Class residue

Defined in File model.hpp

Inheritance Relationships

Derived Types

public cif::mm::monomer (Class monomer)
public cif::mm::sugar (Class sugar)

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.

bool has_alternate_atoms_for(const std::string &atomID) const: Return true if this residue has alternate atoms for the atom atomID.

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.

virtual atom create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation)

Create a new atom and add it to the list.

Returns: newly created atom

Friends

friend class structure

friend std::ostream &operator<<(std::ostream &os, const residue &res): Write the residue res to the std::ostream os.