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
  52 namespace gmx
  53 {
  54 class MDLogger;
  55 }
  56 struct PreprocessResidue;
  57 struct t_symtab;
  58
  59 /*! \brief
  60  * Search for an entry in the rtp database.
  61  *
  62  * A mismatch of one character is allowed,
  63  * if there is only one nearly matching entry in the database,
  64  * a warning will be generated.
  65  *
  66  * \param[in] key The atomname to search for.
  67  * \param[in] rtpDBEntry Database with residue information.
  68  * \param[in] logger Logging object.
  69  * \returns The rtp residue name.
  70  */
  71 std::string searchResidueDatabase(const std::string&                     key,
  72                                   gmx::ArrayRef<const PreprocessResidue> rtpDBEntry,
  73                                   const gmx::MDLogger&                   logger);
  74
  75 /*! \brief
  76  * Returns matching entry in database.
  77  *
  78  * \param[in] rtpname Name of the entry looked for.
  79  * \param[in] rtpDBEntry Database to search.
  80  * \throws If the name can not be found in the database.
  81  */
  82 gmx::ArrayRef<const PreprocessResidue>::const_iterator
  83 getDatabaseEntry(const std::string& rtpname, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry);
  84
  85 /*! \brief
  86  * Read atom types into database.
  87  *
  88  * \param[in] ffdir Force field directory.
  89  * \param[in] tab Symbol table for names.
  90  * \returns Atom type database.
  91  */
  92 PreprocessingAtomTypes read_atype(const char* ffdir, t_symtab* tab);
  93
  94 /*! \brief
  95  * Read in database, append to exisiting.
  96  *
  97  * \param[in] resdb Name of database file.
  98  * \param[inout] rtpDBEntry Database to populate.
  99  * \param[inout] atype Atomtype information.
 100  * \param[inout] tab Symbol table for names.
 101  * \param[in] logger MDLogger interface.
 102  * \param[in] bAllowOverrideRTP If entries can be overwritten in the database.
 103  */
 104 void readResidueDatabase(const std::string&              resdb,
 105                          std::vector<PreprocessResidue>* rtpDBEntry,
 106                          PreprocessingAtomTypes*         atype,
 107                          t_symtab*                       tab,
 108                          const gmx::MDLogger&            logger,
 109                          bool                            bAllowOverrideRTP);
 110
 111 /*! \brief
 112  * Print out database.
 113  *
 114  * \param[in] out File to write to.
 115  * \param[in] rtpDBEntry Database to write out.
 116  * \param[in] atype Atom type information.
 117  */
 118 void print_resall(FILE*                                  out,
 119                   gmx::ArrayRef<const PreprocessResidue> rtpDBEntry,
 120                   const PreprocessingAtomTypes&          atype);
 121
 122 #endif