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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"
53 static const char *pp_pat[] = { "C", "N", "CA", "C", "N" };
54 #define NPP (sizeof(pp_pat)/sizeof(pp_pat[0]))
56 static bool d_comp(const t_dih &a, const t_dih &b)
58 if (a.ai[1] < b.ai[1])
62 else if (a.ai[1] == b.ai[1])
64 return a.ai[2] < b.ai[2];
73 static void calc_dihs(t_xrama *xr)
76 rvec r_ij, r_kj, r_kl, m, n;
79 gmx_rmpbc_t gpbc = nullptr;
81 gpbc = gmx_rmpbc_init(xr->idef, xr->ePBC, xr->natoms);
82 gmx_rmpbc(gpbc, xr->natoms, xr->box, xr->x);
85 for (i = 0; (i < xr->ndih); i++)
88 dd->ang = dih_angle(xr->x[dd->ai[0]], xr->x[dd->ai[1]],
89 xr->x[dd->ai[2]], xr->x[dd->ai[3]],
91 r_ij, r_kj, r_kl, m, n, &sign, &t1, &t2, &t3);
95 gmx_bool new_data(t_xrama *xr)
97 if (!read_next_x(xr->oenv, xr->traj, &xr->t, xr->x, xr->box))
107 static int find_atom(const char *find, char ***names, int start, int nr)
111 for (i = start; (i < nr); i++)
113 if (std::strcmp(find, *names[i]) == 0)
121 static void add_xr(t_xrama *xr, int ff[5], const t_atoms *atoms)
126 srenew(xr->dih, xr->ndih+2);
127 for (i = 0; (i < 4); i++)
129 xr->dih[xr->ndih].ai[i] = ff[i];
131 for (i = 0; (i < 4); i++)
133 xr->dih[xr->ndih+1].ai[i] = ff[i+1];
137 srenew(xr->pp, xr->npp+1);
138 xr->pp[xr->npp].iphi = xr->ndih-2;
139 xr->pp[xr->npp].ipsi = xr->ndih-1;
140 xr->pp[xr->npp].bShow = FALSE;
141 sprintf(buf, "%s-%d", *atoms->resinfo[atoms->atom[ff[1]].resind].name,
142 atoms->resinfo[atoms->atom[ff[1]].resind].nr);
143 xr->pp[xr->npp].label = gmx_strdup(buf);
147 static void get_dih(t_xrama *xr, const t_atoms *atoms)
153 for (i = 0; (i < atoms->nr); )
156 for (j = 0; (j < NPP); j++)
158 if ((ff[j] = find_atom(pp_pat[j], atoms->atomname, found, atoms->nr)) == -1)
168 add_xr(xr, ff, atoms);
171 fprintf(stderr, "Found %d phi-psi combinations\n", xr->npp);
174 static void min_max(t_xrama *xr)
178 xr->amin = xr->natoms;
180 for (i = 0; (i < xr->ndih); i++)
182 for (j = 0; (j < 4); j++)
184 ai = xr->dih[i].ai[j];
189 else if (ai > xr->amax)
197 static void get_dih_props(t_xrama *xr, const t_idef *idef, int mult)
199 int i, ft, ftype, nra;
203 ia = idef->il[F_PDIHS].iatoms;
204 for (i = 0; (i < idef->il[F_PDIHS].nr); )
207 ftype = idef->functype[ft];
208 nra = interaction_function[ftype].nratoms;
210 if (ftype != F_PDIHS)
212 gmx_incons("ftype is not a dihedral");
217 dd = std::lower_bound(xr->dih, xr->dih+xr->ndih, key, d_comp);
218 if (dd < xr->dih+xr->ndih && !d_comp(key, *dd))
220 dd->mult = idef->iparams[ft].pdihs.mult;
221 dd->phi0 = idef->iparams[ft].pdihs.phiA;
227 /* Fill in defaults for values not in the topology */
228 for (i = 0; (i < xr->ndih); i++)
230 if (xr->dih[i].mult == 0)
233 "Dihedral around %d,%d not found in topology. Using mult=%d\n",
234 xr->dih[i].ai[1], xr->dih[i].ai[2], mult);
235 xr->dih[i].mult = mult;
236 xr->dih[i].phi0 = 180;
243 t_topology *init_rama(gmx_output_env_t *oenv, const char *infile,
244 const char *topfile, t_xrama *xr, int mult)
249 top = read_top(topfile, &xr->ePBC);
251 /*get_dih2(xr,top->idef.functype,&(top->idef.bondeds),&(top->atoms));*/
252 get_dih(xr, &(top->atoms));
253 get_dih_props(xr, &(top->idef), mult);
254 xr->natoms = read_first_x(oenv, &xr->traj, infile, &t, &(xr->x), xr->box);
255 xr->idef = &(top->idef);