

inline const std::string &get_compound_id() const

Return the compound_id.

inline void set_compound_id(const std::string &id)

Set the compound_id to id.

inline structure *get_structure() const

Return the structure this residue belongs to

inline std::vector<atom> &atoms()

Return a list of the atoms for this residue

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

Return a const list of the atoms for this residue

void add_atom(atom &atom)

Add atom atom to the atoms in this residue

std::vector<atom> unique_atoms() const

Unique atoms returns only the atoms without alternates and the first of each alternate atom id.

atom get_atom_by_atom_id(const std::string &atomID) const

Return the atom with atom_id atomID.

std::vector<atom> get_atoms_by_id(const std::string &atomID) const

Return the list of atoms having ID atomID.

This includes all alternate atoms with this ID whereas get_atom_by_atom_id only returns the first unique atom

bool is_entity() const

Is this residue a single entity?

inline bool is_water() const

Is this residue a water molecule?

bool has_alternate_atoms() const

Return true if this residue has alternate atoms.

std::set<std::string> get_alternate_ids() const

Return the list of unique alt ID’s present in this residue.

std::set<std::string> get_atom_ids() const

Return the list of unique atom ID’s.

std::tuple<point, float> center_and_radius() const

Return a tuple containing the center location and the radius for the atoms of this residue.

inline bool operator==(const residue &rhs) const

Return true if this residue is equal to rhs.

Friends

friend class structure
friend std::ostream &operator<<(std::ostream &os, const residue &res)

Write the residue res to the std::ostream os.