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44 #include "gromacs/fileio/matio.h"
45 #include "gromacs/gmxana/gstat.h"
46 #include "gromacs/math/units.h"
47 #include "gromacs/math/utilities.h"
48 #include "gromacs/utility/fatalerror.h"
49 #include "gromacs/utility/futil.h"
50 #include "gromacs/utility/gmxassert.h"
51 #include "gromacs/utility/pleasecite.h"
52 #include "gromacs/utility/smalloc.h"
61 static real interpolate(real phi, real psi, t_shiftdata* sd)
63 int iphi, ipsi, iphi1, ipsi1;
64 real fphi, fpsi, wx0, wx1, wy0, wy1;
67 if (phi > 2*M_PI) phi -= 2*M_PI;
69 if (psi > 2*M_PI) psi -= 2*M_PI;
84 iphi = static_cast<int>(fphi);
85 ipsi = static_cast<int>(fpsi);
86 fphi -= iphi; /* Fraction (offset from gridpoint) */
95 iphi1 = (iphi + 1) % sd->nx;
96 ipsi1 = (ipsi + 1) % sd->ny;
98 return (sd->data[iphi][ipsi] * wx0 * wy0 + sd->data[iphi1][ipsi] * wx1 * wy0
99 + sd->data[iphi][ipsi1] * wx0 * wy1 + sd->data[iphi1][ipsi1] * wx1 * wy1);
102 static void dump_sd(const char* fn, t_shiftdata* sd)
107 int nnx, nny, nfac = 4, nlevels = 20;
108 real phi, psi, *x_phi, *y_psi, **newdata;
110 t_rgb rlo = { 1, 0, 0 }, rhi = { 0, 0, 1 };
112 nnx = sd->nx * nfac + 1;
113 nny = sd->ny * nfac + 1;
119 for (i = 0; (i < nnx); i++)
121 snew(newdata[i], nny);
122 phi = i * 2 * M_PI / (nnx - 1);
123 x_phi[i] = phi * gmx::c_rad2Deg - 180;
124 for (j = 0; (j < nny); j++)
126 psi = j * 2 * M_PI / (nny - 1);
129 y_psi[j] = psi * gmx::c_rad2Deg - 180;
131 /*if (((i % nfac) == 0) && ((j % nfac) == 0))
132 newdata[i][j] = sd->data[i/nfac][j/nfac];
134 newdata[i][j] = interpolate(phi, psi, sd);
135 lo = std::min(lo, newdata[i][j]);
136 hi = std::max(hi, newdata[i][j]);
139 sprintf(buf, "%s.xpm", fn);
140 fp = gmx_ffopen(buf, "w");
141 write_xpm(fp, 0, fn, fn, "Phi", "Psi", nnx, nny, x_phi, y_psi, newdata, lo, hi, rlo, rhi, &nlevels);
142 for (i = 0; (i < nnx); i++)
151 static t_shiftdata* read_shifts(const char* fn)
158 gmx::FilePtr fp = gmx::openLibraryFile(fn);
159 if (2 != fscanf(fp.get(), "%d%d", &nx, &ny))
161 gmx_fatal(FARGS, "Error reading from file %s", fn);
163 GMX_ASSERT(nx > 0, "");
166 sd->dx = nx / (2 * M_PI);
167 sd->dy = ny / (2 * M_PI);
168 snew(sd->data, nx + 1);
169 for (i = 0; (i <= nx); i++)
171 snew(sd->data[i], ny + 1);
172 for (j = 0; (j < ny); j++)
176 sd->data[i][j] = sd->data[0][j];
180 if (1 != fscanf(fp.get(), "%lf", &xx))
182 gmx_fatal(FARGS, "Error reading from file %s", fn);
187 sd->data[i][j] = sd->data[i][0];
199 static void done_shifts(t_shiftdata* sd)
203 for (i = 0; (i <= sd->nx); i++)
211 void do_pp2shifts(FILE* fp, int nf, gmx::ArrayRef<const t_dlist> dlist, real** dih)
213 /* Read the shift files */
214 t_shiftdata* ca_sd = read_shifts("ca-shift.dat");
215 t_shiftdata* cb_sd = read_shifts("cb-shift.dat");
216 t_shiftdata* ha_sd = read_shifts("ha-shift.dat");
217 t_shiftdata* co_sd = read_shifts("co-shift.dat");
219 fprintf(fp, "\n *** Chemical shifts from the chemical shift index ***\n");
220 please_cite(fp, "Wishart98a");
222 "%12s %10s %10s %10s %10s\n",
228 for (const auto& dihedral : dlist)
230 if ((has_dihedral(edPhi, dihedral)) && (has_dihedral(edPsi, dihedral)))
232 int Phi = dihedral.j0[edPhi];
233 int Psi = dihedral.j0[edPsi];
234 real ca = 0, cb = 0, co = 0, ha = 0;
235 for (int j = 0; (j < nf); j++)
237 real phi = dih[Phi][j];
238 real psi = dih[Psi][j];
240 ca += interpolate(phi, psi, ca_sd);
241 cb += interpolate(phi, psi, cb_sd);
242 co += interpolate(phi, psi, co_sd);
243 ha += interpolate(phi, psi, ha_sd);
245 fprintf(fp, "%12s %10g %10g %10g %10g\n", dihedral.name, ca / nf, ha / nf, co / nf, cb / nf);