src/gromacs/topology/residuetypes.h

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  35 #ifndef GMX_TOPOLOGY_RESIDUETYPES_H
  36 #define GMX_TOPOLOGY_RESIDUETYPES_H
  37
  38 #include <optional>
  39 #include <string>
  40
  41 #include "gromacs/utility/basedefinitions.h"
  42 #include "gromacs/utility/classhelpers.h"
  43
  44 struct ResidueTypeEntry;
  45
  46 class ResidueType
  47 {
  48 public:
  49     //! Default constructor.
  50     ResidueType();
  51     //! Default destructor.
  52     ~ResidueType();
  53
  54     //! Get handle to underlying residue type data.
  55     ResidueTypeEntry* ResidueTypes();
  56
  57     //! Get number of entries in ResidueTypes.
  58     int numberOfEntries() const;
  59     /*! \brief
  60      * Return true if residue \p residueName is found or false otherwise.
  61      *
  62      * \param[in] residueName Residue name to search database for.
  63      * \returns true if successful.
  64      */
  65     bool nameIndexedInResidueTypes(const std::string& residueName);
  66     /*! \brief
  67      * Add entry to ResidueTypes if unique.
  68      *
  69      * \param[in] residueName Name of new residue.
  70      * \param[in] residueType Type of new residue.
  71      */
  72     void addResidue(const std::string& residueName, const std::string& residueType);
  73     /*! \brief
  74      * Checks if the indicated \p residueName if of \p residueType.
  75      *
  76      * \param[in] residueName Residue that should be checked.
  77      * \param[in] residueType Which ResidueType the residue should have.
  78      * \returns If the check was successful.
  79      */
  80     bool namedResidueHasType(const std::string& residueName, const std::string& residueType);
  81     /*! \brief
  82      * Get index to entry in ResidueTypes with name \p residueName.
  83      *
  84      * \param[in] residueName Name of the residue being searched.
  85      * \returns The index or -1 if not found.
  86      */
  87     int indexFromResidueName(const std::string& residueName) const;
  88     /*! \brief
  89      * Get the name of the entry in ResidueTypes with \p index.
  90      *
  91      * \param[in] index Which entry should be returned.
  92      * \returns The name of the entry at \p index, or nullptr.
  93      */
  94     std::string nameFromResidueIndex(int index) const;
  95     /*! \brief
  96      * Return the residue type if a residue with that name exists, or "Other"
  97      *
  98      * \param[in] residueName Name of the residue to search for.
  99      * \returns The residue type of any matching residue, or "Other"
 100      */
 101     std::string typeOfNamedDatabaseResidue(const std::string& residueName);
 102     /*! \brief
 103      * Return an optional residue type if a residue with that name exists
 104      *
 105      * \param[in] residueName Name of the residue to search for.
 106      * \returns An optional containing the residue type of any matching residue
 107      */
 108     std::optional<std::string> optionalTypeOfNamedDatabaseResidue(const std::string& residueName);
 109
 110 private:
 111     //! Implementation pointer.
 112     class Impl;
 113
 114     gmx::PrivateImplPointer<Impl> impl_;
 115 };
 116
 117 #endif