* This file is part of the GROMACS molecular simulation package.
*
* 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.
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2013,2014, 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
* 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 <ctype.h>
-#include "sysstuff.h"
-#include "strdb.h"
-#include "futil.h"
-#include "macros.h"
-#include "string2.h"
-#include "statutil.h"
-#include "confio.h"
-#include "typedefs.h"
-#include "index.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "index.h"
-
-#define MAXNAMES 30
-#define NAME_LEN 30
+#include <string.h>
+
+#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/math/vec.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
+/* It's not nice to have size limits, but we should not spend more time
+ * on this ancient tool, but instead use the new selection library.
+ */
+#define MAXNAMES 1024
+#define NAME_LEN 1024
gmx_bool bCase = FALSE;
{
c = (*string)[0];
(*string)++;
- s = strdup((*string));
+ s = gmx_strdup((*string));
sp = strchr(s, c);
if (sp != NULL)
{
{
block->index[i] = block->index[i+1]-shift;
}
- name = strdup((*gn)[nr]);
+ name = gmx_strdup((*gn)[nr]);
sfree((*gn)[nr]);
for (i = nr; i < block->nr-1; i++)
{
{
sprintf(buf, "%s_%s_%d", (*gn)[sel_nr], name, atoms->resinfo[resind].nr);
}
- (*gn)[block->nr-1] = strdup(buf);
+ (*gn)[block->nr-1] = gmx_strdup(buf);
}
block->a[block->nra] = a;
block->nra++;
{
rvec_sub(x[ca_end], x[i], vec);
}
+ else
+ {
+ break;
+ }
}
- while ((i < natoms) && (norm(vec) < 0.45));
+ while (norm(vec) < 0.45);
end[nchain] = ca_end;
while ((end[nchain]+1 < natoms) &&
srenew(block->index, block->nr+1);
srenew(*gn, block->nr);
sprintf(buf, "%s_chain%d", (*gn)[sel_nr], j+1);
- (*gn)[block->nr-1] = strdup(buf);
+ (*gn)[block->nr-1] = gmx_strdup(buf);
for (i = block->index[sel_nr]; i < block->index[sel_nr+1]; i++)
{
a = block->a[i];
{
sscanf(string, "%s", gname);
sfree((*gn)[sel_nr]);
- (*gn)[sel_nr] = strdup(gname);
+ (*gn)[sel_nr] = gmx_strdup(gname);
}
}
}
copy2block(nr, index, block);
srenew(*gn, block->nr);
newgroup = block->nr-1;
- (*gn)[newgroup] = strdup(gname);
+ (*gn)[newgroup] = gmx_strdup(gname);
}
else
{
int gmx_make_ndx(int argc, char *argv[])
{
const char *desc[] = {
- "Index groups are necessary for almost every gromacs program.",
+ "Index groups are necessary for almost every GROMACS program.",
"All these programs can generate default index groups. You ONLY",
- "have to use [TT]make_ndx[tt] when you need SPECIAL index groups.",
+ "have to use [THISMODULE] when you need SPECIAL index groups.",
"There is a default index group for the whole system, 9 default",
"index groups for proteins, and a default index group",
"is generated for every other residue name.[PAR]",
- "When no index file is supplied, also [TT]make_ndx[tt] will generate the",
+ "When no index file is supplied, also [THISMODULE] will generate the",
"default groups.",
"With the index editor you can select on atom, residue and chain names",
"and numbers.",
"When a run input file is supplied you can also select on atom type.",
"You can use NOT, AND and OR, you can split groups",
"into chains, residues or atoms. You can delete and rename groups.[PAR]",
- "The atom numbering in the editor and the index file starts at 1."
+ "The atom numbering in the editor and the index file starts at 1.[PAR]",
+ "The [TT]-twin[tt] switch duplicates all index groups with an offset of",
+ "[TT]-natoms[tt], which is useful for Computational Electrophysiology",
+ "double-layer membrane setups."
};
- static int natoms = 0;
- static gmx_bool bVerbose = FALSE;
- t_pargs pa[] = {
+ static int natoms = 0;
+ static gmx_bool bVerbose = FALSE;
+ static gmx_bool bDuplicate = FALSE;
+ t_pargs pa[] = {
{ "-natoms", FALSE, etINT, {&natoms},
"set number of atoms (default: read from coordinate or index file)" },
+ { "-twin", FALSE, etBOOL, {&bDuplicate},
+ "Duplicate all index groups with an offset of -natoms" },
{ "-verbose", FALSE, etBOOL, {&bVerbose},
"HIDDENVerbose output" }
};
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc,
- 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc,
+ 0, NULL, &oenv))
+ {
+ return 0;
+ }
stxfile = ftp2fn_null(efSTX, NFILE, fnm);
if (opt2bSet("-n", NFILE, fnm))
edit_index(natoms, atoms, x, block, &gnames, bVerbose);
- write_index(ndxoutfile, block, gnames);
+ write_index(ndxoutfile, block, gnames, bDuplicate, natoms);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff