#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
-static void norm_princ(const t_atoms *atoms, int isize, int *index, int natoms,
- rvec *x)
+static void norm_princ(const t_atoms* atoms, int isize, int* index, int natoms, rvec* x)
{
int i, m;
rvec princ, vec;
}
}
-int gmx_rms(int argc, char *argv[])
+int gmx_rms(int argc, char* argv[])
{
- const char *desc[] =
- {
+ const char* desc[] = {
"[THISMODULE] compares two structures by computing the root mean square",
"deviation (RMSD), the size-independent [GRK]rho[grk] similarity parameter",
"([TT]rho[tt]) or the scaled [GRK]rho[grk] ([TT]rhosc[tt]), ",
"analogously to the [TT]-m[tt] option. Only bonds between atoms in the",
"comparison group are considered."
};
- static gmx_bool bPBC = TRUE, bFitAll = TRUE, bSplit = FALSE;
- static gmx_bool bDeltaLog = FALSE;
- static int prev = 0, freq = 1, freq2 = 1, nlevels = 80, avl = 0;
- static real rmsd_user_max = -1, rmsd_user_min = -1, bond_user_max = -1,
- bond_user_min = -1, delta_maxy = 0.0;
+ static gmx_bool bPBC = TRUE, bFitAll = TRUE, bSplit = FALSE;
+ static gmx_bool bDeltaLog = FALSE;
+ static int prev = 0, freq = 1, freq2 = 1, nlevels = 80, avl = 0;
+ static real rmsd_user_max = -1, rmsd_user_min = -1, bond_user_max = -1, bond_user_min = -1,
+ delta_maxy = 0.0;
/* strings and things for selecting difference method */
enum
{
- ewSel, ewRMSD, ewRho, ewRhoSc, ewNR
+ ewSel,
+ ewRMSD,
+ ewRho,
+ ewRhoSc,
+ ewNR
};
int ewhat;
- const char *what[ewNR + 1] =
- { nullptr, "rmsd", "rho", "rhosc", nullptr };
- const char *whatname[ewNR] =
- { nullptr, "RMSD", "Rho", "Rho sc" };
- const char *whatlabel[ewNR] =
- { nullptr, "RMSD (nm)", "Rho", "Rho sc" };
- const char *whatxvgname[ewNR] =
- { nullptr, "RMSD", "\\8r\\4", "\\8r\\4\\ssc\\N" };
- const char *whatxvglabel[ewNR] =
- { nullptr, "RMSD (nm)", "\\8r\\4", "\\8r\\4\\ssc\\N" };
+ const char* what[ewNR + 1] = { nullptr, "rmsd", "rho", "rhosc", nullptr };
+ const char* whatname[ewNR] = { nullptr, "RMSD", "Rho", "Rho sc" };
+ const char* whatlabel[ewNR] = { nullptr, "RMSD (nm)", "Rho", "Rho sc" };
+ const char* whatxvgname[ewNR] = { nullptr, "RMSD", "\\8r\\4", "\\8r\\4\\ssc\\N" };
+ const char* whatxvglabel[ewNR] = { nullptr, "RMSD (nm)", "\\8r\\4", "\\8r\\4\\ssc\\N" };
/* strings and things for fitting methods */
enum
{
- efSel, efFit, efReset, efNone, efNR
+ efSel,
+ efFit,
+ efReset,
+ efNone,
+ efNR
};
int efit;
- const char *fit[efNR + 1] =
- { nullptr, "rot+trans", "translation", "none", nullptr };
- const char *fitgraphlabel[efNR + 1] =
- { nullptr, "lsq fit", "translational fit", "no fit" };
- static int nrms = 1;
- static gmx_bool bMassWeighted = TRUE;
- t_pargs pa[] =
- {
- { "-what", FALSE, etENUM,
- { what }, "Structural difference measure" },
- { "-pbc", FALSE, etBOOL,
- { &bPBC }, "PBC check" },
- { "-fit", FALSE, etENUM,
- { fit }, "Fit to reference structure" },
- { "-prev", FALSE, etINT,
- { &prev }, "Compare with previous frame" },
- { "-split", FALSE, etBOOL,
- { &bSplit }, "Split graph where time is zero" },
