src/gromacs/topology/residuetypes.cpp

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  35 #include "gmxpre.h"
  36
  37 #include "residuetypes.h"
  38
  39 #include <cassert>
  40 #include <cstdio>
  41
  42 #include <algorithm>
  43 #include <iterator>
  44 #include <string>
  45
  46 #include "gromacs/compat/optional.h"
  47 #include "gromacs/utility/arrayref.h"
  48 #include "gromacs/utility/cstringutil.h"
  49 #include "gromacs/utility/fatalerror.h"
  50 #include "gromacs/utility/futil.h"
  51 #include "gromacs/utility/smalloc.h"
  52 #include "gromacs/utility/strdb.h"
  53
  54 //! Definition for residue type that is not known.
  55 const std::string c_undefinedResidueType = "Other";
  56
  57 //! Single ResidueType entry object
  58 struct ResidueTypeEntry
  59 {
  60     //! Default constructor creates complete object.
  61     ResidueTypeEntry(const std::string &rName, const std::string &rType)
  62         : residueName(rName), residueType(rType)
  63     {}
  64     //! Name of the residue in the entry.
  65     std::string residueName;
  66     //! Type of the residue in the entry.
  67     std::string residueType;
  68 };
  69
  70 //! Implementation detail for ResidueTypes
  71 class ResidueType::Impl
  72 {
  73     public:
  74         //! Storage object for entries.
  75         std::vector<ResidueTypeEntry> entry;
  76 };
  77
  78 ResidueType::ResidueType()
  79     : impl_(new Impl)
  80 {
  81     char                    line[STRLEN];
  82     char                    resname[STRLEN], restype[STRLEN], dum[STRLEN];
  83
  84     gmx::FilePtr            db = gmx::openLibraryFile("residuetypes.dat");
  85
  86     while (get_a_line(db.get(), line, STRLEN))
  87     {
  88         strip_comment(line);
  89         trim(line);
  90         if (line[0] != '\0')
  91         {
  92             if (sscanf(line, "%1000s %1000s %1000s", resname, restype, dum) != 2)
  93             {
  94                 gmx_fatal(FARGS, "Incorrect number of columns (2 expected) for line in residuetypes.dat  ");
  95             }
  96             addResidue(resname, restype);
  97         }
  98     }
  99 }
 100
 101 ResidueType::~ResidueType()
 102 {
 103 }
 104
 105 /*! \brief
 106  * Return an optional const iterator to a residue entry that matches the given name.
 107  *
 108  * \param[in] entries Currently registered residue entries in the database.
 109  * \param[in] residueName Name of a residue to compare to database.
 110  * \returns An optional iterator to the residue entry that was found.
 111  */
 112 static gmx::compat::optional<gmx::ArrayRef<const ResidueTypeEntry>::const_iterator>
 113 findResidueEntryWithName(gmx::ArrayRef<const ResidueTypeEntry> entries, const std::string &residueName)
 114 {
 115     auto foundIt = std::find_if(entries.begin(), entries.end(),
 116                                 [&residueName](const ResidueTypeEntry &old)
 117                                 { return gmx::equalCaseInsensitive(residueName, old.residueName); });
 118     return (foundIt != entries.end()) ? gmx::compat::make_optional(foundIt) : gmx::compat::nullopt;
 119 }
 120
 121 bool ResidueType::nameIndexedInResidueTypes(const std::string &residueName)
 122 {
 123     return findResidueEntryWithName(impl_->entry, residueName).has_value();
 124 }
 125
 126 void ResidueType::addResidue(const std::string &residueName, const std::string &residueType)
 127 {
 128     if (auto foundIt = findResidueEntryWithName(impl_->entry, residueName))
 129     {
 130         if (!gmx::equalCaseInsensitive((*foundIt)->residueType, residueType))
 131         {
 132             fprintf(stderr, "Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.\n",
 133                     residueName.c_str(), (*foundIt)->residueType.c_str(), residueType.c_str());
 134         }
 135     }
 136     else
 137     {
 138         impl_->entry.emplace_back(residueName, residueType);
 139     }
 140 }
 141
 142 bool ResidueType::namedResidueHasType(const std::string &residueName, const std::string &residueType)
 143 {
 144     auto foundIt = findResidueEntryWithName(impl_->entry, residueName);
 145     return foundIt ? gmx::equalCaseInsensitive(residueType, (*foundIt)->residueType) : false;
 146 }
 147
 148 int ResidueType::numberOfEntries() const
 149 {
 150     return impl_->entry.size();
 151 }
 152
 153 int ResidueType::indexFromResidueName(const std::string &residueName) const
 154 {
 155     gmx::ArrayRef<const ResidueTypeEntry> temp(impl_->entry);
 156     auto foundIt = findResidueEntryWithName(temp, residueName);
 157     return foundIt ? std::distance(temp.begin(), *foundIt) : -1;
 158 }
 159
 160 std::string ResidueType::nameFromResidueIndex(int index) const
 161 {
 162     if (index >= 0 && index < gmx::ssize(impl_->entry))
 163     {
 164         return impl_->entry[index].residueName;
 165     }
 166     else
 167     {
 168         return "";
 169     }
 170 }
 171
 172 std::string
 173 ResidueType::typeOfNamedDatabaseResidue(const std::string &residueName)
 174 {
 175     auto foundIt = findResidueEntryWithName(impl_->entry, residueName);
 176     return foundIt ? (*foundIt)->residueType : c_undefinedResidueType;
 177 }
 178
 179 gmx::compat::optional<std::string>
 180 ResidueType::optionalTypeOfNamedDatabaseResidue(const std::string &residueName)
 181 {
 182     auto foundIt = findResidueEntryWithName(impl_->entry, residueName);
 183     return foundIt ? gmx::compat::make_optional((*foundIt)->residueType) : gmx::compat::nullopt;
 184 }