real ellipticity(int nres, t_bb bb[])
{
- typedef struct {
+ typedef struct
+ {
real phi, psi, w;
} t_ppwstr;
// Avoid warnings about narrowing conversions from double to real
#ifdef _MSC_VER
-#pragma warning(disable: 4838)
+# pragma warning(disable : 4838)
#endif
- static const t_ppwstr ppw[] = {
- { -67, -44, 0.31 },
- { -66, -41, 0.31 },
- { -59, -44, 0.44 },
- { -57, -47, 0.56 },
- { -53, -52, 0.78 },
- { -48, -57, 1.00 },
- { -70.5, -35.8, 0.15 },
- { -57, -79, 0.23 },
- { -38, -78, 1.20 },
- { -60, -30, 0.24 },
- { -54, -28, 0.46 },
- { -44, -33, 0.68 }
- };
+ static const t_ppwstr ppw[] = { { -67, -44, 0.31 }, { -66, -41, 0.31 }, { -59, -44, 0.44 },
+ { -57, -47, 0.56 }, { -53, -52, 0.78 }, { -48, -57, 1.00 },
+ { -70.5, -35.8, 0.15 }, { -57, -79, 0.23 }, { -38, -78, 1.20 },
+ { -60, -30, 0.24 }, { -54, -28, 0.46 }, { -44, -33, 0.68 } };
#ifdef _MSC_VER
-#pragma warning(default: 4838)
+# pragma warning(default : 4838)
#endif
#define NPPW asize(ppw)
- int i, j;
- real ell, pp2, phi, psi;
+ int i, j;
+ real ell, pp2, phi, psi;
ell = 0;
for (i = 0; (i < nres); i++)
psi = bb[i].psi;
for (j = 0; (j < NPPW); j++)
{
- pp2 = gmx::square(phi-ppw[j].phi)+gmx::square(psi-ppw[j].psi);
+ pp2 = gmx::square(phi - ppw[j].phi) + gmx::square(psi - ppw[j].psi);
if (pp2 < 64)
{
bb[i].nhx++;
{
rvec dx;
- rvec_sub(x[index[0]], x[index[gnx-1]], dx);
+ rvec_sub(x[index[0]], x[index[gnx - 1]], dx);
return norm(dx);
}
-real radius(FILE *fp, int nca, const int ca_index[], rvec x[])
+real radius(FILE* fp, int nca, const int ca_index[], rvec x[])
/* Assume we have all the backbone */
{
real dl2, dlt;
for (i = 0; (i < nca); i++)
{
ai = ca_index[i];
- dl2 = gmx::square(x[ai][XX])+gmx::square(x[ai][YY]);
+ dl2 = gmx::square(x[ai][XX]) + gmx::square(x[ai][YY]);
if (fp)
{
fprintf(fp, "\n");
}
- return std::sqrt(dlt/nca);
+ return std::sqrt(dlt / nca);
}
static real rot(rvec x1, const rvec x2)
phi1 = std::atan2(x1[YY], x1[XX]);
cp = std::cos(phi1);
sp = std::sin(phi1);
- xx = cp*x2[XX]+sp*x2[YY];
- yy = -sp*x2[XX]+cp*x2[YY];
+ xx = cp * x2[XX] + sp * x2[YY];
+ yy = -sp * x2[XX] + cp * x2[YY];
- dphi = RAD2DEG*std::atan2(yy, xx);
+ dphi = RAD2DEG * std::atan2(yy, xx);
return dphi;
}
dphi += 360;
}
pt += dphi;
- a0 = a1;
+ a0 = a1;
}
- return (pt/(nca-1));
+ return (pt / (nca - 1));
}
real ca_phi(int gnx, const int index[], rvec x[])
}
phitot = 0;
- for (i = 0; (i < gnx-4); i++)
+ for (i = 0; (i < gnx - 4); i++)
{
- ai = index[i+0];
- aj = index[i+1];
- ak = index[i+2];
- al = index[i+3];
- phi = RAD2DEG*
- dih_angle(x[ai], x[aj], x[ak], x[al], nullptr,
- r_ij, r_kj, r_kl, m, n,
- &t1, &t2, &t3);
+ ai = index[i + 0];
+ aj = index[i + 1];
+ ak = index[i + 2];
+ al = index[i + 3];
+ phi = RAD2DEG
+ * dih_angle(x[ai], x[aj], x[ak], x[al], nullptr, r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3);
phitot += phi;
}
- return (phitot/(gnx-4.0));
+ return (phitot / (gnx - 4.0));
}
real dip(int nbb, int const bbind[], const rvec x[], const t_atom atom[])
q = atom[ai].q;
for (m = 0; (m < DIM); m++)
{
- dipje[m] += x[ai][m]*q;
+ dipje[m] += x[ai][m] * q;
}
}
return norm(dipje);
ztot = 0;
for (i = 1; (i < gnx); i++)
{
- ai = index[i];
- z = x[ai][ZZ];
- ztot += (z-z0);
- z0 = z;
+ ai = index[i];
+ z = x[ai][ZZ];
+ ztot += (z - z0);
+ z0 = z;
}
- return (ztot/(gnx-1.0));
+ return (ztot / (gnx - 1.0));
}
-void av_hblen(FILE *fp3, FILE *fp3a,
- FILE *fp4, FILE *fp4a,
- FILE *fp5, FILE *fp5a,
- real t, int nres, t_bb bb[])
+void av_hblen(FILE* fp3, FILE* fp3a, FILE* fp4, FILE* fp4a, FILE* fp5, FILE* fp5a, real t, int nres, t_bb bb[])
{
int i, n3 = 0, n4 = 0, n5 = 0;
real d3 = 0, d4 = 0, d5 = 0;
- for (i = 0; (i < nres-3); i++)
+ for (i = 0; (i < nres - 3); i++)
{
if (bb[i].bHelix)
{
- fprintf(fp3a, "%10g", bb[i].d3);
+ fprintf(fp3a, "%10g", bb[i].d3);
n3++;
d3 += bb[i].d3;
- if (i < nres-4)
+ if (i < nres - 4)
{
fprintf(fp4a, "%10g", bb[i].d4);
n4++;
d4 += bb[i].d4;
}
- if (i < nres-5)
+ if (i < nres - 5)
{
fprintf(fp5a, "%10g", bb[i].d5);
n5++;
}
}
}
- fprintf(fp3, "%10g %10g\n", t, d3/n3);
- fprintf(fp4, "%10g %10g\n", t, d4/n4);
- fprintf(fp5, "%10g %10g\n", t, d5/n5);
+ fprintf(fp3, "%10g %10g\n", t, d3 / n3);
+ fprintf(fp4, "%10g %10g\n", t, d4 / n4);
+ fprintf(fp5, "%10g %10g\n", t, d5 / n5);
fprintf(fp3a, "\n");
fprintf(fp4a, "\n");
fprintf(fp5a, "\n");
-
}
-void av_phipsi(FILE *fphi, FILE *fpsi, FILE *fphi2, FILE *fpsi2,
- real t, int nres, t_bb bb[])
+void av_phipsi(FILE* fphi, FILE* fpsi, FILE* fphi2, FILE* fpsi2, real t, int nres, t_bb bb[])
{
int i, n = 0;
real phi = 0, psi = 0;
n++;
}
}
- fprintf(fphi, "%10g %10g\n", t, (phi/n));
- fprintf(fpsi, "%10g %10g\n", t, (psi/n));
+ fprintf(fphi, "%10g %10g\n", t, (phi / n));
+ fprintf(fpsi, "%10g %10g\n", t, (psi / n));
fprintf(fphi2, "\n");
fprintf(fpsi2, "\n");
}
for (n = 0; (n < nbb); n++)
{
- pp2 = gmx::square(bb[n].phi-PHI_AHX)+gmx::square(bb[n].psi-PSI_AHX);
+ pp2 = gmx::square(bb[n].phi - PHI_AHX) + gmx::square(bb[n].psi - PSI_AHX);
bb[n].bHelix = FALSE;
if (pp2 < 2500)
{
- if ((bb[n].d4 < 0.36) || ((n > 0) && bb[n-1].bHelix))
+ if ((bb[n].d4 < 0.36) || ((n > 0) && bb[n - 1].bHelix))
{
bb[n].bHelix = TRUE;
}
}
}
-t_bb *mkbbind(const char *fn, int *nres, int *nbb, int res0,
- int *nall, int **index,
- char ***atomname, t_atom atom[],
- t_resinfo *resinfo)
+t_bb* mkbbind(const char* fn,
+ int* nres,
+ int* nbb,
+ int res0,
+ int* nall,
+ int** index,
+ char*** atomname,
+ t_atom atom[],
+ t_resinfo* resinfo)
{
- static const char * bb_nm[] = { "N", "H", "CA", "C", "O", "HN" };
+ static const char* bb_nm[] = { "N", "H", "CA", "C", "O", "HN" };
#define NBB asize(bb_nm)
- t_bb *bb;
- char *grpname;
- int ai, i, i0, i1, j, k, rnr, gnx, r0, r1;
+ t_bb* bb;
+ char* grpname;
+ int ai, i, i0, i1, j, k, rnr, gnx, r0, r1;
fprintf(stderr, "Please select a group containing the entire backbone\n");
rd_index(fn, 1, &gnx, index, &grpname);
r0 = std::min(r0, atom[(*index)[i]].resind);
r1 = std::max(r1, atom[(*index)[i]].resind);
}
- rnr = r1-r0+1;
+ rnr = r1 - r0 + 1;
fprintf(stderr, "There are %d residues\n", rnr);
snew(bb, rnr);
for (i = 0; (i < rnr); i++)
{
- bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1; bb[i].resno = res0+i;
+ bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1;
+ bb[i].resno = res0 + i;
}
for (i = j = 0; (i < gnx); i++)
int resindex = atom[ai].resind;
// Create an index into the residues present in the selected
// index group.
- int bbindex = resindex -r0;
+ int bbindex = resindex - r0;
if (std::strcmp(*(resinfo[resindex].name), "PRO") == 0)
{
// For PRO in a peptide, there is no H bound to backbone
}
switch (k)
{
- case 0:
- bb[bbindex].N = ai;
- break;
+ case 0: bb[bbindex].N = ai; break;
case 1:
case 5:
/* No attempt to address the case where some weird input has both H and HN atoms in the group */
bb[bbindex].H = ai;
break;
- case 2:
- bb[bbindex].CA = ai;
- break;
- case 3:
- bb[bbindex].C = ai;
- break;
- case 4:
- bb[bbindex].O = ai;
- break;
- default:
- break;
+ case 2: bb[bbindex].CA = ai; break;
+ case 3: bb[bbindex].C = ai; break;
+ case 4: bb[bbindex].O = ai; break;
+ default: break;
}
}
for (i0 = 0; (i0 < rnr); i0++)
{
- if ((bb[i0].N != -1) && (bb[i0].H != -1) &&
- (bb[i0].CA != -1) &&
- (bb[i0].C != -1) && (bb[i0].O != -1))
+ if ((bb[i0].N != -1) && (bb[i0].H != -1) && (bb[i0].CA != -1) && (bb[i0].C != -1)
+ && (bb[i0].O != -1))
{
break;
}
}
- for (i1 = rnr-1; (i1 >= 0); i1--)
+ for (i1 = rnr - 1; (i1 >= 0); i1--)
{
- if ((bb[i1].N != -1) && (bb[i1].H != -1) &&
- (bb[i1].CA != -1) &&
- (bb[i1].C != -1) && (bb[i1].O != -1))
+ if ((bb[i1].N != -1) && (bb[i1].H != -1) && (bb[i1].CA != -1) && (bb[i1].C != -1)
+ && (bb[i1].O != -1))
{
break;
}
{
i0++;
}
- if (i1 == rnr-1)
+ if (i1 == rnr - 1)
{
i1--;
}
for (i = i0; (i < i1); i++)
{
- bb[i].Cprev = bb[i-1].C;
- bb[i].Nnext = bb[i+1].N;
+ bb[i].Cprev = bb[i - 1].C;
+ bb[i].Nnext = bb[i + 1].N;
}
- rnr = std::max(0, i1-i0+1);
- fprintf(stderr, "There are %d complete backbone residues (from %d to %d)\n",
- rnr, bb[i0].resno, bb[i1].resno);
+ rnr = std::max(0, i1 - i0 + 1);
+ fprintf(stderr, "There are %d complete backbone residues (from %d to %d)\n", rnr, bb[i0].resno,
+ bb[i1].resno);
if (rnr == 0)
{
gmx_fatal(FARGS, "Zero complete backbone residues were found, cannot proceed");
}
*nres = rnr;
- *nbb = rnr*asize(bb_nm);
+ *nbb = rnr * asize(bb_nm);
return bb;
}
-real pprms(FILE *fp, int nbb, t_bb bb[])
+real pprms(FILE* fp, int nbb, t_bb bb[])
{
int i, n;
real rms, rmst, rms2;
{
if (bb[i].bHelix)
{
- rms = std::sqrt(bb[i].pprms2);
+ rms = std::sqrt(bb[i].pprms2);
rmst += rms;
rms2 += bb[i].pprms2;
fprintf(fp, "%10g ", rms);
}
}
fprintf(fp, "\n");
- rms = std::sqrt(rms2/n-gmx::square(rmst/n));
+ rms = std::sqrt(rms2 / n - gmx::square(rmst / n));
return rms;
}
{
ao = bb[i].O;
bb[i].d4 = bb[i].d3 = bb[i].d5 = 0;
- if (i < nres-3)
+ if (i < nres - 3)
{
- an = bb[i+3].N;
+ an = bb[i + 3].N;
rvec_sub(x[ao], x[an], dx);
bb[i].d3 = norm(dx);
}
- if (i < nres-4)
+ if (i < nres - 4)
{
- an = bb[i+4].N;
+ an = bb[i + 4].N;
rvec_sub(x[ao], x[an], dx);
bb[i].d4 = norm(dx);
}
- if (i < nres-5)
+ if (i < nres - 5)
{
- an = bb[i+5].N;
+ an = bb[i + 5].N;
rvec_sub(x[ao], x[an], dx);
bb[i].d5 = norm(dx);
}
- bb[i].phi = RAD2DEG*
- dih_angle(x[bb[i].Cprev], x[bb[i].N], x[bb[i].CA], x[bb[i].C], nullptr,
- r_ij, r_kj, r_kl, m, n,
- &t1, &t2, &t3);
- bb[i].psi = RAD2DEG*
- dih_angle(x[bb[i].N], x[bb[i].CA], x[bb[i].C], x[bb[i].Nnext], nullptr,
- r_ij, r_kj, r_kl, m, n,
- &t1, &t2, &t3);
- bb[i].pprms2 = gmx::square(bb[i].phi-PHI_AHX)+gmx::square(bb[i].psi-PSI_AHX);
-
- bb[i].jcaha +=
- 1.4*std::sin((bb[i].psi+138.0)*DEG2RAD) -
- 4.1*std::cos(2.0*DEG2RAD*(bb[i].psi+138.0)) +
- 2.0*std::cos(2.0*DEG2RAD*(bb[i].phi+30.0));
+ bb[i].phi = RAD2DEG
+ * dih_angle(x[bb[i].Cprev], x[bb[i].N], x[bb[i].CA], x[bb[i].C], nullptr, r_ij,
+ r_kj, r_kl, m, n, &t1, &t2, &t3);
+ bb[i].psi = RAD2DEG
+ * dih_angle(x[bb[i].N], x[bb[i].CA], x[bb[i].C], x[bb[i].Nnext], nullptr, r_ij,
+ r_kj, r_kl, m, n, &t1, &t2, &t3);
+ bb[i].pprms2 = gmx::square(bb[i].phi - PHI_AHX) + gmx::square(bb[i].psi - PSI_AHX);
+
+ bb[i].jcaha += 1.4 * std::sin((bb[i].psi + 138.0) * DEG2RAD)
+ - 4.1 * std::cos(2.0 * DEG2RAD * (bb[i].psi + 138.0))
+ + 2.0 * std::cos(2.0 * DEG2RAD * (bb[i].phi + 30.0));
}
}
-static void check_ahx(int nres, t_bb bb[],
- int *hstart, int *hend)
+static void check_ahx(int nres, t_bb bb[], int* hstart, int* hend)
{
- int h0, h1, h0sav, h1sav;
+ int h0, h1, h0sav, h1sav;
set_ahcity(nres, bb);
h0 = h0sav = h1sav = 0;
do
{
- for (; (!bb[h0].bHelix) && (h0 < nres-4); h0++)
- {
- ;
- }
- for (h1 = h0; bb[h1+1].bHelix && (h1 < nres-1); h1++)
- {
- ;
- }
+ for (; (!bb[h0].bHelix) && (h0 < nres - 4); h0++) {}
+ for (h1 = h0; bb[h1 + 1].bHelix && (h1 < nres - 1); h1++) {}
if (h1 > h0)
{
/*fprintf(stderr,"Helix from %d to %d\n",h0,h1);*/
- if (h1-h0 > h1sav-h0sav)
+ if (h1 - h0 > h1sav - h0sav)
{
h0sav = h0;
h1sav = h1;
}
}
- h0 = h1+1;
- }
- while (h1 < nres-1);
+ h0 = h1 + 1;
+ } while (h1 < nres - 1);
*hstart = h0sav;
*hend = h1sav;
}
-void do_start_end(int nres, t_bb bb[], int *nbb, int bbindex[],
- int *nca, int caindex[],
- gmx_bool bRange, int rStart, int rEnd)
+void do_start_end(int nres, t_bb bb[], int* nbb, int bbindex[], int* nca, int caindex[], gmx_bool bRange, int rStart, int rEnd)
{
- int i, j, hstart = 0, hend = 0;
+ int i, j, hstart = 0, hend = 0;
if (bRange)
{
/* Find start and end of longest helix fragment */
check_ahx(nres, bb, &hstart, &hend);
}
- fprintf(stderr, "helix from: %d through %d\n",
- bb[hstart].resno, bb[hend].resno);
+ fprintf(stderr, "helix from: %d through %d\n", bb[hstart].resno, bb[hend].resno);
for (j = 0, i = hstart; (i <= hend); i++)
{
- bbindex[j++] = bb[i].N;
- bbindex[j++] = bb[i].H;
- bbindex[j++] = bb[i].CA;
- bbindex[j++] = bb[i].C;
- bbindex[j++] = bb[i].O;
- caindex[i-hstart] = bb[i].CA;
+ bbindex[j++] = bb[i].N;
+ bbindex[j++] = bb[i].H;
+ bbindex[j++] = bb[i].CA;
+ bbindex[j++] = bb[i].C;
+ bbindex[j++] = bb[i].O;
+ caindex[i - hstart] = bb[i].CA;
}
*nbb = j;
- *nca = (hend-hstart+1);
+ *nca = (hend - hstart + 1);
}
-void pr_bb(FILE *fp, int nres, t_bb bb[])
+void pr_bb(FILE* fp, int nres, t_bb bb[])
{
int i;
fprintf(fp, "\n");
- fprintf(fp, "%3s %3s %3s %3s %3s %7s %7s %7s %7s %7s %3s\n",
- "AA", "N", "Ca", "C", "O", "Phi", "Psi", "D3", "D4", "D5", "Hx?");
+ fprintf(fp, "%3s %3s %3s %3s %3s %7s %7s %7s %7s %7s %3s\n", "AA", "N", "Ca", "C", "O", "Phi",
+ "Psi", "D3", "D4", "D5", "Hx?");
for (i = 0; (i < nres); i++)
{
- fprintf(fp, "%3d %3d %3d %3d %3d %7.2f %7.2f %7.3f %7.3f %7.3f %3s\n",
- bb[i].resno, bb[i].N, bb[i].CA, bb[i].C, bb[i].O,
- bb[i].phi, bb[i].psi, bb[i].d3, bb[i].d4, bb[i].d5,
+ fprintf(fp, "%3d %3d %3d %3d %3d %7.2f %7.2f %7.3f %7.3f %7.3f %3s\n", bb[i].resno, bb[i].N,
+ bb[i].CA, bb[i].C, bb[i].O, bb[i].phi, bb[i].psi, bb[i].d3, bb[i].d4, bb[i].d5,
bb[i].bHelix ? "Yes" : "No");
}
fprintf(fp, "\n");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff