src/gromacs/gmxpreprocess/add_par.cpp

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  38 /* This file is completely threadsafe - keep it that way! */
  39 #include "gmxpre.h"
  40
  41 #include "add_par.h"
  42
  43 #include <cstring>
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/gmxpreprocess/grompp_impl.h"
  48 #include "gromacs/gmxpreprocess/notset.h"
  49 #include "gromacs/gmxpreprocess/toputil.h"
  50 #include "gromacs/utility/cstringutil.h"
  51 #include "gromacs/utility/fatalerror.h"
  52 #include "gromacs/utility/smalloc.h"
  53
  54 #include "hackblock.h"
  55
  56 void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s)
  57 {
  58     if ((ai < 0) || (aj < 0))
  59     {
  60         gmx_fatal(FARGS, "Trying to add impossible atoms: ai=%d, aj=%d", ai, aj);
  61     }
  62     std::vector<int>  atoms = { ai, aj };
  63     std::vector<real> forceParm(c.begin(), c.end());
  64
  65     ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
  66 }
  67
  68 void add_cmap_param(InteractionsOfType* ps, int ai, int aj, int ak, int al, int am, const char* s)
  69 {
  70     std::vector<int> atoms = { ai, aj, ak, al, am };
  71     ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
  72 }
  73
  74 void add_vsite2_param(InteractionsOfType* ps, int ai, int aj, int ak, real c0)
  75 {
  76     std::vector<int>  atoms     = { ai, aj, ak };
  77     std::vector<real> forceParm = { c0 };
  78     ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
  79 }
  80
  81 void add_vsite3_param(InteractionsOfType* ps, int ai, int aj, int ak, int al, real c0, real c1)
  82 {
  83     std::vector<int>  atoms     = { ai, aj, ak, al };
  84     std::vector<real> forceParm = { c0, c1 };
  85     ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
  86 }
  87
  88 void add_vsite3_atoms(InteractionsOfType* ps, int ai, int aj, int ak, int al, bool bSwapParity)
  89 {
  90     std::vector<int> atoms = { ai, aj, ak, al };
  91     ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
  92
  93     if (bSwapParity)
  94     {
  95         ps->interactionTypes.back().setForceParameter(1, -1);
  96     }
  97 }
  98
  99 void add_vsite4_atoms(InteractionsOfType* ps, int ai, int aj, int ak, int al, int am)
 100 {
 101     std::vector<int> atoms = { ai, aj, ak, al, am };
 102     ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
 103 }
 104
 105 int search_jtype(const PreprocessResidue& localPpResidue, const char* name, bool bNterm)
 106 {
 107     int    niter, jmax;
 108     size_t k, kmax, minstrlen;
 109     char * rtpname, searchname[12];
 110
 111     strcpy(searchname, name);
 112
 113     /* Do a best match comparison */
 114     /* for protein N-terminus, allow renaming of H1, H2 and H3 to H */
 115     if (bNterm && (strlen(searchname) == 2) && (searchname[0] == 'H')
 116         && ((searchname[1] == '1') || (searchname[1] == '2') || (searchname[1] == '3')))
 117     {
 118         niter = 2;
 119     }
 120     else
 121     {
 122         niter = 1;
 123     }
 124     kmax = 0;
 125     jmax = -1;
 126     for (int iter = 0; (iter < niter && jmax == -1); iter++)
 127     {
 128         if (iter == 1)
 129         {
 130             /* Try without the hydrogen number in the N-terminus */
 131             searchname[1] = '\0';
 132         }
 133         for (int j = 0; (j < localPpResidue.natom()); j++)
 134         {
 135             rtpname = *(localPpResidue.atomname[j]);
 136             if (gmx_strcasecmp(searchname, rtpname) == 0)
 137             {
 138                 jmax = j;
 139                 kmax = strlen(searchname);
 140                 break;
 141             }
 142             if (iter == niter - 1)
 143             {
 144                 minstrlen = std::min(strlen(searchname), strlen(rtpname));
 145                 for (k = 0; k < minstrlen; k++)
 146                 {
 147                     if (searchname[k] != rtpname[k])
 148                     {
 149                         break;
 150                     }
 151                 }
 152                 if (k > kmax)
 153                 {
 154                     kmax = k;
 155                     jmax = j;
 156                 }
 157             }
 158         }
 159     }
 160     if (jmax == -1)
 161     {
 162         gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s", searchname,
 163                   localPpResidue.resname.c_str());
 164     }
 165     if (kmax != strlen(searchname))
 166     {
 167         gmx_fatal(FARGS,
 168                   "Atom %s not found in rtp database in residue %s, "
 169                   "it looks a bit like %s",
 170                   searchname, localPpResidue.resname.c_str(), *(localPpResidue.atomname[jmax]));
 171     }
 172     return jmax;
 173 }