"0000000000000000000000000000000000000000000000000000000000000",
"0000000000000000000000000000000000000000000000000000000000000",
"0000000000000000000000000000000000000000000000000000000000000" };
-#define NPP asize(map)
- int x, y;
+ int x, y;
-#define INDEX(ppp) (((static_cast<int>(360 + (ppp)*RAD2DEG)) % 360) / 6)
+#define INDEX(ppp) (((static_cast<int>(360 + (ppp)*gmx::c_rad2Deg)) % 360) / 6)
x = INDEX(phi);
y = INDEX(psi);
#undef INDEX
}
else if (debug)
{
- fprintf(debug, "Res. %d has imcomplete occupancy or bfacs > %g\n",
- dlist[i].resnr, bfac_max);
+ fprintf(debug, "Res. %d has imcomplete occupancy or bfacs > %g\n", dlist[i].resnr, bfac_max);
}
}
else
break;
default:
sprintf(hisfile, "histo-chi%d%s", Dih - NONCHI + 1, residue_name);
- sprintf(title, "\\xc\\f{}\\s%d\\N Distribution for %s", Dih - NONCHI + 1,
- residue_name);
+ sprintf(title, "\\xc\\f{}\\s%d\\N Distribution for %s", Dih - NONCHI + 1, residue_name);
}
std::strcpy(hhisfile, hisfile);
std::strcat(hhisfile, ".xvg");
Psi = dlist[i].j0[edPsi];
for (j = 0; (j < nf); j++)
{
- phi = RAD2DEG * dih[Phi][j];
- psi = RAD2DEG * dih[Psi][j];
+ phi = gmx::c_rad2Deg * dih[Phi][j];
+ psi = gmx::c_rad2Deg * dih[Psi][j];
fprintf(fp, "%10g %10g\n", phi, psi);
if (bViol)
{
- fprintf(gp, "%d\n", static_cast<int>(!bAllowed(dih[Phi][j], RAD2DEG * dih[Psi][j])));
+ fprintf(gp,
+ "%d\n",
+ static_cast<int>(!bAllowed(dih[Phi][j], gmx::c_rad2Deg * dih[Psi][j])));
}
if (bOm)
{
- omega = RAD2DEG * dih[Om][j];
+ omega = gmx::c_rad2Deg * dih[Om][j];
mat[static_cast<int>(((phi * NMAT) / 360) + gmx::exactDiv(NMAT, 2))]
[static_cast<int>(((psi * NMAT) / 360) + gmx::exactDiv(NMAT, 2))] += omega;
}
lo += 180;
hi += 180;
nlevels = 20;
- write_xpm3(fp, 0, "Omega/Ramachandran Plot", "Deg", "Phi", "Psi", NMAT, NMAT, axis,
- axis, mat, lo, 180.0, hi, rlo, rmid, rhi, &nlevels);
+ write_xpm3(fp,
+ 0,
+ "Omega/Ramachandran Plot",
+ "Deg",
+ "Phi",
+ "Psi",
+ NMAT,
+ NMAT,
+ axis,
+ axis,
+ mat,
+ lo,
+ 180.0,
+ hi,
+ rlo,
+ rmid,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
for (j = 0; (j < NMAT); j++)
{
if ((has_dihedral(edChi1, &(dlist[i]))) && (has_dihedral(edChi2, &(dlist[i]))))
{
sprintf(fn, "ramaX1X2%s.xvg", dlist[i].name);
- fp = rama_file(fn, "\\8c\\4\\s1\\N-\\8c\\4\\s2\\N Ramachandran Plot",
- "\\8c\\4\\s1\\N (deg)", "\\8c\\4\\s2\\N (deg)", oenv);
+ fp = rama_file(fn,
+ "\\8c\\4\\s1\\N-\\8c\\4\\s2\\N Ramachandran Plot",
+ "\\8c\\4\\s1\\N (deg)",
+ "\\8c\\4\\s2\\N (deg)",
+ oenv);
Xi1 = dlist[i].j0[edChi1];
Xi2 = dlist[i].j0[edChi2];
for (j = 0; (j < nf); j++)
{
- fprintf(fp, "%10g %10g\n", RAD2DEG * dih[Xi1][j], RAD2DEG * dih[Xi2][j]);
+ fprintf(fp, "%10g %10g\n", gmx::c_rad2Deg * dih[Xi1][j], gmx::c_rad2Deg * dih[Xi2][j]);
}
xvgrclose(fp);
}
/* must correspond with enum in pp2shift.h:38 */
char* leg[edMax];
-#define NLEG asize(leg)
leg[0] = gmx_strdup("Phi");
leg[1] = gmx_strdup("Psi");
z0 *= 10.0; /* nm -> angstrom */
for (i = 0; (i < 10); i++)
{
- gmx_fprintf_pdb_atomline(fp, epdbATOM, atoms->nr + 1 + i, "CA", ' ', "LEG", ' ',
- atoms->nres + 1, ' ', x0, y0, z0 + (1.2 * i), 0.0, -0.1 * i,
+ gmx_fprintf_pdb_atomline(fp,
+ PdbRecordType::Atom,
+ atoms->nr + 1 + i,
+ "CA",
+ ' ',
+ "LEG",
+ ' ',
+ atoms->nres + 1,
+ ' ',
+ x0,
+ y0,
+ z0 + (1.2 * i),
+ 0.0,
+ -0.1 * i,
"");
}
gmx_ffclose(fp);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
sfree(ppa);
return 0;
snew(dih, ndih);
/* COMPUTE ALL DIHEDRALS! */
- read_ang_dih(ftp2fn(efTRX, NFILE, fnm), FALSE, TRUE, FALSE, bPBC, 1, &idum, &nf, &time, isize,
- index, &trans_frac, &aver_angle, dih, oenv);
+ read_ang_dih(
+ ftp2fn(efTRX, NFILE, fnm), FALSE, TRUE, FALSE, bPBC, 1, &idum, &nf, &time, isize, index, &trans_frac, &aver_angle, dih, oenv);
dt = (time[nf - 1] - time[0]) / (nf - 1); /* might want this for corr or n. transit*/
if (bCorr)
}
/* Histogramming & J coupling constants & calc of S2 order params */
- histogramming(log, nbin, &rt, nf, maxchi, dih, nlist, dlist, index, bPhi, bPsi, bOmega, bChi,
- bNormHisto, bSSHisto, ftp2fn(efDAT, NFILE, fnm), bfac_max, &atoms, bDo_jc,
- opt2fn("-jc", NFILE, fnm), oenv);
+ histogramming(log,
+ nbin,
+ &rt,
+ nf,
+ maxchi,
+ dih,
+ nlist,
+ dlist,
+ index,
+ bPhi,
+ bPsi,
+ bOmega,
+ bChi,
+ bNormHisto,
+ bSSHisto,
+ ftp2fn(efDAT, NFILE, fnm),
+ bfac_max,
+ &atoms,
+ bDo_jc,
+ opt2fn("-jc", NFILE, fnm),
+ oenv);
/* transitions
*
}
- low_ana_dih_trans(bDo_ot, opt2fn("-ot", NFILE, fnm), bDo_oh, opt2fn("-oh", NFILE, fnm), maxchi, dih,
- nlist, dlist, nf, nactdih, grpname, multiplicity, time, FALSE, core_frac, oenv);
+ low_ana_dih_trans(bDo_ot,
+ opt2fn("-ot", NFILE, fnm),
+ bDo_oh,
+ opt2fn("-oh", NFILE, fnm),
+ maxchi,
+ dih,
+ nlist,
+ dlist,
+ nf,
+ nactdih,
+ grpname,
+ multiplicity,
+ time,
+ FALSE,
+ core_frac,
+ oenv);
/* Order parameters */
- order_params(log, opt2fn("-o", NFILE, fnm), maxchi, nlist, dlist, ftp2fn_null(efPDB, NFILE, fnm),
- bfac_init, &atoms, x, pbcType, box, bPhi, bPsi, bChi, oenv);
+ order_params(log,
+ opt2fn("-o", NFILE, fnm),
+ maxchi,
+ nlist,
+ dlist,
+ ftp2fn_null(efPDB, NFILE, fnm),
+ bfac_init,
+ &atoms,
+ x,
+ pbcType,
+ box,
+ bPhi,
+ bPsi,
+ bChi,
+ oenv);
/* Print ramachandran maps! */
if (bRama)
}
mk_chi_lookup(chi_lookup, maxchi, nlist, dlist);
- get_chi_product_traj(dih, nf, nlist, maxchi, dlist, time, chi_lookup, multiplicity, FALSE,
- bNormHisto, core_frac, bAll, opt2fn("-cp", NFILE, fnm), oenv);
+ get_chi_product_traj(dih,
+ nf,
+ nlist,
+ maxchi,
+ dlist,
+ time,
+ chi_lookup,
+ multiplicity,
+ FALSE,
+ bNormHisto,
+ core_frac,
+ bAll,
+ opt2fn("-cp", NFILE, fnm),
+ oenv);
for (i = 0; i < nlist; i++)
{
/* Correlation comes last because it messes up the angles */
if (bCorr)
{
- do_dihcorr(opt2fn("-corr", NFILE, fnm), nf, ndih, dih, dt, nlist, dlist, time, maxchi, bPhi,
- bPsi, bChi, bOmega, oenv);
+ do_dihcorr(opt2fn("-corr", NFILE, fnm), nf, ndih, dih, dt, nlist, dlist, time, maxchi, bPhi, bPsi, bChi, bOmega, oenv);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff