2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2010,2014,2018,2019,2020, 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.
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.
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.
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.
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.
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.
35 #ifndef GMX_TOPOLOGY_RESIDUETYPES_H
36 #define GMX_TOPOLOGY_RESIDUETYPES_H
41 #include "gromacs/utility/basedefinitions.h"
42 #include "gromacs/utility/classhelpers.h"
44 struct ResidueTypeEntry
;
49 //! Default constructor.
51 //! Default destructor.
54 //! Get handle to underlying residue type data.
55 ResidueTypeEntry
* ResidueTypes();
57 //! Get number of entries in ResidueTypes.
58 int numberOfEntries() const;
60 * Return true if residue \p residueName is found or false otherwise.
62 * \param[in] residueName Residue name to search database for.
63 * \returns true if successful.
65 bool nameIndexedInResidueTypes(const std::string
& residueName
);
67 * Add entry to ResidueTypes if unique.
69 * \param[in] residueName Name of new residue.
70 * \param[in] residueType Type of new residue.
72 void addResidue(const std::string
& residueName
, const std::string
& residueType
);
74 * Checks if the indicated \p residueName if of \p residueType.
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.
80 bool namedResidueHasType(const std::string
& residueName
, const std::string
& residueType
);
82 * Get index to entry in ResidueTypes with name \p residueName.
84 * \param[in] residueName Name of the residue being searched.
85 * \returns The index or -1 if not found.
87 int indexFromResidueName(const std::string
& residueName
) const;
89 * Get the name of the entry in ResidueTypes with \p index.
91 * \param[in] index Which entry should be returned.
92 * \returns The name of the entry at \p index, or nullptr.
94 std::string
nameFromResidueIndex(int index
) const;
96 * Return the residue type if a residue with that name exists, or "Other"
98 * \param[in] residueName Name of the residue to search for.
99 * \returns The residue type of any matching residue, or "Other"
101 std::string
typeOfNamedDatabaseResidue(const std::string
& residueName
);
103 * Return an optional residue type if a residue with that name exists
105 * \param[in] residueName Name of the residue to search for.
106 * \returns An optional containing the residue type of any matching residue
108 std::optional
<std::string
> optionalTypeOfNamedDatabaseResidue(const std::string
& residueName
);
111 //! Implementation pointer.
114 gmx::PrivateImplPointer
<Impl
> impl_
;