src/gromacs/gmxpreprocess/h_db.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "h_db.h"
  41
  42 #include <cctype>
  43 #include <cstdlib>
  44 #include <cstring>
  45
  46 #include <algorithm>
  47 #include <string>
  48 #include <vector>
  49
  50 #include "gromacs/gmxpreprocess/fflibutil.h"
  51 #include "gromacs/gmxpreprocess/notset.h"
  52 #include "gromacs/topology/atoms.h"
  53 #include "gromacs/utility/arraysize.h"
  54 #include "gromacs/utility/cstringutil.h"
  55 #include "gromacs/utility/fatalerror.h"
  56 #include "gromacs/utility/futil.h"
  57 #include "gromacs/utility/smalloc.h"
  58 #include "gromacs/utility/stringutil.h"
  59
  60 #include "hackblock.h"
  61
  62 /* Number of control atoms for each 'add' type.
  63  *
  64  * There are 11 types of adding hydrogens, numbered from 1 thru
  65  * 11. Each of these has a specific number of control atoms, that
  66  * determine how the hydrogens are added.  Here these number are
  67  * given. Because arrays start at 0, an extra dummy for index 0 is
  68  * added.
  69  */
  70 const int ncontrol[] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3, 1, 1 };
  71 #define maxcontrol asize(ncontrol)
  72
  73 void print_ab(FILE *out, const MoleculePatch &hack, const char *nname)
  74 {
  75     fprintf(out, "%d\t%d\t%s", hack.nr, hack.tp, nname);
  76     for (int i = 0; (i < hack.nctl); i++)
  77     {
  78         fprintf(out, "\t%s", hack.a[i].c_str());
  79     }
  80     fprintf(out, "\n");
  81 }
  82
  83
  84 void read_ab(char *line, const char *fn, MoleculePatch *hack)
  85 {
  86     int  nh, tp, ns;
  87     char a[4][12];
  88     char hn[32];
  89
  90     ns = sscanf(line, "%d%d%s%s%s%s%s", &nh, &tp, hn, a[0], a[1], a[2], a[3]);
  91     if (ns < 4)
  92     {
  93         gmx_fatal(FARGS, "wrong format in input file %s on line\n%s\n", fn, line);
  94     }
  95
  96     hack->nr = nh;
  97     hack->tp = tp;
  98     if ((tp < 1) || (tp >= maxcontrol))
  99     {
 100         gmx_fatal(FARGS, "Error in hdb file %s:\nH-type should be in 1-%d. Offending line:\n%s", fn, maxcontrol-1, line);
 101     }
 102
 103     hack->nctl = ns - 3;
 104     if ((hack->nctl != ncontrol[hack->tp]) && (ncontrol[hack->tp] != -1))
 105     {
 106         gmx_fatal(FARGS, "Error in hdb file %s:\nWrong number of control atoms (%d instead of %d) on line:\n%s\n", fn, hack->nctl, ncontrol[hack->tp], line);
 107     }
 108     for (int i = 0; (i < hack->nctl); i++)
 109     {
 110         hack->a[i] = a[i];
 111     }
 112     hack->oname.clear();
 113     hack->nname = hn;
 114     hack->atom.clear();
 115     hack->cgnr  = NOTSET;
 116     hack->bXSet = false;
 117     for (int i = 0; i < DIM; i++)
 118     {
 119         hack->newx[i] = NOTSET;
 120     }
 121 }
 122
 123 static void read_h_db_file(const char *hfn, std::vector<MoleculePatchDatabase> *globalPatches)
 124 {
 125     char         filebase[STRLEN], line[STRLEN], buf[STRLEN];
 126
 127     fflib_filename_base(hfn, filebase, STRLEN);
 128     /* Currently filebase is read and set, but not used.
 129      * hdb entries from any hdb file and be applied to rtp entries
 130      * in any rtp file.
 131      */
 132
 133     FILE *in = fflib_open(hfn);
 134
 135     while (fgets2(line, STRLEN-1, in))
 136     {
 137         // Skip lines that are only whitespace
 138         if (gmx::countWords(line) == 0)
 139         {
 140             continue;
 141         }
 142         int n;
 143         if (sscanf(line, "%s%n", buf, &n) != 1)
 144         {
 145             int size = globalPatches->size();
 146             fprintf(stderr, "Error in hdb file: nah = %d\nline = '%s'\n",
 147                     size, line);
 148             break;
 149         }
 150         globalPatches->emplace_back(MoleculePatchDatabase());
 151         MoleculePatchDatabase *block = &globalPatches->back();
 152         clearModificationBlock(block);
 153         block->name     = buf;
 154         block->filebase = filebase;
 155
 156         int nab;
 157         if (sscanf(line+n, "%d", &nab) == 1)
 158         {
 159             for (int i = 0; (i < nab); i++)
 160             {
 161                 if (feof(in))
 162                 {
 163                     gmx_fatal(FARGS, "Expected %d lines of hydrogens, found only %d "
 164                               "while reading Hydrogen Database %s residue %s",
 165                               nab, i-1, block->name.c_str(), hfn);
 166                 }
 167                 if (nullptr == fgets(buf, STRLEN, in))
 168                 {
 169                     gmx_fatal(FARGS, "Error reading from file %s", hfn);
 170                 }
 171                 block->hack.emplace_back(MoleculePatch());
 172                 read_ab(buf, hfn, &block->hack.back());
 173             }
 174         }
 175     }
 176     gmx_ffclose(in);
 177
 178     if (!globalPatches->empty())
 179     {
 180         /* Sort the list for searching later */
 181         std::sort(globalPatches->begin(), globalPatches->end(),
 182                   [](const MoleculePatchDatabase &a1, const MoleculePatchDatabase &a2)
 183                   { return std::lexicographical_compare(a1.name.begin(), a1.name.end(),
 184                                                         a2.name.begin(), a2.name.end(),
 185                                                         [](const char &c1, const char &c2)
 186                                                         { return std::toupper(c1) < std::toupper(c2); }); });
 187     }
 188 }
 189
 190 int read_h_db(const char *ffdir, std::vector<MoleculePatchDatabase> *globalPatches)
 191 {
 192     /* Read the hydrogen database file(s).
 193      * Do not generate an error when no files are found.
 194      */
 195
 196     std::vector<std::string> hdbf = fflib_search_file_end(ffdir, ".hdb", FALSE);
 197     globalPatches->clear();
 198     for (const auto &filename : hdbf)
 199     {
 200         read_h_db_file(filename.c_str(), globalPatches);
 201     }
 202     return globalPatches->size();
 203 }
 204
 205 gmx::ArrayRef<MoleculePatchDatabase>::iterator
 206 search_h_db(gmx::ArrayRef<MoleculePatchDatabase> globalPatches, char *key)
 207 {
 208     return std::find_if(globalPatches.begin(), globalPatches.end(),
 209                         [&key](const MoleculePatchDatabase &a)
 210                         { return gmx::equalCaseInsensitive(key, a.name); });
 211 }