src/gromacs/topology/residuetypes.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2013,2014,2015,2016 by the GROMACS development team.
   5  * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
   6  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   7  * and including many others, as listed in the AUTHORS file in the
   8  * top-level source directory and at http://www.gromacs.org.
   9  *
  10  * GROMACS is free software; you can redistribute it and/or
  11  * modify it under the terms of the GNU Lesser General Public License
  12  * as published by the Free Software Foundation; either version 2.1
  13  * of the License, or (at your option) any later version.
  14  *
  15  * GROMACS is distributed in the hope that it will be useful,
  16  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  17  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  18  * Lesser General Public License for more details.
  19  *
  20  * You should have received a copy of the GNU Lesser General Public
  21  * License along with GROMACS; if not, see
  22  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  23  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  24  *
  25  * If you want to redistribute modifications to GROMACS, please
  26  * consider that scientific software is very special. Version
  27  * control is crucial - bugs must be traceable. We will be happy to
  28  * consider code for inclusion in the official distribution, but
  29  * derived work must not be called official GROMACS. Details are found
  30  * in the README & COPYING files - if they are missing, get the
  31  * official version at http://www.gromacs.org.
  32  *
  33  * To help us fund GROMACS development, we humbly ask that you cite
  34  * the research papers on the package. Check out http://www.gromacs.org.
  35  */
  36 #include "gmxpre.h"
  37
  38 #include "residuetypes.h"
  39
  40 #include <cassert>
  41 #include <cstdio>
  42
  43 #include <algorithm>
  44 #include <iterator>
  45 #include <optional>
  46 #include <string>
  47
  48 #include "gromacs/utility/arrayref.h"
  49 #include "gromacs/utility/cstringutil.h"
  50 #include "gromacs/utility/fatalerror.h"
  51 #include "gromacs/utility/futil.h"
  52 #include "gromacs/utility/smalloc.h"
  53 #include "gromacs/utility/strdb.h"
  54
  55 //! Definition for residue type that is not known.
  56 const std::string c_undefinedResidueType = "Other";
  57
  58 //! Single ResidueType entry object
  59 struct ResidueTypeEntry
  60 {
  61     //! Default constructor creates complete object.
  62     ResidueTypeEntry(const std::string& rName, const std::string& rType) :
  63         residueName(rName),
  64         residueType(rType)
  65     {
  66     }
  67     //! Name of the residue in the entry.
  68     std::string residueName;
  69     //! Type of the residue in the entry.
  70     std::string residueType;
  71 };
  72
  73 //! Implementation detail for ResidueTypes
  74 class ResidueType::Impl
  75 {
  76 public:
  77     //! Storage object for entries.
  78     std::vector<ResidueTypeEntry> entry;
  79 };
  80
  81 ResidueType::ResidueType() : impl_(new Impl)
  82 {
  83     char line[STRLEN];
  84     char resname[STRLEN], restype[STRLEN], dum[STRLEN];
  85
  86     gmx::FilePtr db = gmx::openLibraryFile("residuetypes.dat");
  87
  88     while (get_a_line(db.get(), line, STRLEN))
  89     {
  90         strip_comment(line);
  91         trim(line);
  92         if (line[0] != '\0')
  93         {
  94             if (sscanf(line, "%1000s %1000s %1000s", resname, restype, dum) != 2)
  95             {
  96                 gmx_fatal(
  97                         FARGS,
  98                         "Incorrect number of columns (2 expected) for line in residuetypes.dat  ");
  99             }
 100             addResidue(resname, restype);
 101         }
 102     }
 103 }
 104
 105 ResidueType::~ResidueType() {}
 106
 107 /*! \brief
 108  * Return an optional const iterator to a residue entry that matches the given name.
 109  *
 110  * \param[in] entries Currently registered residue entries in the database.
 111  * \param[in] residueName Name of a residue to compare to database.
 112  * \returns An optional iterator to the residue entry that was found.
 113  */
 114 static std::optional<gmx::ArrayRef<const ResidueTypeEntry>::const_iterator>
 115 findResidueEntryWithName(gmx::ArrayRef<const ResidueTypeEntry> entries, const std::string& residueName)
 116 {
 117     auto foundIt =
 118             std::find_if(entries.begin(), entries.end(), [&residueName](const ResidueTypeEntry& old) {
 119                 return gmx::equalCaseInsensitive(residueName, old.residueName);
 120             });
 121     return (foundIt != entries.end()) ? std::make_optional(foundIt) : std::nullopt;
 122 }
 123
 124 bool ResidueType::nameIndexedInResidueTypes(const std::string& residueName)
 125 {
 126     return findResidueEntryWithName(impl_->entry, residueName).has_value();
 127 }
 128
 129 void ResidueType::addResidue(const std::string& residueName, const std::string& residueType)
 130 {
 131     if (auto foundIt = findResidueEntryWithName(impl_->entry, residueName))
 132     {
 133         if (!gmx::equalCaseInsensitive((*foundIt)->residueType, residueType))
 134         {
 135             fprintf(stderr,
 136                     "Warning: Residue '%s' already present with type '%s' in database, ignoring "
 137                     "new type '%s'.\n",
 138                     residueName.c_str(), (*foundIt)->residueType.c_str(), residueType.c_str());
 139         }
 140     }
 141     else
 142     {
 143         impl_->entry.emplace_back(residueName, residueType);
 144     }
 145 }
 146
 147 bool ResidueType::namedResidueHasType(const std::string& residueName, const std::string& residueType)
 148 {
 149     auto foundIt = findResidueEntryWithName(impl_->entry, residueName);
 150     return foundIt ? gmx::equalCaseInsensitive(residueType, (*foundIt)->residueType) : false;
 151 }
 152
 153 int ResidueType::numberOfEntries() const
 154 {
 155     return impl_->entry.size();
 156 }
 157
 158 int ResidueType::indexFromResidueName(const std::string& residueName) const
 159 {
 160     gmx::ArrayRef<const ResidueTypeEntry> temp(impl_->entry);
 161     auto                                  foundIt = findResidueEntryWithName(temp, residueName);
 162     return foundIt ? std::distance(temp.begin(), *foundIt) : -1;
 163 }
 164
 165 std::string ResidueType::nameFromResidueIndex(int index) const
 166 {
 167     if (index >= 0 && index < gmx::ssize(impl_->entry))
 168     {
 169         return impl_->entry[index].residueName;
 170     }
 171     else
 172     {
 173         return "";
 174     }
 175 }
 176
 177 std::string ResidueType::typeOfNamedDatabaseResidue(const std::string& residueName)
 178 {
 179     auto foundIt = findResidueEntryWithName(impl_->entry, residueName);
 180     return foundIt ? (*foundIt)->residueType : c_undefinedResidueType;
 181 }
 182
 183 std::optional<std::string> ResidueType::optionalTypeOfNamedDatabaseResidue(const std::string& residueName)
 184 {
 185     auto foundIt = findResidueEntryWithName(impl_->entry, residueName);
 186     return foundIt ? std::make_optional((*foundIt)->residueType) : std::nullopt;
 187 }