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38 #ifndef GMX_TOPOLOGY_MTOP_UTIL_H
39 #define GMX_TOPOLOGY_MTOP_UTIL_H
46 #include <boost/stl_interfaces/iterator_interface.hpp>
48 #include "gromacs/topology/topology.h"
49 #include "gromacs/utility/enumerationhelpers.h"
51 struct gmx_localtop_t;
57 // TODO All of the functions taking a const gmx_mtop * are deprecated
58 // and should be replaced by versions taking const gmx_mtop & when
59 // their callers are refactored similarly.
61 /* Counts the number of atoms of each type. State should be 0 for
62 * state A and 1 for state B types. typecount should have at
63 * least mtop->ffparams.atnr elements.
65 void gmx_mtop_count_atomtypes(const gmx_mtop_t& mtop, int state, int typecount[]);
67 /*!\brief Returns the total number of molecules in mtop
69 * \param[in] mtop The global topology
71 int gmx_mtop_num_molecules(const gmx_mtop_t& mtop);
73 /* Returns the total number of residues in mtop. */
74 int gmx_mtop_nres(const gmx_mtop_t& mtop);
78 //! Proxy object returned from AtomIterator
82 //! Default constructor.
83 AtomProxy(const AtomIterator* it) : it_(it) {}
84 //! Access current global atom number.
85 int globalAtomNumber() const;
86 //! Access current t_atom struct.
87 const t_atom& atom() const;
88 //! Access current name of the atom.
89 const char* atomName() const;
90 //! Access current name of the residue the atom is in.
91 const char* residueName() const;
92 //! Access current residue number.
93 int residueNumber() const;
94 //! Access current molecule type.
95 const gmx_moltype_t& moleculeType() const;
96 //! Access the position of the current atom in the molecule.
97 int atomNumberInMol() const;
100 const AtomIterator* it_;
104 * Object that allows looping over all atoms in an mtop.
107 public boost::stl_interfaces::proxy_iterator_interface<AtomIterator, std::forward_iterator_tag, t_atom, AtomProxy>
110 boost::stl_interfaces::proxy_iterator_interface<AtomIterator, std::forward_iterator_tag, t_atom, AtomProxy>;
113 //! Construct from topology and optionalally a global atom number.
114 explicit AtomIterator(const gmx_mtop_t& mtop, int globalAtomNumber = 0);
116 //! Prefix increment.
117 AtomIterator& operator++();
118 using Base:: operator++;
120 //! Equality comparison.
121 bool operator==(const AtomIterator& o) const;
123 //! Dereference operator. Returns proxy.
124 AtomProxy operator*() const { return { this }; }
128 const gmx_mtop_t* mtop_;
129 //! Current molecule block.
131 //! The atoms of the current molecule.
132 const t_atoms* atoms_;
133 //! The current molecule.
134 int currentMolecule_;
135 //! Current highest number for residues.
136 int highestResidueNumber_;
137 //! Current local atom number.
138 int localAtomNumber_;
139 //! Global current atom number.
140 int globalAtomNumber_;
142 friend class AtomProxy;
145 //! Range over all atoms of topology.
149 //! Default constructor.
150 explicit AtomRange(const gmx_mtop_t& mtop) : begin_(mtop), end_(mtop, mtop.natoms) {}
151 //! Iterator to begin of range.
152 AtomIterator& begin() { return begin_; }
153 //! Iterator to end of range.
154 AtomIterator& end() { return end_; }
157 AtomIterator begin_, end_;
162 //! Proxy object returned from IListIterator
166 //! Default constructor.
167 IListProxy(const IListIterator* it) : it_(it) {}
168 //! Access current global atom number.
169 const InteractionLists& list() const;
170 //! Access current molecule.
174 const IListIterator* it_;
178 * Object that allows looping over all atoms in an mtop.
180 class IListIterator :
181 public boost::stl_interfaces::proxy_iterator_interface<IListIterator, std::forward_iterator_tag, InteractionLists, IListProxy>
184 boost::stl_interfaces::proxy_iterator_interface<IListIterator, std::forward_iterator_tag, InteractionLists, IListProxy>;
187 //! Construct from topology.
188 explicit IListIterator(const gmx_mtop_t& mtop, size_t mblock = 0);
190 //! Prefix increment.
191 IListIterator& operator++();
192 using Base:: operator++;
194 //! Equality comparison.
195 bool operator==(const IListIterator& o) const;
197 //! Dereference operator. Returns proxy.
198 IListProxy operator*() const { return { this }; }
202 const gmx_mtop_t* mtop_;
203 //! Index of molecule block corresponding to the current location.
206 friend class IListProxy;
211 * Range over all interaction lists of topology.
213 * Includes the intermolecular interactions as the final element in the
219 //! Default constructor.
220 explicit IListRange(const gmx_mtop_t& mtop);
221 //! Iterator to begin of range.
222 IListIterator& begin() { return begin_; }
223 //! Iterator to end of range.
224 IListIterator& end() { return end_; }
227 IListIterator begin_, end_;
230 /* Abstract type for atom loop over atoms in all molecule blocks */
231 typedef struct gmx_mtop_atomloop_block* gmx_mtop_atomloop_block_t;
233 /* Initialize an atom loop over atoms in all molecule blocks the system.
235 gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t& mtop);
237 /* Loop to the next atom.
238 * When not at the end:
240 * sets the pointer atom to the t_atom struct of that atom
241 * and return the number of molecules corresponding to this atom.
242 * When at the end, destroys aloop and returns FALSE.
244 * gmx_mtop_atomloop_block_t aloop;
245 * aloop = gmx_mtop_atomloop_block_init(mtop)
246 * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
250 gmx_bool gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom** atom, int* nmol);
253 /* Returns the total number of interactions in the system of type ftype */
254 int gmx_mtop_ftype_count(const gmx_mtop_t& mtop, int ftype);
256 /* Returns the total number of interactions in the system with all interaction flags that are set in \p if_flags set */
257 int gmx_mtop_interaction_count(const gmx_mtop_t& mtop, int unsigned if_flags);
259 /* Returns the count of atoms for each particle type */
260 gmx::EnumerationArray<ParticleType, int> gmx_mtop_particletype_count(const gmx_mtop_t& mtop);
262 /* Returns a single t_atoms struct for the whole system */
263 t_atoms gmx_mtop_global_atoms(const gmx_mtop_t& mtop);
265 /*! \brief Return whether the atom with the given index is within a
266 * 1-4 interaction within the given molecule type and its charge is
269 * Some 1-4 interactions like F_COUL14 have the charges stored in the
270 * iparams list, but others do not. The commonly used F_LJ14 gets its
271 * charges from the topology, so we need more detailed checks for it,
272 * when FEP is active.
274 * \param[in] atomIndex Index within range [0, molt.nr)
275 * \param[in] molt Moleculetype to consider
276 * \return Whether this atom is in a 1-4 interaction and charge is perturbed
278 bool atomHasPerturbedChargeIn14Interaction(int atomIndex, const gmx_moltype_t& molt);
281 * Populate a 'local' topology for the whole system.
283 * When freeEnergyInteractionsAtEnd == true, the free energy interactions will
284 * be sorted to the end.
286 * \param[in] mtop The global topology used to populate the local one.
287 * \param[in,out] top New local topology populated from global \p mtop.
288 * \param[in] freeEnergyInteractionsAtEnd If free energy interactions will be sorted.
290 void gmx_mtop_generate_local_top(const gmx_mtop_t& mtop, gmx_localtop_t* top, bool freeEnergyInteractionsAtEnd);
293 /*!\brief Creates and returns a struct with begin/end atom indices of all molecules
295 * \param[in] mtop The global topology
296 * \returns A RangePartitioning object with numBlocks() equal to the number
297 * of molecules and atom indices such that molecule m contains atoms a with:
298 * index[m] <= a < index[m+1].
300 gmx::RangePartitioning gmx_mtop_molecules(const gmx_mtop_t& mtop);
303 * Returns the index range from residue begin to end for each residue in a molecule block.
305 * Note that residues will always have consecutive atoms numbers internally.
307 * \param[in] moltype Molecule Type to parse for start and end.
308 * \returns Vector of ranges for all residues.
310 std::vector<gmx::Range<int>> atomRangeOfEachResidue(const gmx_moltype_t& moltype);
312 /* Converts a gmx_mtop_t struct to t_topology.
314 * If the lifetime of the returned topology should be longer than that
315 * of mtop, your need to pass freeMtop==true.
316 * If freeMTop == true, memory related to mtop will be freed so that done_top()
317 * on the result value will free all memory.
318 * If freeMTop == false, mtop and the return value will share some of their
319 * memory, and there is currently no way to consistently free all the memory.
321 t_topology gmx_mtop_t_to_t_topology(gmx_mtop_t* mtop, bool freeMTop);
323 /*! \brief Get vector of atoms indices from topology
325 * This function returns the indices of all particles with type
326 * eptAtom, that is shells, vsites etc. are left out.
327 * \param[in] mtop Molecular topology
328 * \returns Vector that will be filled with the atom indices
330 std::vector<int> get_atom_index(const gmx_mtop_t& mtop);
332 /*! \brief Converts a t_atoms struct to an mtop struct
334 * All pointers contained in \p atoms will be copied into \p mtop.
335 * Note that this will produce one moleculetype encompassing the whole system.
337 * \param[in] symtab The symbol table
338 * \param[in] name Pointer to the name for the topology
339 * \param[in] atoms The atoms to convert
340 * \param[out] mtop The molecular topology output containing atoms.
342 void convertAtomsToMtop(t_symtab* symtab, char** name, t_atoms* atoms, gmx_mtop_t* mtop);
344 //! Checks and returns whether non-bonded interactions are perturbed for free-energy calculations
345 bool haveFepPerturbedNBInteractions(const gmx_mtop_t& mtop);
347 //! Checks whether masses are perturbed for free-energy calculations
348 bool haveFepPerturbedMasses(const gmx_mtop_t& mtop);
350 //! Checks whether masses are perturbed for free-energy calculations in SETTLE interactions
351 bool haveFepPerturbedMassesInSettles(const gmx_mtop_t& mtop);
353 //! Checks whether constraints are perturbed for free-energy calculations
354 bool havePerturbedConstraints(const gmx_mtop_t& mtop);