*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* 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 <stdio.h>
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "gstat.h"
-#include "macros.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 "physics.h"
-#include "index.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
-#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "xvgr.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.");
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
for (i = 0; (i < NJC); i++)
{
sfree(leg[i]);
}
}
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
- gmx_ffclose(fp);
+ xvgrclose(fp);
if (bSSHisto)
{
for (k = 0; (k < 3); k++)
{
gmx_ffclose(gp);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
if (bOm)
{
sprintf(fn, "ramomega%s.xpm", dlist[i].name);
{
fprintf(fp, "%10g %10g\n", RAD2DEG*dih[Xi1][j], RAD2DEG*dih[Xi2][j]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
else
{
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",
/* fprintf(fp,"%12s\n",dlist[i].name); this confuses xmgrace */
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
static void order_params(FILE *log,
for (i = 0; i < NLEG; i++)
{
- leg[i] = strdup(const_leg[i]);
+ leg[i] = gmx_strdup(const_leg[i]);
}
/* Print order parameters */
fprintf(fp, "\n");
/* fprintf(fp,"%12s\n",dlist[i].name); this confuses xmgrace */
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
if (NULL != pdbfn)
{
"With option [TT]-all[tt], the angles themselves as a function of time for",
"each residue are printed to separate files [TT](dihedral)(RESIDUE)(nresnr).xvg[tt].",
"These can be in radians or degrees.[PAR]",
- "A log file (argument [TT]-g[tt]) is also written. This contains [BR]",
- "(a) information about the number of residues of each type.[BR]",
- "(b) The NMR ^3J coupling constants from the Karplus equation.[BR]",
- "(c) a table for each residue of the number of transitions between ",
- "rotamers per nanosecond, and the order parameter S^2 of each dihedral.[BR]",
- "(d) a table for each residue of the rotamer occupancy.[PAR]",
+ "A log file (argument [TT]-g[tt]) is also written. This contains",
+ "",
+ " * information about the number of residues of each type.",
+ " * The NMR ^3J coupling constants from the Karplus equation.",
+ " * a table for each residue of the number of transitions between ",
+ " rotamers per nanosecond, and the order parameter S^2 of each dihedral.",
+ " * a table for each residue of the rotamer occupancy.",
+ "",
"All rotamers are taken as 3-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals",
"to planar groups (i.e. [GRK]chi[grk][SUB]2[sub] of aromatics, Asp and Asn; [GRK]chi[grk][SUB]3[sub] of Glu",
"and Gln; and [GRK]chi[grk][SUB]4[sub] of Arg), which are 2-fold. \"rotamer 0\" means ",
"that the dihedral was not in the core region of each rotamer. ",
"The width of the core region can be set with [TT]-core_rotamer[tt][PAR]",
- "The S^2 order parameters are also output to an [TT].xvg[tt] file",
- "(argument [TT]-o[tt] ) and optionally as a [TT].pdb[tt] file with",
+ "The S^2 order parameters are also output to an [REF].xvg[ref] file",
+ "(argument [TT]-o[tt] ) and optionally as a [REF].pdb[ref] file with",
"the S^2 values as B-factor (argument [TT]-p[tt]). ",
"The total number of rotamer transitions per timestep",
"(argument [TT]-ot[tt]), the number of transitions per rotamer",
"(argument [TT]-rt[tt]), and the ^3J couplings (argument [TT]-jc[tt]), ",
- "can also be written to [TT].xvg[tt] files. Note that the analysis",
+ "can also be written to [REF].xvg[ref] files. Note that the analysis",
"of rotamer transitions assumes that the supplied trajectory frames",
"are equally spaced in time.[PAR]",
{ "-binwidth", FALSE, etINT, {&ndeg},
"bin width for histograms (degrees)" },
{ "-core_rotamer", FALSE, etREAL, {&core_frac},
- "only the central [TT]-core_rotamer[tt]*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
+ "only the central [TT]-core_rotamer[tt]\\*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
{ "-maxchi", FALSE, etENUM, {maxchistr},
"calculate first ndih [GRK]chi[grk] dihedrals" },
{ "-normhisto", FALSE, etBOOL, {&bNormHisto},
"Normalize histograms" },
{ "-ramomega", FALSE, etBOOL, {&bRamOmega},
- "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [TT].xpm[tt] plot" },
+ "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [REF].xpm[ref] plot" },
{ "-bfact", FALSE, etREAL, {&bfac_init},
- "B-factor value for [TT].pdb[tt] file for atoms with no calculated dihedral order parameter"},
+ "B-factor value for [REF].pdb[ref] file for atoms with no calculated dihedral order parameter"},
{ "-chi_prod", FALSE, etBOOL, {&bChiProduct},
"compute a single cumulative rotamer for each residue"},
{ "-HChi", FALSE, etBOOL, {&bHChi},
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))
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff