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