* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdio.h>
#include <string.h>
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/residuetypes.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
-#include "gstat.h"
-#include "macros.h"
-#include "gromacs/math/utilities.h"
-#include "physics.h"
-#include "index.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "viewit.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
static gmx_bool bAllowed(real phi, real psi)
{
return j;
}
-static void histogramming(FILE *log, int nbin, gmx_residuetype_t rt,
+static void histogramming(FILE *log, int nbin, gmx_residuetype_t *rt,
int nf, int maxchi, real **dih,
int nlist, t_dlist dlist[],
atom_id index[],
snew(leg, NJC);
for (i = 0; (i < NKKKPHI); i++)
{
- leg[i] = strdup(kkkphi[i].name);
+ leg[i] = gmx_strdup(kkkphi[i].name);
}
for (i = 0; (i < NKKKPSI); i++)
{
- leg[i+NKKKPHI] = strdup(kkkpsi[i].name);
+ leg[i+NKKKPHI] = gmx_strdup(kkkpsi[i].name);
}
for (i = 0; (i < NKKKCHI); i++)
{
- leg[i+NKKKPHI+NKKKPSI] = strdup(kkkchi1[i].name);
+ leg[i+NKKKPHI+NKKKPSI] = gmx_strdup(kkkchi1[i].name);
}
xvgr_legend(fp, NJC, (const char**)leg, oenv);
fprintf(fp, "%5s ", "#Res.");
strcpy(hhisfile, hisfile);
strcat(hhisfile, ".xvg");
fp = xvgropen(hhisfile, title, "Degrees", "", oenv);
- fprintf(fp, "@ with g0\n");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@ with g0\n");
+ }
xvgr_world(fp, -180, 0, 180, 0.1, oenv);
- fprintf(fp, "# this effort to set graph size fails unless you run with -autoscale none or -autoscale y flags\n");
- fprintf(fp, "@ xaxis tick on\n");
- fprintf(fp, "@ xaxis tick major 90\n");
- fprintf(fp, "@ xaxis tick minor 30\n");
- fprintf(fp, "@ xaxis ticklabel prec 0\n");
- fprintf(fp, "@ yaxis tick off\n");
- fprintf(fp, "@ yaxis ticklabel off\n");
- fprintf(fp, "@ type xy\n");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "# this effort to set graph size fails unless you run with -autoscale none or -autoscale y flags\n");
+ fprintf(fp, "@ xaxis tick on\n");
+ fprintf(fp, "@ xaxis tick major 90\n");
+ fprintf(fp, "@ xaxis tick minor 30\n");
+ fprintf(fp, "@ xaxis ticklabel prec 0\n");
+ fprintf(fp, "@ yaxis tick off\n");
+ fprintf(fp, "@ yaxis ticklabel off\n");
+ fprintf(fp, "@ type xy\n");
+ }
if (bSSHisto)
{
for (k = 0; (k < 3); k++)
}
}
}
- fprintf(fp, "&\n");
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
gmx_ffclose(fp);
if (bSSHisto)
{
for (k = 0; (k < 3); k++)
{
- fprintf(ssfp[k], "&\n");
+ fprintf(ssfp[k], "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
gmx_ffclose(ssfp[k]);
}
}
FILE *fp;
fp = xvgropen(fn, title, xaxis, yaxis, oenv);
- fprintf(fp, "@ with g0\n");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@ with g0\n");
+ }
xvgr_world(fp, -180, -180, 180, 180, oenv);
- fprintf(fp, "@ xaxis tick on\n");
- fprintf(fp, "@ xaxis tick major 90\n");
- fprintf(fp, "@ xaxis tick minor 30\n");
- fprintf(fp, "@ xaxis ticklabel prec 0\n");
- fprintf(fp, "@ yaxis tick on\n");
- fprintf(fp, "@ yaxis tick major 90\n");
- fprintf(fp, "@ yaxis tick minor 30\n");
- fprintf(fp, "@ yaxis ticklabel prec 0\n");
- fprintf(fp, "@ s0 type xy\n");
- fprintf(fp, "@ s0 symbol 2\n");
- fprintf(fp, "@ s0 symbol size 0.410000\n");
- fprintf(fp, "@ s0 symbol fill 1\n");
- fprintf(fp, "@ s0 symbol color 1\n");
- fprintf(fp, "@ s0 symbol linewidth 1\n");
- fprintf(fp, "@ s0 symbol linestyle 1\n");
- fprintf(fp, "@ s0 symbol center false\n");
- fprintf(fp, "@ s0 symbol char 0\n");
- fprintf(fp, "@ s0 skip 0\n");
- fprintf(fp, "@ s0 linestyle 0\n");
- fprintf(fp, "@ s0 linewidth 1\n");
- fprintf(fp, "@ type xy\n");
-
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@ xaxis tick on\n");
+ fprintf(fp, "@ xaxis tick major 90\n");
+ fprintf(fp, "@ xaxis tick minor 30\n");
+ fprintf(fp, "@ xaxis ticklabel prec 0\n");
+ fprintf(fp, "@ yaxis tick on\n");
+ fprintf(fp, "@ yaxis tick major 90\n");
+ fprintf(fp, "@ yaxis tick minor 30\n");
+ fprintf(fp, "@ yaxis ticklabel prec 0\n");
+ fprintf(fp, "@ s0 type xy\n");
+ fprintf(fp, "@ s0 symbol 2\n");
+ fprintf(fp, "@ s0 symbol size 0.410000\n");
+ fprintf(fp, "@ s0 symbol fill 1\n");
+ fprintf(fp, "@ s0 symbol color 1\n");
+ fprintf(fp, "@ s0 symbol linewidth 1\n");
+ fprintf(fp, "@ s0 symbol linestyle 1\n");
+ fprintf(fp, "@ s0 symbol center false\n");
+ fprintf(fp, "@ s0 symbol char 0\n");
+ fprintf(fp, "@ s0 skip 0\n");
+ fprintf(fp, "@ s0 linestyle 0\n");
+ fprintf(fp, "@ s0 linewidth 1\n");
+ fprintf(fp, "@ type xy\n");
+ }
return fp;
}
char *leg[edMax];
#define NLEG asize(leg)
- leg[0] = strdup("Phi");
- leg[1] = strdup("Psi");
- leg[2] = strdup("Omega");
- leg[3] = strdup("Chi1");
- leg[4] = strdup("Chi2");
- leg[5] = strdup("Chi3");
- leg[6] = strdup("Chi4");
- leg[7] = strdup("Chi5");
- leg[8] = strdup("Chi6");
+ leg[0] = gmx_strdup("Phi");
+ leg[1] = gmx_strdup("Psi");
+ leg[2] = gmx_strdup("Omega");
+ leg[3] = gmx_strdup("Chi1");
+ leg[4] = gmx_strdup("Chi2");
+ leg[5] = gmx_strdup("Chi3");
+ leg[6] = gmx_strdup("Chi4");
+ leg[7] = gmx_strdup("Chi5");
+ leg[8] = gmx_strdup("Chi6");
/* Print order parameters */
fp = xvgropen(fn, "Dihedral Rotamer Transitions", "Residue", "Transitions/ns",
{
FILE *fp;
int nh[edMax];
- char buf[STRLEN];
int i, Dih, Xi;
real S2Max, S2Min;
for (i = 0; i < NLEG; i++)
{
- leg[i] = strdup(const_leg[i]);
+ leg[i] = gmx_strdup(const_leg[i]);
}
/* Print order parameters */
x0 *= 10.0; /* nm -> angstrom */
y0 *= 10.0; /* nm -> angstrom */
z0 *= 10.0; /* nm -> angstrom */
- sprintf(buf, "%s%%6.f%%6.2f\n", get_pdbformat());
for (i = 0; (i < 10); i++)
{
- fprintf(fp, buf, "ATOM ", 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, epdbATOM, atoms->nr+1+i, "CA", ' ', "LEG", ' ', atoms->nres+1, ' ',
+ x0, y0, z0+(1.2*i), 0.0, -0.1*i, "");
}
gmx_ffclose(fp);
}
gmx_bool bDo_rt, bDo_oh, bDo_ot, bDo_jc;
real dt = 0, traj_t_ns;
output_env_t oenv;
- gmx_residuetype_t rt;
+ gmx_residuetype_t *rt;
atom_id isize, *index;
int ndih, nactdih, nf;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
&oenv))
{
}
}
- /* Correlation comes last because it fucks up the angles */
+ /* Correlation comes last because it messes up the angles */
if (bCorr)
{
do_dihcorr(opt2fn("-corr", NFILE, fnm), nf, ndih, dih, dt, nlist, dlist, time,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff