/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
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* of the License, or (at your option) any later version.
*
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+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <stdio.h>
-#include <math.h>
+#include "gmxpre.h"
-#include "confio.h"
-#include "pdbio.h"
-#include "gmx_fatal.h"
-#include "futil.h"
-#include "gstat.h"
-#include "macros.h"
-#include "maths.h"
-#include "physics.h"
-#include "index.h"
-#include "smalloc.h"
-#include "statutil.h"
-#include "tpxio.h"
+#include <math.h>
+#include <stdio.h>
#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "strdb.h"
-#include "xvgr.h"
-#include "matio.h"
-#include "gmx_ana.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 "gromacs/utility/smalloc.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[],
rt_size = gmx_residuetype_get_size(rt);
if (bSSHisto)
{
- fp = ffopen(ssdump, "r");
+ fp = gmx_ffopen(ssdump, "r");
if (1 != fscanf(fp, "%d", &nres))
{
gmx_fatal(FARGS, "Error reading from file %s", ssdump);
gmx_fatal(FARGS, "Error reading from file %s", ssdump);
}
- ffclose(fp);
+ gmx_ffclose(fp);
/* Four dimensional array... Very cool */
snew(his_aa_ss, 3);
for (i = 0; (i < 3); i++)
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");
}
- ffclose(fp);
+ gmx_ffclose(fp);
for (i = 0; (i < NJC); i++)
{
sfree(leg[i]);
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++)
{
sprintf(sshisfile, "%s-%s.xvg", hisfile, sss[k]);
- ssfp[k] = ffopen(sshisfile, "w");
+ ssfp[k] = gmx_ffopen(sshisfile, "w");
}
}
for (j = 0; (j < nbin); j++)
}
}
}
- fprintf(fp, "&\n");
- ffclose(fp);
+ 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");
- ffclose(ssfp[k]);
+ 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;
}
if (bViol)
{
sprintf(fn, "violPhiPsi%s.xvg", dlist[i].name);
- gp = ffopen(fn, "w");
+ gp = gmx_ffopen(fn, "w");
}
Phi = dlist[i].j0[edPhi];
Psi = dlist[i].j0[edPsi];
}
if (bViol)
{
- ffclose(gp);
+ gmx_ffclose(gp);
}
- ffclose(fp);
+ gmx_ffclose(fp);
if (bOm)
{
sprintf(fn, "ramomega%s.xpm", dlist[i].name);
- fp = ffopen(fn, "w");
+ fp = gmx_ffopen(fn, "w");
lo = hi = 0;
for (j = 0; (j < NMAT); j++)
{
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);
- ffclose(fp);
+ gmx_ffclose(fp);
for (j = 0; (j < NMAT); j++)
{
sfree(mat[j]);
{
fprintf(fp, "%10g %10g\n", RAD2DEG*dih[Xi1][j], RAD2DEG*dih[Xi2][j]);
}
- ffclose(fp);
+ gmx_ffclose(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");
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
static void order_params(FILE *log,
{
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 */
fprintf(fp, "\n");
/* fprintf(fp,"%12s\n",dlist[i].name); this confuses xmgrace */
}
- ffclose(fp);
+ gmx_ffclose(fp);
if (NULL != pdbfn)
{
}
}
- fp = ffopen(pdbfn, "w");
+ fp = gmx_ffopen(pdbfn, "w");
fprintf(fp, "REMARK generated by g_chi\n");
fprintf(fp, "REMARK "
"B-factor field contains negative of dihedral order parameters\n");
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, "");
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
fprintf(log, "Dihedrals with S2 > 0.8\n");
int gmx_chi(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_chi[tt] computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk], and [GRK]chi[grk] dihedrals for all your ",
+ "[THISMODULE] computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk],",
+ "and [GRK]chi[grk] dihedrals for all your",
"amino acid backbone and sidechains.",
"It can compute dihedral angle as a function of time, and as",
"histogram distributions.",
const char *bugs[] = {
"Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.",
- "[GRK]phi[grk] and [GRK]psi[grk] dihedrals are calculated in a non-standard way, using H-N-CA-C for [GRK]phi[grk] instead of C(-)-N-CA-C, and N-CA-C-O for [GRK]psi[grk] instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like [TT]g_rama[tt].",
+ "[GRK]phi[grk] and [GRK]psi[grk] dihedrals are calculated in a "
+ "non-standard way, using H-N-CA-C for [GRK]phi[grk] instead of "
+ "C(-)-N-CA-C, and N-CA-C-O for [GRK]psi[grk] instead of N-CA-C-N(+). "
+ "This causes (usually small) discrepancies with the output of other "
+ "tools like [gmx-rama].",
"[TT]-r0[tt] option does not work properly",
"Rotamers with multiplicity 2 are printed in [TT]chi.log[tt] as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0"
};
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))
{
sscanf(maxchistr[0], "%d", &maxchi);
bChi = (maxchi > 0);
- log = ffopen(ftp2fn(efLOG, NFILE, fnm), "w");
+ log = gmx_ffopen(ftp2fn(efLOG, NFILE, fnm), "w");
if (bRamOmega)
{
traj_t_ns = 0.001 * (time[nf-1]-time[0]);
pr_dlist(log, nlist, dlist, traj_t_ns, edPrintST, bPhi, bPsi, bChi, bOmega, maxchi);
pr_dlist(log, nlist, dlist, traj_t_ns, edPrintRO, bPhi, bPsi, bChi, bOmega, maxchi);
- ffclose(log);
+ gmx_ffclose(log);
/* transitions to xvg */
if (bDo_rt)
{
}
}
- /* 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