-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
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- * This source code is part of
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include <ctype.h>
-#include "pdbio.h"
-#include "confio.h"
-#include "symtab.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "copyrite.h"
-#include "statutil.h"
-#include "string2.h"
-#include "strdb.h"
-#include "index.h"
-#include "vec.h"
-#include "typedefs.h"
-#include "gbutil.h"
-#include "strdb.h"
-#include "physics.h"
-#include "atomprop.h"
-#include "tpxio.h"
-#include "pbc.h"
+
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/math/units.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
#include "princ.h"
-#include "txtdump.h"
-#include "viewit.h"
-#include "rmpbc.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
typedef struct
{
char sanm[12];
for (i = 0; i < nat; i++)
{
- fprintf(out, get_pdbformat(), "ATOM", a0 + i, "C", "BOX", 'K' + i
- / NCUCVERT, r0 + i, 10 * vert[i][XX], 10 * vert[i][YY], 10
- * vert[i][ZZ]);
- fprintf(out, "\n");
+ gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / NCUCVERT, r0 + i, ' ',
+ 10*vert[i][XX], 10*vert[i][YY], 10*vert[i][ZZ], 1.0, 0.0, "");
}
edge = compact_unitcell_edges();
{
for (x = 0; x <= 1; x++)
{
- fprintf(out, get_pdbformat(), "ATOM", a0 + i, "C", "BOX", 'K' + i
- / 8, r0 + i, x * 10 * box[XX][XX],
- y * 10 * box[YY][YY], z * 10 * box[ZZ][ZZ]);
- fprintf(out, "\n");
+ gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i/8, r0+i, ' ',
+ x * 10 * box[XX][XX], y * 10 * box[YY][YY], z * 10 * box[ZZ][ZZ], 1.0, 0.0, "");
i++;
}
}
int gmx_editconf(int argc, char *argv[])
{
- const char
- *desc[] =
+ const char *desc[] =
{
- "[TT]editconf[tt] converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
+ "[THISMODULE] converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
"or [TT].pdb[tt].",
"[PAR]",
"The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
"[PAR]",
"To convert a truncated octrahedron file produced by a package which uses",
"a cubic box with the corners cut off (such as GROMOS), use:[BR]",
- "[TT]editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out[tt][BR]",
+ "[TT]gmx editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out[tt][BR]",
"where [TT]veclen[tt] is the size of the cubic box times [SQRT]3[sqrt]/2."
};
const char *bugs[] =
{
"For complex molecules, the periodicity removal routine may break down, "
- "in that case you can use [TT]trjconv[tt]."
+ "in that case you can use [gmx-trjconv]."
};
static real dist = 0.0, rbox = 0.0, to_diam = 0.0;
static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
- asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
bIndex = opt2bSet("-n", NFILE, fnm) || bNDEF;
bMead = opt2bSet("-mead", NFILE, fnm);
if (outftp == efPDB)
{
- out = ffopen(outfile, "w");
+ out = gmx_ffopen(outfile, "w");
write_pdbfile_indexed(out, title, &atoms, x, ePBC, box, ' ', 1, isize, index, conect, TRUE);
- ffclose(out);
+ gmx_ffclose(out);
}
else
{
if ((outftp == efPDB) || (outftp == efPQR))
{
- out = ffopen(outfile, "w");
+ out = gmx_ffopen(outfile, "w");
if (bMead)
{
- set_pdb_wide_format(TRUE);
fprintf(out, "REMARK "
"The B-factors in this file hold atomic radii\n");
fprintf(out, "REMARK "
visualize_box(out, bLegend ? atoms.nr+12 : atoms.nr,
bLegend ? atoms.nres = 12 : atoms.nres, box, visbox);
}
- ffclose(out);
+ gmx_ffclose(out);
}
else
{
do_view(oenv, outfile, NULL);
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff