src/gromacs/topology/residuetypes.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2014,2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 #ifndef GMX_TOPOLOGY_RESIDUETYPES_H
  36 #define GMX_TOPOLOGY_RESIDUETYPES_H
  37
  38 #include <string>
  39
  40 #include "gromacs/compat/optional.h"
  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
 102         typeOfNamedDatabaseResidue(const std::string &residueName);
 103         /*! \brief
 104          * Return an optional residue type if a residue with that name exists
 105          *
 106          * \param[in] residueName Name of the residue to search for.
 107          * \returns An optional containing the residue type of any matching residue
 108          */
 109         gmx::compat::optional<std::string>
 110         optionalTypeOfNamedDatabaseResidue(const std::string &residueName);
 111
 112     private:
 113         //! Implementation pointer.
 114         class Impl;
 115
 116         gmx::PrivateImplPointer<Impl> impl_;
 117 };
 118
 119 #endif