src/gromacs/gmxpreprocess/genhydro.h

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  37
  38 #ifndef GMX_GMXPREPROCESS_GENHYDRO_H
  39 #define GMX_GMXPREPROCESS_GENHYDRO_H
  40
  41 #include "gromacs/math/vectypes.h"
  42 #include "gromacs/utility/arrayref.h"
  43
  44 struct t_atoms;
  45 struct t_symtab;
  46 struct MoleculePatchDatabase;
  47
  48 /*! \brief
  49  * Generate hydrogen atoms and N and C terminal patches.
  50  *
  51  * \param[inout] initialAtoms The input atoms data structure to be modified.
  52  * \param[inout] localAtoms The extra atoms for reassigning the new entries.
  53  * \param[inout] xptr Coordinates to be updated with those for new atoms.
  54  * \param[in] globalPatches The atom modifications to use.
  55  * \param[inout] symtab Global symbol table for atom names.
  56  * \param[in] nterpairs Number of termini pairs in the molecule.
  57  * \param[in] ntdb Entries for N-terminus in each chain, each entry can be valid or nullptr.
  58  * \param[in] ctdb Entries for C-terminus in each cahin, each entry can be valid or nullptr.
  59  * \param[in] rN Residue number of the N-terminus of each chain.
  60  * \param[in] rC Residue number of the C-terminus of each chain.
  61  * \param[in] bMissing If routine should continue if atoms are not found.
  62  * \returns New total number of atoms.
  63  */
  64 int add_h(t_atoms**                                   initialAtoms,
  65           t_atoms**                                   localAtoms,
  66           std::vector<gmx::RVec>*                     xptr,
  67           gmx::ArrayRef<const MoleculePatchDatabase>  globalPatches,
  68           t_symtab*                                   symtab,
  69           int                                         nterpairs,
  70           gmx::ArrayRef<MoleculePatchDatabase* const> ntdb,
  71           gmx::ArrayRef<MoleculePatchDatabase* const> ctdb,
  72           gmx::ArrayRef<const int>                    rN,
  73           gmx::ArrayRef<const int>                    rC,
  74           bool                                        bMissing);
  75 #endif