src/gromacs/gmxpreprocess/resall.h

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  37 /*! \file
  38  * \internal \brief
  39  * Methods to get residue information during preprocessing.
  40  */
  41 #ifndef GMX_GMXPREPROCESS_RESALL_H
  42 #define GMX_GMXPREPROCESS_RESALL_H
  43
  44 #include <cstdio>
  45
  46 #include <vector>
  47
  48 #include "gromacs/utility/arrayref.h"
  49
  50 class PreprocessingAtomTypes;
  51 struct PreprocessResidue;
  52 struct t_symtab;
  53
  54 /*! \brief
  55  * Search for an entry in the rtp database.
  56  *
  57  * A mismatch of one character is allowed,
  58  * if there is only one nearly matching entry in the database,
  59  * a warning will be generated.
  60  *
  61  * \param[in] key The atomname to search for.
  62  * \param[in] rtpDBEntry Database with residue information.
  63  * \returns The rtp residue name.
  64  */
  65 std::string searchResidueDatabase(const std::string &key, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry);
  66
  67 /*! \brief
  68  * Returns matching entry in database.
  69  *
  70  * \param[in] rtpname Name of the entry looked for.
  71  * \param[in] rtpDBEntry Database to search.
  72  * \throws If the name can not be found in the database.
  73  */
  74 gmx::ArrayRef<const PreprocessResidue>::const_iterator
  75 getDatabaseEntry(const std::string &rtpname, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry);
  76
  77 /*! \brief
  78  * Read atom types into database.
  79  *
  80  * \param[in] ffdir Force field directory.
  81  * \param[in] tab Symbol table for names.
  82  * \returns Atom type database.
  83  */
  84 PreprocessingAtomTypes read_atype(const char *ffdir, t_symtab *tab);
  85
  86 /*! \brief
  87  * Read in database, append to exisiting.
  88  *
  89  * \param[in] resdb Name of database file.
  90  * \param[inout] rtpDBEntry Database to populate.
  91  * \param[inout] atype Atomtype information.
  92  * \param[inout] tab Symbol table for names.
  93  * \param[in] bAllowOverrideRTP If entries can be overwritten in the database.
  94  */
  95 void readResidueDatabase(const std::string               &resdb,
  96                          std::vector<PreprocessResidue>  *rtpDBEntry,
  97                          PreprocessingAtomTypes          *atype,
  98                          t_symtab                        *tab,
  99                          bool                             bAllowOverrideRTP);
 100
 101 /*! \brief
 102  * Print out database.
 103  *
 104  * \param[in] out File to write to.
 105  * \param[in] rtpDBEntry Database to write out.
 106  * \param[in] atype Atom type information.
 107  */
 108 void print_resall(FILE *out, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry,
 109                   const PreprocessingAtomTypes &atype);
 110
 111 #endif