-/* -*- 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.
*
- *
- * This source code is part of
- *
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- * GROningen MAchine for Chemical Simulations
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- * 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.
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-
- * This program is free software; you can redistribute it and/or
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+ * 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,
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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 "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
-#include "symtab.h"
-#include "smalloc.h"
-#include "macros.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 "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 "pbc.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++;
}
}
gmx_fatal(FARGS, "Output file should be a .pdb file"
" when using the -grasp option\n");
}
- if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
- (fn2ftp(infile) == efTPA) ||
- (fn2ftp(infile) == efTPB)))
+ if ((bMead || bGrasp) && (fn2ftp(infile) != efTPR))
{
- gmx_fatal(FARGS, "Input file should be a .tp[abr] file"
+ gmx_fatal(FARGS, "Input file should be a .tpr file"
" when using the -mead option\n");
}
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
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff