
.. _program_listing_file_cif++_model.hpp:

Program Listing for File model.hpp
==================================

|exhale_lsh| :ref:`Return to documentation for file <file_cif++_model.hpp>` (``cif++/model.hpp``)

.. |exhale_lsh| unicode:: U+021B0 .. UPWARDS ARROW WITH TIP LEFTWARDS

.. code-block:: cpp

   /*-
    * SPDX-License-Identifier: BSD-2-Clause
    *
    * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
    *
    * Redistribution and use in source and binary forms, with or without
    * modification, are permitted provided that the following conditions are met:
    *
    * 1. Redistributions of source code must retain the above copyright notice, this
    *    list of conditions and the following disclaimer
    * 2. Redistributions in binary form must reproduce the above copyright notice,
    *    this list of conditions and the following disclaimer in the documentation
    *    and/or other materials provided with the distribution.
    *
    * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
    * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
    * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
    * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
    * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
    * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
    * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
    * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
    * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    */
   
   #pragma once
   
   #include "cif++/atom_type.hpp"
   #include "cif++/datablock.hpp"
   #include "cif++/point.hpp"
   
   #include <memory>
   #include <numeric>
   
   #if __cpp_lib_format
   #include <format>
   #endif
   
   namespace cif::mm
   {
   
   class atom;
   class residue;
   class monomer;
   class polymer;
   class structure;
   
   // --------------------------------------------------------------------
   
   class atom
   {
     private:
       struct atom_impl : public std::enable_shared_from_this<atom_impl>
       {
           atom_impl(const datablock &db, std::string_view id)
               : m_db(db)
               , m_cat(db["atom_site"])
               , m_id(id)
           {
               auto r = row();
               if (r)
                   tie(m_location.m_x, m_location.m_y, m_location.m_z) = r.get("Cartn_x", "Cartn_y", "Cartn_z");
           }
   
           // constructor for a symmetry copy of an atom
           atom_impl(const atom_impl &impl, const point &loc, const std::string &sym_op)
               : atom_impl(impl)
           {
               m_location = loc;
               m_symop = sym_op;
           }
   
           atom_impl(const atom_impl &i) = default;
   
           void prefetch();
   
           int compare(const atom_impl &b) const;
   
           // bool getAnisoU(float anisou[6]) const;
   
           int get_charge() const;
   
           void moveTo(const point &p);
   
           // const compound *compound() const;
   
           std::string get_property(std::string_view name) const;
           int get_property_int(std::string_view name) const;
           float get_property_float(std::string_view name) const;
   
           void set_property(const std::string_view name, const std::string &value);
   
           row_handle row()
           {
               return m_cat[{ { "id", m_id } }];
           }
   
           const row_handle row() const
           {
               return m_cat[{ { "id", m_id } }];
           }
   
           row_handle row_aniso()
           {
               auto cat = m_db.get("atom_site_anisotrop");
               return cat ? cat->operator[]({ { "id", m_id } }) : row_handle{};
           }
   
           const row_handle row_aniso() const
           {
               auto cat = m_db.get("atom_site_anisotrop");
               return cat ? cat->operator[]({ { "id", m_id } }) : row_handle{};
           }
   
           const datablock &m_db;
           const category &m_cat;
           std::string m_id;
           point m_location;
           std::string m_symop = "1_555";
       };
     public:
       atom() {}
   
       atom(std::shared_ptr<atom_impl> impl)
           : m_impl(impl)
       {
       }
   
       atom(const atom &rhs)
           : m_impl(rhs.m_impl)
       {
       }
   
       atom(const datablock &db, const row_handle &row)
           : atom(std::make_shared<atom_impl>(db, row["id"].as<std::string>()))
       {
       }
   
       atom(const atom &rhs, const point &symmmetry_location, const std::string &symmetry_operation)
           : atom(std::make_shared<atom_impl>(*rhs.m_impl, symmmetry_location, symmetry_operation))
       {
       }
   
       explicit operator bool() const { return (bool)m_impl; }
   
       atom &operator=(const atom &rhs) = default;
   
       std::string get_property(std::string_view name) const
       {
           if (not m_impl)
               throw std::logic_error("Error trying to fetch a property from an uninitialized atom");
           return m_impl->get_property(name);
       }
   
       int get_property_int(std::string_view name) const
       {
           if (not m_impl)
               throw std::logic_error("Error trying to fetch a property from an uninitialized atom");
           return m_impl->get_property_int(name);
       }
   
       float get_property_float(std::string_view name) const
       {
           if (not m_impl)
               throw std::logic_error("Error trying to fetch a property from an uninitialized atom");
           return m_impl->get_property_float(name);
       }
   
       void set_property(const std::string_view name, const std::string &value)
       {
           if (not m_impl)
               throw std::logic_error("Error trying to modify an uninitialized atom");
           m_impl->set_property(name, value);
       }
   
       template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
       void set_property(const std::string_view name, const T &value)
       {
           set_property(name, std::to_string(value));
       }
   
       const std::string &id() const { return impl().m_id; }
   
       cif::atom_type get_type() const { return atom_type_traits(get_property("type_symbol")).type(); }
   
       point get_location() const { return impl().m_location; }
   
       void set_location(point p)
       {
           if (not m_impl)
               throw std::logic_error("Error trying to modify an uninitialized atom");
           m_impl->moveTo(p);
       }
   
       void translate(point t)
       {
           set_location(get_location() + t);
       }
   
       void rotate(quaternion q)
       {
           auto loc = get_location();
           loc.rotate(q);
           set_location(loc);
       }
   
       void rotate(quaternion q, point p)
       {
           auto loc = get_location();
           loc.rotate(q, p);
           set_location(loc);
       }
   
       void translate_and_rotate(point t, quaternion q)
       {
           auto loc = get_location();
           loc += t;
           loc.rotate(q);
           set_location(loc);
       }
   
       void translate_rotate_and_translate(point t1, quaternion q, point t2)
       {
           auto loc = get_location();
           loc += t1;
           loc.rotate(q);
           loc += t2;
           set_location(loc);
       }
   
       const row_handle get_row() const { return impl().row(); }
   
       const row_handle get_row_aniso() const { return impl().row_aniso(); }
   
       bool is_symmetry_copy() const { return impl().m_symop != "1_555"; }
   
       std::string symmetry() const { return impl().m_symop; }
   
       bool is_water() const
       {
           auto comp_id = get_label_comp_id();
           return comp_id == "HOH" or comp_id == "H2O" or comp_id == "WAT";
       }
   
       int get_charge() const { return impl().get_charge(); }
   
       float get_occupancy() const { return get_property_float("occupancy"); }
   
       // specifications
   
       std::string get_label_asym_id() const { return get_property("label_asym_id"); }     
       int get_label_seq_id() const { return get_property_int("label_seq_id"); }           
       std::string get_label_atom_id() const { return get_property("label_atom_id"); }     
       std::string get_label_alt_id() const { return get_property("label_alt_id"); }       
       std::string get_label_comp_id() const { return get_property("label_comp_id"); }     
       std::string get_label_entity_id() const { return get_property("label_entity_id"); } 
   
       std::string get_auth_asym_id() const { return get_property("auth_asym_id"); }      
       std::string get_auth_seq_id() const { return get_property("auth_seq_id"); }        
       std::string get_auth_atom_id() const { return get_property("auth_atom_id"); }      
       std::string get_auth_alt_id() const { return get_property("auth_alt_id"); }        
       std::string get_auth_comp_id() const { return get_property("auth_comp_id"); }      
       std::string get_pdb_ins_code() const { return get_property("pdbx_PDB_ins_code"); } 
   
       bool is_alternate() const
       {
           if (auto alt_id = get_label_alt_id(); alt_id.empty() or alt_id == ".")
               return false;
           return true;
       }
   
       std::string pdb_id() const
       {
           return get_label_comp_id() + '_' + get_auth_asym_id() + '_' + get_auth_seq_id() + get_pdb_ins_code();
       }
   
       bool operator==(const atom &rhs) const
       {
           if (m_impl == rhs.m_impl)
               return true;
   
           if (not(m_impl and rhs.m_impl))
               return false;
   
           return &m_impl->m_db == &rhs.m_impl->m_db and m_impl->m_id == rhs.m_impl->m_id;
       }
   
       bool operator!=(const atom &rhs) const
       {
           return not operator==(rhs);
       }
   
       bool is_back_bone() const
       {
           auto atomID = get_label_atom_id();
           return atomID == "N" or atomID == "O" or atomID == "C" or atomID == "CA";
       }
   
       void swap(atom &b)
       {
           std::swap(m_impl, b.m_impl);
       }
   
       int compare(const atom &b) const { return impl().compare(*b.m_impl); }
   
       bool operator<(const atom &rhs) const
       {
           return compare(rhs) < 0;
       }
   
       friend std::ostream &operator<<(std::ostream &os, const atom &atom);
   
     private:
       friend class structure;
   
       const atom_impl &impl() const
       {
           if (not m_impl)
               throw std::runtime_error("Uninitialized atom, not found?");
           return *m_impl;
       }
   
       std::shared_ptr<atom_impl> m_impl;
   };
   
   inline void swap(atom &a, atom &b)
   {
       a.swap(b);
   }
   
   inline float distance(const atom &a, const atom &b)
   {
       return distance(a.get_location(), b.get_location());
   }
   
   inline float distance_squared(const atom &a, const atom &b)
   {
       return distance_squared(a.get_location(), b.get_location());
   }
   
   // --------------------------------------------------------------------
   
   enum class EntityType
   {
       Polymer,    
       NonPolymer, 
       Macrolide,  
       Water,      
       Branched    
   };
   
   // --------------------------------------------------------------------
   
   class residue
   {
     public:
       friend class structure;
   
       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)
           : m_structure(&structure)
           , m_compound_id(compoundID)
           , m_asym_id(asymID)
           , m_seq_id(seqID)
           , m_auth_asym_id(authAsymID)
           , m_auth_seq_id(authSeqID)
           , m_pdb_ins_code(pdbInsCode)
       {
       }
   
       residue(structure &structure, const std::vector<atom> &atoms);
   
       residue(const residue &rhs) = delete;
       residue &operator=(const residue &rhs) = delete;
   
       residue(residue &&rhs) = default;
       residue &operator=(residue &&rhs) = default;
   
       virtual ~residue() = default;
       std::string get_entity_id() const;
   
       EntityType entity_type() const;
   
       const std::string &get_asym_id() const { return m_asym_id; } 
       int get_seq_id() const { return m_seq_id; }                  
   
       const std::string get_auth_asym_id() const { return m_auth_asym_id; } 
       const std::string get_auth_seq_id() const { return m_auth_seq_id; }   
       std::string get_pdb_ins_code() const { return m_pdb_ins_code; }       
   
       const std::string &get_compound_id() const { return m_compound_id; } 
       void set_compound_id(const std::string &id) { m_compound_id = id; }  
   
       structure *get_structure() const { return m_structure; }
   
       std::vector<atom> &atoms()
       {
           return m_atoms;
       }
   
       const std::vector<atom> &atoms() const
       {
           return m_atoms;
       }
   
       void add_atom(atom &atom);
   
       std::vector<atom> unique_atoms() const;
   
       atom get_atom_by_atom_id(const std::string &atomID) const;
   
       std::vector<atom> get_atoms_by_id(const std::string &atomID) const;
   
       bool is_entity() const;
   
       bool is_water() const { return m_compound_id == "HOH"; }
   
       bool has_alternate_atoms() const;
   
       bool has_alternate_atoms_for(const std::string &atomID) const;
   
       std::set<std::string> get_alternate_ids() const;
   
       std::set<std::string> get_atom_ids() const;
   
       std::tuple<point, float> center_and_radius() const;
   
       friend std::ostream &operator<<(std::ostream &os, const residue &res);
   
       bool operator==(const residue &rhs) const
       {
           return this == &rhs or (m_structure == rhs.m_structure and
                                      m_seq_id == rhs.m_seq_id and
                                      m_asym_id == rhs.m_asym_id and
                                      m_compound_id == rhs.m_compound_id and
                                      m_auth_seq_id == rhs.m_auth_seq_id);
       }
   
       virtual atom create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation);
   
     protected:
       residue() {}
   
       structure *m_structure = nullptr;
       std::string m_compound_id, m_asym_id;
       int m_seq_id = 0;
       std::string m_auth_asym_id, m_auth_seq_id, m_pdb_ins_code;
       std::vector<atom> m_atoms;
   };
   
   // --------------------------------------------------------------------
   
   class monomer : public residue
   {
     public:
       monomer(const monomer &rhs) = delete;
       monomer &operator=(const monomer &rhs) = delete;
   
       monomer(monomer &&rhs);
   
       monomer &operator=(monomer &&rhs);
   
       monomer(const polymer &polymer, std::size_t index, int seqID, const std::string &authSeqID,
           const std::string &pdbInsCode, const std::string &compoundID);
   
       bool is_first_in_chain() const; 
       bool is_last_in_chain() const;  
   
       // convenience
       bool has_alpha() const; 
       bool has_kappa() const; 
   
       // Assuming this is really an amino acid...
   
       float phi() const;   
       float psi() const;   
       float alpha() const; 
       float kappa() const; 
       float tco() const;   
       float omega() const; 
   
       // torsion angles
       std::size_t nr_of_chis() const; 
       float chi(std::size_t i) const; 
   
       bool is_cis() const; 
   
       bool is_complete() const;
   
       bool has_alternate_backbone_atoms() const;
   
       atom CAlpha() const { return get_atom_by_atom_id("CA"); } 
       atom C() const { return get_atom_by_atom_id("C"); }       
       atom N() const { return get_atom_by_atom_id("N"); }       
       atom O() const { return get_atom_by_atom_id("O"); }       
       atom H() const { return get_atom_by_atom_id("H"); }       
   
       bool is_bonded_to(const monomer &rhs) const
       {
           return this != &rhs and are_bonded(*this, rhs);
       }
   
       static bool are_bonded(const monomer &a, const monomer &b, float errorMargin = 0.5f);
   
       static bool is_cis(const monomer &a, const monomer &b);
   
       static float omega(const monomer &a, const monomer &b);
   
       float chiral_volume() const;
   
       bool operator==(const monomer &rhs) const
       {
           return m_polymer == rhs.m_polymer and m_index == rhs.m_index;
       }
   
       atom create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation) override;
   
     private:
       const polymer *m_polymer;
       std::size_t m_index;
   };
   
   // --------------------------------------------------------------------
   
   class polymer : public std::vector<monomer>
   {
     public:
       polymer(structure &s, const std::string &entityID, const std::string &asymID, const std::string &auth_asym_id);
   
       polymer(const polymer &) = delete;
       polymer &operator=(const polymer &) = delete;
   
       structure *get_structure() const { return m_structure; } 
   
       std::string get_asym_id() const { return m_asym_id; }           
       std::string get_auth_asym_id() const { return m_auth_asym_id; } 
       std::string get_entity_id() const { return m_entity_id; }       
   
     private:
       structure *m_structure;
       std::string m_entity_id;
       std::string m_asym_id;
       std::string m_auth_asym_id;
   };
   
   // --------------------------------------------------------------------
   // sugar and branch, to describe glycosylation sites
   
   class branch;
   
   class sugar : public residue
   {
     public:
       sugar(branch &branch, const std::string &compoundID,
           const std::string &asymID, int authSeqID);
   
       sugar(sugar &&rhs);
       sugar &operator=(sugar &&rhs);
       int num() const
       {
           int result;
           auto r = std::from_chars(m_auth_seq_id.data(), m_auth_seq_id.data() + m_auth_seq_id.length(), result);
           if ((bool)r.ec)
               throw std::runtime_error("The auth_seq_id should be a number for a sugar");
           return result;
       }
   
       std::string name() const;
   
       atom get_link() const { return m_link; }
   
       void set_link(atom link) { m_link = link; }
   
       std::size_t get_link_nr() const
       {
           std::size_t result = 0;
           if (m_link)
               result = m_link.get_property_int("auth_seq_id");
           return result;
       }
   
       atom add_atom(row_initializer atom_info);
   
     private:
       branch *m_branch;
       atom m_link;
   };
   
   class branch : public std::vector<sugar>
   {
     public:
       branch(structure &structure, const std::string &asym_id, const std::string &entity_id);
   
       branch(const branch &) = delete;
       branch &operator=(const branch &) = delete;
   
       branch(branch &&) = default;
       branch &operator=(branch &&) = default;
       void link_atoms();
   
       std::string name() const;
   
       float weight() const;
   
       std::string get_asym_id() const { return m_asym_id; }     
       std::string get_entity_id() const { return m_entity_id; } 
   
       structure &get_structure() { return *m_structure; }       
       structure &get_structure() const { return *m_structure; } 
   
       sugar &get_sugar_by_num(int nr);
   
       const sugar &get_sugar_by_num(int nr) const
       {
           return const_cast<branch *>(this)->get_sugar_by_num(nr);
       }
   
       sugar &construct_sugar(const std::string &compound_id);
   
       sugar &construct_sugar(const std::string &compound_id, const std::string &atom_id,
           int linked_sugar_nr, const std::string &linked_atom_id);
   
     private:
       friend sugar;
   
       std::string name(const sugar &s) const;
   
       structure *m_structure;
       std::string m_asym_id, m_entity_id;
   };
   
   // --------------------------------------------------------------------
   
   enum class StructureOpenOptions
   {
       SkipHydrogen = 1 << 0 
   };
   
   constexpr inline bool operator&(StructureOpenOptions a, StructureOpenOptions b)
   {
       return static_cast<int>(a) bitand static_cast<int>(b);
   }
   
   // --------------------------------------------------------------------
   
   class structure
   {
     public:
       structure(file &p, std::size_t modelNr = 1, StructureOpenOptions options = {});
   
       structure(datablock &db, std::size_t modelNr = 1, StructureOpenOptions options = {});
   
       structure(structure &&s) = default;
       // structures cannot be copied.
   
       structure(const structure &) = delete;
       structure &operator=(const structure &) = delete;
       ~structure() = default;
   
       std::size_t get_model_nr() const { return m_model_nr; }
   
       const std::vector<atom> &atoms() const { return m_atoms; }
   
       EntityType get_entity_type_for_entity_id(const std::string entityID) const; 
       EntityType get_entity_type_for_asym_id(const std::string asymID) const;     
   
       const std::list<polymer> &polymers() const { return m_polymers; } 
       std::list<polymer> &polymers() { return m_polymers; }             
   
       polymer &get_polymer_by_asym_id(const std::string &asymID);            
       const polymer &get_polymer_by_asym_id(const std::string &asymID) const 
       {
           return const_cast<structure *>(this)->get_polymer_by_asym_id(asymID);
       }
   
       const std::list<branch> &branches() const { return m_branches; } 
       std::list<branch> &branches() { return m_branches; }             
   
       branch &get_branch_by_asym_id(const std::string &asymID);             
       const branch &get_branch_by_asym_id(const std::string &asymID) const; 
   
       const std::vector<residue> &non_polymers() const { return m_non_polymers; } 
   
       bool has_atom_id(const std::string &id) const;    
       atom get_atom_by_id(const std::string &id) const; 
   
       atom get_atom_by_label(const std::string &atomID, const std::string &asymID,
           const std::string &compID, int seqID, const std::string &altID = "");
   
       atom get_atom_by_position(point p) const;
   
       atom get_atom_by_position_and_type(point p, std::string_view type, std::string_view res_type) const;
   
       residue &create_residue(const std::vector<atom> &atoms);
   
       residue &get_residue(const std::string &asymID)
       {
           return get_residue(asymID, 0, "");
       }
   
       const residue &get_residue(const std::string &asymID) const
       {
           return get_residue(asymID, 0, "");
       }
   
       residue &get_residue(const std::string &asymID, int seqID, const std::string &authSeqID);
   
       const residue &get_residue(const std::string &asymID, int seqID, const std::string &authSeqID) const
       {
           return const_cast<structure *>(this)->get_residue(asymID, seqID, authSeqID);
       }
   
       residue &get_residue(const std::string &asymID, const std::string &compID, int seqID, const std::string &authSeqID);
   
       const residue &get_residue(const std::string &asymID, const std::string &compID, int seqID, const std::string &authSeqID) const
       {
           return const_cast<structure *>(this)->get_residue(asymID, compID, seqID, authSeqID);
       }
   
       residue &get_residue(const atom &atom)
       {
           return get_residue(atom.get_label_asym_id(), atom.get_label_comp_id(), atom.get_label_seq_id(), atom.get_auth_seq_id());
       }
   
       const residue &get_residue(const atom &atom) const
       {
           return get_residue(atom.get_label_asym_id(), atom.get_label_comp_id(), atom.get_label_seq_id(), atom.get_auth_seq_id());
       }
   
       // Actions. Originally a lot more actions were expected here
   
       void remove_atom(atom &a)
       {
           remove_atom(a, true);
       }
   
       void swap_atoms(atom a1, atom a2); 
       void move_atom(atom a, point p);   
   
       void change_residue(residue &res, const std::string &newcompound,
           const std::vector<std::tuple<std::string, std::string>> &remappedAtoms);
   
       void remove_residue(const std::string &asym_id, int seq_id, const std::string &auth_seq_id);
   
       std::string create_non_poly_entity(const std::string &mon_id);
   
       std::string create_non_poly(const std::string &entity_id, const std::vector<atom> &atoms);
   
       std::string create_non_poly(const std::string &entity_id, std::vector<row_initializer> atoms);
   
       void create_water(row_initializer atom);
   
       branch &create_branch();
   
       // /// \brief Create a new (sugar) branch with one first NAG containing atoms constructed from \a atoms
       // branch &create_branch(std::vector<row_initializer> atoms);
   
       // /// \brief Extend an existing (sugar) branch identified by \a asymID with one sugar containing atoms constructed from \a atom_info
       // ///
       // /// \param asym_id      The asym id of the branch to extend
       // /// \param atom_info    Array containing the info for the atoms to construct for the new sugar
       // /// \param link_sugar   The sugar to link to, note: this is the sugar number (1 based)
       // /// \param link_atom    The atom id of the atom linked in the sugar
       // branch &extend_branch(const std::string &asym_id, std::vector<row_initializer> atom_info,
       //  int link_sugar, const std::string &link_atom);
   
       void remove_branch(branch &branch);
   
       void remove_residue(residue &res);
   
       void translate(point t);
   
       void rotate(quaternion t);
   
       void translate_and_rotate(point t, quaternion q);
   
       void translate_rotate_and_translate(point t1, quaternion q, point t2);
   
       void cleanup_empty_categories();
   
       category &get_category(std::string_view name) const
       {
           return m_db[name];
       }
   
       datablock &get_datablock() const
       {
           return m_db;
       }
   
       void validate_atoms() const;
   
       template <typename... Args>
       atom &emplace_atom(Args &...args)
       {
           return emplace_atom(atom{ std::forward<Args>(args)... });
       }
   
       atom &emplace_atom(atom &&atom);
   
       void reorder_atoms();
   
     private:
       friend polymer;
       friend residue;
   
       void load_atoms_for_model(StructureOpenOptions options);
   
       std::string insert_compound(const std::string &compoundID, bool is_entity);
   
       std::string create_entity_for_branch(branch &branch);
   
       void load_data();
   
       void remove_atom(atom &a, bool removeFromResidue);
       void remove_sugar(sugar &sugar);
   
       datablock &m_db;
       std::size_t m_model_nr;
       std::vector<atom> m_atoms;
       std::vector<std::size_t> m_atom_index;
       std::list<polymer> m_polymers;
       std::list<branch> m_branches;
       std::vector<residue> m_non_polymers;
   };
   
   } // namespace cif::mm