- { "-fitall", FALSE, etBOOL,
- { &bFitAll }, "HIDDENFit all pairs of structures in matrix" },
- { "-skip", FALSE, etINT,
- { &freq }, "Only write every nr-th frame to matrix" },
- { "-skip2", FALSE, etINT,
- { &freq2 }, "Only write every nr-th frame to matrix" },
- { "-max", FALSE, etREAL,
- { &rmsd_user_max }, "Maximum level in comparison matrix" },
- { "-min", FALSE, etREAL,
- { &rmsd_user_min }, "Minimum level in comparison matrix" },
- { "-bmax", FALSE, etREAL,
- { &bond_user_max }, "Maximum level in bond angle matrix" },
- { "-bmin", FALSE, etREAL,
- { &bond_user_min }, "Minimum level in bond angle matrix" },
- { "-mw", FALSE, etBOOL,
- { &bMassWeighted }, "Use mass weighting for superposition" },
- { "-nlevels", FALSE, etINT,
- { &nlevels }, "Number of levels in the matrices" },
- { "-ng", FALSE, etINT,
- { &nrms }, "Number of groups to compute RMS between" },
- { "-dlog", FALSE, etBOOL,
- { &bDeltaLog },
- "HIDDENUse a log x-axis in the delta t matrix" },
- { "-dmax", FALSE, etREAL,
- { &delta_maxy }, "HIDDENMaximum level in delta matrix" },
- { "-aver", FALSE, etINT,
- { &avl },
- "HIDDENAverage over this distance in the RMSD matrix" }
+ const char* fit[efNR + 1] = { nullptr, "rot+trans", "translation", "none", nullptr };
+ const char* fitgraphlabel[efNR + 1] = { nullptr, "lsq fit", "translational fit", "no fit" };
+ static int nrms = 1;
+ static gmx_bool bMassWeighted = TRUE;
+ t_pargs pa[] = {
+ { "-what", FALSE, etENUM, { what }, "Structural difference measure" },
+ { "-pbc", FALSE, etBOOL, { &bPBC }, "PBC check" },
+ { "-fit", FALSE, etENUM, { fit }, "Fit to reference structure" },
+ { "-prev", FALSE, etINT, { &prev }, "Compare with previous frame" },
+ { "-split", FALSE, etBOOL, { &bSplit }, "Split graph where time is zero" },
+ { "-fitall", FALSE, etBOOL, { &bFitAll }, "HIDDENFit all pairs of structures in matrix" },
+ { "-skip", FALSE, etINT, { &freq }, "Only write every nr-th frame to matrix" },
+ { "-skip2", FALSE, etINT, { &freq2 }, "Only write every nr-th frame to matrix" },
+ { "-max", FALSE, etREAL, { &rmsd_user_max }, "Maximum level in comparison matrix" },
+ { "-min", FALSE, etREAL, { &rmsd_user_min }, "Minimum level in comparison matrix" },
+ { "-bmax", FALSE, etREAL, { &bond_user_max }, "Maximum level in bond angle matrix" },
+ { "-bmin", FALSE, etREAL, { &bond_user_min }, "Minimum level in bond angle matrix" },
+ { "-mw", FALSE, etBOOL, { &bMassWeighted }, "Use mass weighting for superposition" },
+ { "-nlevels", FALSE, etINT, { &nlevels }, "Number of levels in the matrices" },
+ { "-ng", FALSE, etINT, { &nrms }, "Number of groups to compute RMS between" },
+ { "-dlog", FALSE, etBOOL, { &bDeltaLog }, "HIDDENUse a log x-axis in the delta t matrix" },
+ { "-dmax", FALSE, etREAL, { &delta_maxy }, "HIDDENMaximum level in delta matrix" },
+ { "-aver", FALSE, etINT, { &avl }, "HIDDENAverage over this distance in the RMSD matrix" }
};
- int natoms_trx, natoms_trx2, natoms;
- int i, j, k, m;
+ int natoms_trx, natoms_trx2, natoms;
+ int i, j, k, m;
#define NFRAME 5000
- int maxframe = NFRAME, maxframe2 = NFRAME;
- real t, *w_rls, *w_rms, *w_rls_m = nullptr, *w_rms_m = nullptr;
- gmx_bool bNorm, bAv, bFreq2, bFile2, bMat, bBond, bDelta, bMirror, bMass;
- gmx_bool bFit, bReset;
- t_topology top;
- int ePBC;
- t_iatom *iatom = nullptr;
+ int maxframe = NFRAME, maxframe2 = NFRAME;
+ real t, *w_rls, *w_rms, *w_rls_m = nullptr, *w_rms_m = nullptr;
+ gmx_bool bNorm, bAv, bFreq2, bFile2, bMat, bBond, bDelta, bMirror, bMass;
+ gmx_bool bFit, bReset;
+ t_topology top;
+ int ePBC;
+ t_iatom* iatom = nullptr;
- matrix box = {{0}};
- rvec *x, *xp, *xm = nullptr, **mat_x = nullptr, **mat_x2, *mat_x2_j = nullptr, vec1,
- vec2;
- t_trxstatus *status;
- char buf[256], buf2[256];
- int ncons = 0;
- FILE *fp;
- real rlstot = 0, **rls, **rlsm = nullptr, *time, *time2, *rlsnorm = nullptr,
- **rmsd_mat = nullptr, **bond_mat = nullptr, *axis, *axis2, *del_xaxis,
- *del_yaxis, rmsd_max, rmsd_min, rmsd_avg, bond_max, bond_min, ang;
- real **rmsdav_mat = nullptr, av_tot, weight, weight_tot;
- real **delta = nullptr, delta_max, delta_scalex = 0, delta_scaley = 0,
- *delta_tot;
- int delta_xsize = 0, del_lev = 100, mx, my, abs_my;
- gmx_bool bA1, bA2, bPrev, bTop, *bInMat = nullptr;
- int ifit, *irms, ibond = 0, *ind_bond1 = nullptr, *ind_bond2 = nullptr, n_ind_m =
- 0;
- int *ind_fit, **ind_rms, *ind_m = nullptr, *rev_ind_m = nullptr, *ind_rms_m =
- nullptr;
- char *gn_fit, **gn_rms;
- t_rgb rlo, rhi;
- gmx_output_env_t *oenv;
+ matrix box = { { 0 } };
+ rvec * x, *xp, *xm = nullptr, **mat_x = nullptr, **mat_x2, *mat_x2_j = nullptr, vec1, vec2;
+ t_trxstatus* status;
+ char buf[256], buf2[256];
+ int ncons = 0;
+ FILE* fp;
+ real rlstot = 0, **rls, **rlsm = nullptr, *time, *time2, *rlsnorm = nullptr,
+ **rmsd_mat = nullptr, **bond_mat = nullptr, *axis, *axis2, *del_xaxis, *del_yaxis,
+ rmsd_max, rmsd_min, rmsd_avg, bond_max, bond_min, ang;
+ real ** rmsdav_mat = nullptr, av_tot, weight, weight_tot;
+ real ** delta = nullptr, delta_max, delta_scalex = 0, delta_scaley = 0, *delta_tot;
+ int delta_xsize = 0, del_lev = 100, mx, my, abs_my;
+ gmx_bool bA1, bA2, bPrev, bTop, *bInMat = nullptr;
+ int ifit, *irms, ibond = 0, *ind_bond1 = nullptr, *ind_bond2 = nullptr, n_ind_m = 0;
+ int * ind_fit, **ind_rms, *ind_m = nullptr, *rev_ind_m = nullptr, *ind_rms_m = nullptr;
+ char * gn_fit, **gn_rms;
+ t_rgb rlo, rhi;
+ gmx_output_env_t* oenv;
gmx_rmpbc_t gpbc = nullptr;
- t_filenm fnm[] =
- {
- { efTPS, nullptr, nullptr, ffREAD },
- { efTRX, "-f", nullptr, ffREAD },
- { efTRX, "-f2", nullptr, ffOPTRD },
- { efNDX, nullptr, nullptr, ffOPTRD },
- { efXVG, nullptr, "rmsd", ffWRITE },
- { efXVG, "-mir", "rmsdmir", ffOPTWR },
- { efXVG, "-a", "avgrp", ffOPTWR },
- { efXVG, "-dist", "rmsd-dist", ffOPTWR },
- { efXPM, "-m", "rmsd", ffOPTWR },
- { efDAT, "-bin", "rmsd", ffOPTWR },
+ t_filenm fnm[] = {
+ { efTPS, nullptr, nullptr, ffREAD }, { efTRX, "-f", nullptr, ffREAD },
+ { efTRX, "-f2", nullptr, ffOPTRD }, { efNDX, nullptr, nullptr, ffOPTRD },
+ { efXVG, nullptr, "rmsd", ffWRITE }, { efXVG, "-mir", "rmsdmir", ffOPTWR },
+ { efXVG, "-a", "avgrp", ffOPTWR }, { efXVG, "-dist", "rmsd-dist", ffOPTWR },
+ { efXPM, "-m", "rmsd", ffOPTWR }, { efDAT, "-bin", "rmsd", ffOPTWR },
{ efXPM, "-bm", "bond", ffOPTWR }
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr,
- &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW, NFILE, fnm,
+ asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
bBond = opt2bSet("-bm", NFILE, fnm);
bDelta = (delta_maxy > 0); /* calculate rmsd vs delta t matrix from *
* your RMSD matrix (hidden option */
- bNorm = opt2bSet("-a", NFILE, fnm);
- bFreq2 = opt2parg_bSet("-skip2", asize(pa), pa);
+ bNorm = opt2bSet("-a", NFILE, fnm);
+ bFreq2 = opt2parg_bSet("-skip2", asize(pa), pa);
if (freq <= 0)
{
- fprintf(stderr, "The number of frames to skip is <= 0. "
+ fprintf(stderr,
+ "The number of frames to skip is <= 0. "
"Writing out all frames.\n\n");
freq = 1;
}
bPrev = (prev > 0);
if (bPrev)
{
- fprintf(stderr, "WARNING: using option -prev with large trajectories will\n"
+ fprintf(stderr,
+ "WARNING: using option -prev with large trajectories will\n"
" require a lot of memory and could lead to crashes\n");
prev = abs(prev);
if (freq != 1)
if (bFile2 && !bMat && !bBond)
{
- fprintf(
- stderr,
+ fprintf(stderr,
"WARNING: second trajectory (-f2) useless when not calculating matrix (-m/-bm),\n"
- " will not read from %s\n", opt2fn("-f2", NFILE,
- fnm));
+ " will not read from %s\n",
+ opt2fn("-f2", NFILE, fnm));
bFile2 = FALSE;
}
{
fprintf(stderr,
"WARNING: second trajectory (-f2) useless when making delta matrix,\n"
- " will not read from %s\n", opt2fn("-f2",
- NFILE, fnm));
+ " will not read from %s\n",
+ opt2fn("-f2", NFILE, fnm));
bFile2 = FALSE;
}
}
- bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xp,
- nullptr, box, TRUE);
+ bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xp, nullptr, box, TRUE);
snew(w_rls, top.atoms.nr);
snew(w_rms, top.atoms.nr);
if (bReset)
{
- fprintf(stderr, "Select group for %s fit\n", bFit ? "least squares"
- : "translational");
- get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &ifit,
- &ind_fit, &gn_fit);
+ fprintf(stderr, "Select group for %s fit\n", bFit ? "least squares" : "translational");
+ get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &ifit, &ind_fit, &gn_fit);
}
else
{
{
if (bFit && ifit < 3)
{
- gmx_fatal(FARGS, "Need >= 3 points to fit!\n" );
+ gmx_fatal(FARGS, "Need >= 3 points to fit!\n");
}
bMass = FALSE;
snew(ind_rms, nrms);
snew(irms, nrms);
- fprintf(stderr, "Select group%s for %s calculation\n",
- (nrms > 1) ? "s" : "", whatname[ewhat]);
- get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm),
- nrms, irms, ind_rms, gn_rms);
+ fprintf(stderr, "Select group%s for %s calculation\n", (nrms > 1) ? "s" : "", whatname[ewhat]);
+ get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm), nrms, irms, ind_rms, gn_rms);
if (bNorm)
{
natoms_trx = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
if (natoms_trx != top.atoms.nr)
{
- fprintf(stderr,
- "\nWARNING: topology has %d atoms, whereas trajectory has %d\n",
+ fprintf(stderr, "\nWARNING: topology has %d atoms, whereas trajectory has %d\n",
top.atoms.nr, natoms_trx);
}
natoms = std::min(top.atoms.nr, natoms_trx);
{
if (IS_CHEMBOND(k))
{
- ncons += top.idef.il[k].nr/3;
+ ncons += top.idef.il[k].nr / 3;
}
}
fprintf(stderr, "Found %d bonds in topology\n", ncons);
if (IS_CHEMBOND(k))
{
iatom = top.idef.il[k].iatoms;
- ncons = top.idef.il[k].nr/3;
+ ncons = top.idef.il[k].nr / 3;
for (i = 0; i < ncons; i++)
{
bA1 = FALSE;
bA2 = FALSE;
for (j = 0; j < irms[0]; j++)
{
- if (iatom[3*i+1] == ind_rms[0][j])
+ if (iatom[3 * i + 1] == ind_rms[0][j])
{
bA1 = TRUE;
}
- if (iatom[3*i+2] == ind_rms[0][j])
+ if (iatom[3 * i + 2] == ind_rms[0][j])
{
bA2 = TRUE;
}
}
if (bA1 && bA2)
{
- ind_bond1[ibond] = rev_ind_m[iatom[3*i+1]];
- ind_bond2[ibond] = rev_ind_m[iatom[3*i+2]];
+ ind_bond1[ibond] = rev_ind_m[iatom[3 * i + 1]];
+ ind_bond2[ibond] = rev_ind_m[iatom[3 * i + 2]];
ibond++;
}
}
{
if (tel_mat >= NFRAME)
{
- srenew(mat_x, tel_mat+1);
+ srenew(mat_x, tel_mat + 1);
}
snew(mat_x[tel_mat], n_ind_m);
for (i = 0; i < n_ind_m; i++)
/*calculate energy of root_least_squares*/
if (bPrev)
{
- j = tel_mat-prev-1;
+ j = tel_mat - prev - 1;
if (j < 0)
{
j = 0;
}
for (j = 0; (j < nrms); j++)
{
- rls[j][teller] =
- calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xp);
+ rls[j][teller] = calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xp);
}
if (bNorm)
{
for (j = 0; (j < irms[0]); j++)
{
- rlsnorm[j] +=
- calc_similar_ind(ewhat != ewRMSD, 1, &(ind_rms[0][j]), w_rms, x, xp);
+ rlsnorm[j] += calc_similar_ind(ewhat != ewRMSD, 1, &(ind_rms[0][j]), w_rms, x, xp);
}
}
for (j = 0; j < nrms; j++)
{
rlsm[j][teller] =
- calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xm);
+ calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xm);
}
}
time[teller] = output_env_conv_time(oenv, t);
}
}
}
- }
- while (read_next_x(oenv, status, &t, x, box));
+ } while (read_next_x(oenv, status, &t, x, box));
close_trx(status);
int tel_mat2 = 0;
fprintf(stderr, "\nWill read second trajectory file\n");
snew(mat_x2, NFRAME);
- natoms_trx2 =
- read_first_x(oenv, &status, opt2fn("-f2", NFILE, fnm), &t, &x, box);
+ natoms_trx2 = read_first_x(oenv, &status, opt2fn("-f2", NFILE, fnm), &t, &x, box);
if (natoms_trx2 != natoms_trx)
{
gmx_fatal(FARGS,
"Second trajectory (%d atoms) does not match the first one"
- " (%d atoms)", natoms_trx2, natoms_trx);
+ " (%d atoms)",
+ natoms_trx2, natoms_trx);
}
frame2 = 0;
do
{
if (tel_mat2 >= NFRAME)
{
- srenew(mat_x2, tel_mat2+1);
+ srenew(mat_x2, tel_mat2 + 1);
}
snew(mat_x2[tel_mat2], n_ind_m);
for (i = 0; i < n_ind_m; i++)
maxframe2 += NFRAME;
srenew(time2, maxframe2);
}
- }
- while (read_next_x(oenv, status, &t, x, box));
+ } while (read_next_x(oenv, status, &t, x, box));
close_trx(status);
}
else
fprintf(stderr, "\n");
if (bMat)
{
- fprintf(stderr, "Building %s matrix, %dx%d elements\n",
- whatname[ewhat], tel_mat, tel_mat2);
+ fprintf(stderr, "Building %s matrix, %dx%d elements\n", whatname[ewhat], tel_mat, tel_mat2);
snew(rmsd_mat, tel_mat);
}
if (bBond)
{
- fprintf(stderr, "Building bond angle matrix, %dx%d elements\n",
- tel_mat, tel_mat2);
+ fprintf(stderr, "Building bond angle matrix, %dx%d elements\n", tel_mat, tel_mat2);
snew(bond_mat, tel_mat);
}
snew(axis, tel_mat);
bond_min = 1e10;
for (j = 0; j < tel_mat2; j++)
{
- axis2[j] = time2[freq2*j];
+ axis2[j] = time2[freq2 * j];
}
if (bDelta)
{
if (bDeltaLog)
{
- delta_scalex = 8.0/std::log(2.0);
- delta_xsize = gmx::roundToInt(std::log(tel_mat/2.)*delta_scalex)+1;
+ delta_scalex = 8.0 / std::log(2.0);
+ delta_xsize = gmx::roundToInt(std::log(tel_mat / 2.) * delta_scalex) + 1;
}
else
{
- delta_xsize = tel_mat/2;
+ delta_xsize = tel_mat / 2;
}
- delta_scaley = 1.0/delta_maxy;
+ delta_scaley = 1.0 / delta_maxy;
snew(delta, delta_xsize);
for (j = 0; j < delta_xsize; j++)
{
- snew(delta[j], del_lev+1);
+ snew(delta[j], del_lev + 1);
}
if (avl > 0)
{
}
for (i = 0; i < tel_mat; i++)
{
- axis[i] = time[freq*i];
+ axis[i] = time[freq * i];
fprintf(stderr, "\r element %5d; time %5.2f ", i, axis[i]);
fflush(stderr);
if (bMat)
{
if (bFile2 || (i < j))
{
- rmsd_mat[i][j] =
- calc_similar_ind(ewhat != ewRMSD, irms[0], ind_rms_m,
- w_rms_m, mat_x[i], mat_x2_j);
+ rmsd_mat[i][j] = calc_similar_ind(ewhat != ewRMSD, irms[0], ind_rms_m,
+ w_rms_m, mat_x[i], mat_x2_j);
if (rmsd_mat[i][j] > rmsd_max)
{
rmsd_max = rmsd_mat[i][j];
rvec_sub(mat_x2_j[ind_bond1[m]], mat_x2_j[ind_bond2[m]], vec2);
ang += std::acos(cos_angle(vec1, vec2));
}
- bond_mat[i][j] = ang*180.0/(M_PI*ibond);
+ bond_mat[i][j] = ang * 180.0 / (M_PI * ibond);
if (bond_mat[i][j] > bond_max)
{
bond_max = bond_mat[i][j];
}
if (bFile2)
{
- rmsd_avg /= static_cast<real>(tel_mat)*static_cast<real>(tel_mat2);
+ rmsd_avg /= static_cast<real>(tel_mat) * static_cast<real>(tel_mat2);
}
else
{
- rmsd_avg /= tel_mat*(tel_mat - 1)/2.;
+ rmsd_avg /= tel_mat * (tel_mat - 1) / 2.;
}
if (bMat && (avl > 0))
{
rmsd_max = 0.0;
rmsd_min = 0.0;
rmsd_avg = 0.0;
- for (j = 0; j < tel_mat-1; j++)
+ for (j = 0; j < tel_mat - 1; j++)
{
- for (i = j+1; i < tel_mat; i++)
+ for (i = j + 1; i < tel_mat; i++)
{
av_tot = 0;
weight_tot = 0;
for (my = -avl; my <= avl; my++)
{
- if ((j+my >= 0) && (j+my < tel_mat))
+ if ((j + my >= 0) && (j + my < tel_mat))
{
abs_my = std::abs(my);
for (mx = -avl; mx <= avl; mx++)
{
- if ((i+mx >= 0) && (i+mx < tel_mat))
+ if ((i + mx >= 0) && (i + mx < tel_mat))
{
- weight = avl+1.0-std::max(std::abs(mx), abs_my);
- av_tot += weight*rmsd_mat[i+mx][j+my];
+ weight = avl + 1.0 - std::max(std::abs(mx), abs_my);
+ av_tot += weight * rmsd_mat[i + mx][j + my];
weight_tot += weight;
}
}
}
}
- rmsdav_mat[i][j] = av_tot/weight_tot;
+ rmsdav_mat[i][j] = av_tot / weight_tot;
rmsdav_mat[j][i] = rmsdav_mat[i][j];
if (rmsdav_mat[i][j] > rmsd_max)
{
if (bMat)
{
- fprintf(stderr, "\n%s: Min %f, Max %f, Avg %f\n",
- whatname[ewhat], rmsd_min, rmsd_max, rmsd_avg);
- rlo.r = 1; rlo.g = 1; rlo.b = 1;
- rhi.r = 0; rhi.g = 0; rhi.b = 0;
+ fprintf(stderr, "\n%s: Min %f, Max %f, Avg %f\n", whatname[ewhat], rmsd_min, rmsd_max, rmsd_avg);
+ rlo.r = 1;
+ rlo.g = 1;
+ rlo.b = 1;
+ rhi.r = 0;
+ rhi.g = 0;
+ rhi.b = 0;
if (rmsd_user_max != -1)
{
rmsd_max = rmsd_user_max;
{
rmsd_min = rmsd_user_min;
}
- if ((rmsd_user_max != -1) || (rmsd_user_min != -1))
+ if ((rmsd_user_max != -1) || (rmsd_user_min != -1))
{
- fprintf(stderr, "Min and Max value set to resp. %f and %f\n",
- rmsd_min, rmsd_max);
+ fprintf(stderr, "Min and Max value set to resp. %f and %f\n", rmsd_min, rmsd_max);
}
sprintf(buf, "%s %s matrix", gn_rms[0], whatname[ewhat]);
write_xpm(opt2FILE("-m", NFILE, fnm, "w"), 0, buf, whatlabel[ewhat],
- output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat, tel_mat2,
- axis, axis2, rmsd_mat, rmsd_min, rmsd_max, rlo, rhi, &nlevels);
+ output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat,
+ tel_mat2, axis, axis2, rmsd_mat, rmsd_min, rmsd_max, rlo, rhi, &nlevels);
/* Print the distribution of RMSD values */
if (opt2bSet("-dist", NFILE, fnm))
{
if (bDelta)
{
snew(delta_tot, delta_xsize);
- for (j = 0; j < tel_mat-1; j++)
+ for (j = 0; j < tel_mat - 1; j++)
{
- for (i = j+1; i < tel_mat; i++)
+ for (i = j + 1; i < tel_mat; i++)
{
- mx = i-j;
- if (mx < tel_mat/2)
+ mx = i - j;
+ if (mx < tel_mat / 2)
{
if (bDeltaLog)
{
- mx = gmx::roundToInt(std::log(static_cast<real>(mx))*delta_scalex);
+ mx = gmx::roundToInt(std::log(static_cast<real>(mx)) * delta_scalex);
}
- my = gmx::roundToInt(rmsd_mat[i][j]*delta_scaley*static_cast<real>(del_lev));
+ my = gmx::roundToInt(rmsd_mat[i][j] * delta_scaley * static_cast<real>(del_lev));
delta_tot[mx] += 1.0;
if ((rmsd_mat[i][j] >= 0) && (rmsd_mat[i][j] <= delta_maxy))
{
{
if (delta_tot[i] > 0.0)
{
- delta_tot[i] = 1.0/delta_tot[i];
+ delta_tot[i] = 1.0 / delta_tot[i];
for (j = 0; j <= del_lev; j++)
{
delta[i][j] *= delta_tot[i];
}
fprintf(stderr, "Maximum in delta matrix: %f\n", delta_max);
snew(del_xaxis, delta_xsize);
- snew(del_yaxis, del_lev+1);
+ snew(del_yaxis, del_lev + 1);
for (i = 0; i < delta_xsize; i++)
{
- del_xaxis[i] = axis[i]-axis[0];
+ del_xaxis[i] = axis[i] - axis[0];
}
- for (i = 0; i < del_lev+1; i++)
+ for (i = 0; i < del_lev + 1; i++)
{
- del_yaxis[i] = delta_maxy*static_cast<real>(i)/static_cast<real>(del_lev);
+ del_yaxis[i] = delta_maxy * static_cast<real>(i) / static_cast<real>(del_lev);
}
sprintf(buf, "%s %s vs. delta t", gn_rms[0], whatname[ewhat]);
fp = gmx_ffopen("delta.xpm", "w");
write_xpm(fp, 0, buf, "density", output_env_get_time_label(oenv), whatlabel[ewhat],
- delta_xsize, del_lev+1, del_xaxis, del_yaxis,
- delta, 0.0, delta_max, rlo, rhi, &nlevels);
+ delta_xsize, del_lev + 1, del_xaxis, del_yaxis, delta, 0.0, delta_max,
+ rlo, rhi, &nlevels);
gmx_ffclose(fp);
}
if (opt2bSet("-bin", NFILE, fnm))
{
bond_min = bond_user_min;
}
- if ((bond_user_max != -1) || (bond_user_min != -1))
+ if ((bond_user_max != -1) || (bond_user_min != -1))
{
- fprintf(stderr, "Bond angle Min and Max set to:\n"
- "Min. angle: %f, Max. angle: %f\n", bond_min, bond_max);
+ fprintf(stderr,
+ "Bond angle Min and Max set to:\n"
+ "Min. angle: %f, Max. angle: %f\n",
+ bond_min, bond_max);
}
- rlo.r = 1; rlo.g = 1; rlo.b = 1;
- rhi.r = 0; rhi.g = 0; rhi.b = 0;
+ rlo.r = 1;
+ rlo.g = 1;
+ rlo.b = 1;
+ rhi.r = 0;
+ rhi.g = 0;
+ rhi.b = 0;
sprintf(buf, "%s av. bond angle deviation", gn_rms[0]);
write_xpm(opt2FILE("-bm", NFILE, fnm, "w"), 0, buf, "degrees",
- output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat, tel_mat2,
- axis, axis2, bond_mat, bond_min, bond_max, rlo, rhi, &nlevels);
+ output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat,
+ tel_mat2, axis, axis2, bond_mat, bond_min, bond_max, rlo, rhi, &nlevels);
}
}
}
else
{
- sprintf(buf, "%s with frame %g %s ago", whatxvgname[ewhat],
- time[prev*freq]-time[0], output_env_get_time_label(oenv).c_str());
+ sprintf(buf, "%s with frame %g %s ago", whatxvgname[ewhat], time[prev * freq] - time[0],
+ output_env_get_time_label(oenv).c_str());
}
fp = xvgropen(opt2fn("-o", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
whatxvglabel[ewhat], oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
- fprintf(fp, "@ subtitle \"%s%s after %s%s%s\"\n",
- (nrms == 1) ? "" : "of ", gn_rms[0], fitgraphlabel[efit],
- bFit ? " to " : "", bFit ? gn_fit : "");
+ fprintf(fp, "@ subtitle \"%s%s after %s%s%s\"\n", (nrms == 1) ? "" : "of ", gn_rms[0],
+ fitgraphlabel[efit], bFit ? " to " : "", bFit ? gn_fit : "");
}
if (nrms != 1)
{
}
for (i = 0; (i < teller); i++)
{
- if (bSplit && i > 0 &&
- std::abs(time[bPrev ? freq*i : i]/output_env_get_time_factor(oenv)) < 1e-5)
+ if (bSplit && i > 0 && std::abs(time[bPrev ? freq * i : i] / output_env_get_time_factor(oenv)) < 1e-5)
{
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
- fprintf(fp, "%12.7f", time[bPrev ? freq*i : i]);
+ fprintf(fp, "%12.7f", time[bPrev ? freq * i : i]);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, " %12.7f", rls[j][i]);
/* Write the mirror RMSD's to file */
sprintf(buf, "%s with Mirror", whatxvgname[ewhat]);
sprintf(buf2, "Mirror %s", whatxvglabel[ewhat]);
- fp = xvgropen(opt2fn("-mir", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
- buf2, oenv);
+ fp = xvgropen(opt2fn("-mir", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv), buf2, oenv);
if (nrms == 1)
{
if (output_env_get_print_xvgr_codes(oenv))
{
- fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n",
- gn_rms[0], bFit ? gn_fit : "");
+ fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n", gn_rms[0],
+ bFit ? gn_fit : "");
}
}
else
fp = xvgropen(opt2fn("-a", NFILE, fnm), buf, "Residue", buf2, oenv);
for (j = 0; (j < nrms); j++)
{
- fprintf(fp, "%10d %10g\n", j, rlstot/static_cast<real>(teller));
+ fprintf(fp, "%10d %10g\n", j, rlstot / static_cast<real>(teller));
}
xvgrclose(fp);
}
fp = xvgropen("aver.xvg", gn_rms[0], "Residue", whatxvglabel[ewhat], oenv);
for (j = 0; (j < irms[0]); j++)
{
- fprintf(fp, "%10d %10g\n", j, rlsnorm[j]/static_cast<real>(teller));
+ fprintf(fp, "%10d %10g\n", j, rlsnorm[j] / static_cast<real>(teller));
}
xvgrclose(fp);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff