src/gromacs/gmxana/nrama.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "nrama.h"
  40
  41 #include <cstdlib>
  42 #include <cstring>
  43
  44 #include "gromacs/listed-forces/bonded.h"
  45 #include "gromacs/pbcutil/rmpbc.h"
  46 #include "gromacs/utility/cstringutil.h"
  47 #include "gromacs/utility/fatalerror.h"
  48 #include "gromacs/utility/futil.h"
  49 #include "gromacs/utility/smalloc.h"
  50
  51 static const char *pp_pat[] = { "C", "N", "CA", "C", "N" };
  52 #define NPP (sizeof(pp_pat)/sizeof(pp_pat[0]))
  53
  54 static int d_comp(const void *a, const void *b)
  55 {
  56     t_dih *da, *db;
  57
  58     da = (t_dih *)a;
  59     db = (t_dih *)b;
  60
  61     if (da->ai[1] < db->ai[1])
  62     {
  63         return -1;
  64     }
  65     else if (da->ai[1] == db->ai[1])
  66     {
  67         return (da->ai[2] - db->ai[2]);
  68     }
  69     else
  70     {
  71         return 1;
  72     }
  73 }
  74
  75
  76 static void calc_dihs(t_xrama *xr)
  77 {
  78     int          i, t1, t2, t3;
  79     rvec         r_ij, r_kj, r_kl, m, n;
  80     real         sign;
  81     t_dih       *dd;
  82     gmx_rmpbc_t  gpbc = NULL;
  83
  84     gpbc = gmx_rmpbc_init(xr->idef, xr->ePBC, xr->natoms);
  85     gmx_rmpbc(gpbc, xr->natoms, xr->box, xr->x);
  86     gmx_rmpbc_done(gpbc);
  87
  88     for (i = 0; (i < xr->ndih); i++)
  89     {
  90         dd      = &(xr->dih[i]);
  91         dd->ang = dih_angle(xr->x[dd->ai[0]], xr->x[dd->ai[1]],
  92                             xr->x[dd->ai[2]], xr->x[dd->ai[3]],
  93                             NULL,
  94                             r_ij, r_kj, r_kl, m, n, &sign, &t1, &t2, &t3);
  95     }
  96 }
  97
  98 gmx_bool new_data(t_xrama *xr)
  99 {
 100     if (!read_next_x(xr->oenv, xr->traj, &xr->t, xr->x, xr->box))
 101     {
 102         return FALSE;
 103     }
 104
 105     calc_dihs(xr);
 106
 107     return TRUE;
 108 }
 109
 110 static int find_atom(const char *find, char ***names, int start, int nr)
 111 {
 112     int i;
 113
 114     for (i = start; (i < nr); i++)
 115     {
 116         if (std::strcmp(find, *names[i]) == 0)
 117         {
 118             return i;
 119         }
 120     }
 121     return -1;
 122 }
 123
 124 static void add_xr(t_xrama *xr, int ff[5], t_atoms *atoms)
 125 {
 126     char buf[12];
 127     int  i;
 128
 129     srenew(xr->dih, xr->ndih+2);
 130     for (i = 0; (i < 4); i++)
 131     {
 132         xr->dih[xr->ndih].ai[i] = ff[i];
 133     }
 134     for (i = 0; (i < 4); i++)
 135     {
 136         xr->dih[xr->ndih+1].ai[i] = ff[i+1];
 137     }
 138     xr->ndih += 2;
 139
 140     srenew(xr->pp, xr->npp+1);
 141     xr->pp[xr->npp].iphi  = xr->ndih-2;
 142     xr->pp[xr->npp].ipsi  = xr->ndih-1;
 143     xr->pp[xr->npp].bShow = FALSE;
 144     sprintf(buf, "%s-%d", *atoms->resinfo[atoms->atom[ff[1]].resind].name,
 145             atoms->resinfo[atoms->atom[ff[1]].resind].nr);
 146     xr->pp[xr->npp].label = gmx_strdup(buf);
 147     xr->npp++;
 148 }
 149
 150 static void get_dih(t_xrama *xr, t_atoms *atoms)
 151 {
 152     int    found, ff[NPP];
 153     int    i;
 154     size_t j;
 155
 156     for (i = 0; (i < atoms->nr); )
 157     {
 158         found = i;
 159         for (j = 0; (j < NPP); j++)
 160         {
 161             if ((ff[j] = find_atom(pp_pat[j], atoms->atomname, found, atoms->nr)) == -1)
 162             {
 163                 break;
 164             }
 165             found = ff[j]+1;
 166         }
 167         if (j != NPP)
 168         {
 169             break;
 170         }
 171         add_xr(xr, ff, atoms);
 172         i = ff[0]+1;
 173     }
 174     fprintf(stderr, "Found %d phi-psi combinations\n", xr->npp);
 175 }
 176
 177 static int search_ff(int thisff[NPP], int ndih, int **ff)
 178 {
 179     int      j, k;
 180     gmx_bool bFound = FALSE;
 181
 182     for (j = 0; (j < ndih); j++)
 183     {
 184         bFound = TRUE;
 185         for (k = 1; (k <= 3); k++)
 186         {
 187             bFound = bFound && (thisff[k] == ff[j][k]);
 188         }
 189         if (bFound)
 190         {
 191             if (thisff[0] == -1)
 192             {
 193                 ff[j][4] = thisff[4];
 194             }
 195             else
 196             {
 197                 ff[j][0] = thisff[0];
 198             }
 199             break;
 200         }
 201     }
 202     if (!bFound)
 203     {
 204         for (k = 0; (k < 5); k++)
 205         {
 206             ff[ndih][k] = thisff[k];
 207         }
 208         ndih++;
 209     }
 210     return ndih;
 211 }
 212
 213 static void min_max(t_xrama *xr)
 214 {
 215     int ai, i, j;
 216
 217     xr->amin = xr->natoms;
 218     xr->amax = 0;
 219     for (i = 0; (i < xr->ndih); i++)
 220     {
 221         for (j = 0; (j < 4); j++)
 222         {
 223             ai = xr->dih[i].ai[j];
 224             if (ai < xr->amin)
 225             {
 226                 xr->amin = ai;
 227             }
 228             else if (ai > xr->amax)
 229             {
 230                 xr->amax = ai;
 231             }
 232         }
 233     }
 234 }
 235
 236 static void get_dih_props(t_xrama *xr, t_idef *idef, int mult)
 237 {
 238     int      i, ft, ftype, nra;
 239     t_iatom *ia;
 240     t_dih   *dd, key;
 241
 242     ia = idef->il[F_PDIHS].iatoms;
 243     for (i = 0; (i < idef->il[F_PDIHS].nr); )
 244     {
 245         ft    = ia[0];
 246         ftype = idef->functype[ft];
 247         nra   = interaction_function[ftype].nratoms;
 248
 249         if (ftype != F_PDIHS)
 250         {
 251             gmx_incons("ftype is not a dihedral");
 252         }
 253
 254         key.ai[1] = ia[2];
 255         key.ai[2] = ia[3];
 256         if ((dd = (t_dih *)bsearch(&key, xr->dih, xr->ndih, (size_t)sizeof(key), d_comp))
 257             != NULL)
 258         {
 259             dd->mult = idef->iparams[ft].pdihs.mult;
 260             dd->phi0 = idef->iparams[ft].pdihs.phiA;
 261         }
 262
 263         i  += nra+1;
 264         ia += nra+1;
 265     }
 266     /* Fill in defaults for values not in the topology */
 267     for (i = 0; (i < xr->ndih); i++)
 268     {
 269         if (xr->dih[i].mult == 0)
 270         {
 271             fprintf(stderr,
 272                     "Dihedral around %d,%d not found in topology. Using mult=%d\n",
 273                     xr->dih[i].ai[1], xr->dih[i].ai[2], mult);
 274             xr->dih[i].mult = mult;
 275             xr->dih[i].phi0 = 180;
 276         }
 277     }
 278 }
 279
 280
 281
 282 t_topology *init_rama(gmx_output_env_t *oenv, const char *infile,
 283                       const char *topfile, t_xrama *xr, int mult)
 284 {
 285     t_topology *top;
 286     real        t;
 287
 288     top = read_top(topfile, &xr->ePBC);
 289
 290     /*get_dih2(xr,top->idef.functype,&(top->idef.bondeds),&(top->atoms));*/
 291     get_dih(xr, &(top->atoms));
 292     get_dih_props(xr, &(top->idef), mult);
 293     xr->natoms = read_first_x(oenv, &xr->traj, infile, &t, &(xr->x), xr->box);
 294     xr->idef   = &(top->idef);
 295     xr->oenv   = oenv;
 296
 297     min_max(xr);
 298     calc_dihs(xr);
 299
 300     return top;
 301 }