*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
#include <ctype.h>
-#include "sysstuff.h"
-#include "macros.h"
-#include "smalloc.h"
-#include "string2.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/confio.h"
-#include "vec.h"
-#include "pbc.h"
+#include "gromacs/math/vec.h"
#include "toputil.h"
#include "topio.h"
#include "gpp_nextnb.h"
-#include "symtab.h"
-#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
#include "pgutil.h"
#include "resall.h"
#include "gen_ad.h"
{
fprintf(debug,
"Something VERY strange is going on in rm2par (gen_ad.c)\n"
- "a[0] %u a[1] %u a[2] %u a[3] %u\n",
+ "a[0] %d a[1] %d a[2] %d a[3] %d\n",
p[i].a[0], p[i].a[1], p[i].a[2], p[i].a[3]);
}
strcpy(p[i].s, "");
t_param *ang, *dih, *pai, *improper;
t_rbondeds *hbang, *hbdih;
char **anm;
+ const char *p;
int res, minres, maxres;
int i, j, j1, k, k1, l, l1, m, n, i1, i2;
int ninc, maxang, maxdih, maxpai;
int nFound;
gmx_bool bFound, bExcl;
-
/* These are the angles, dihedrals and pairs that we generate
* from the bonds. The ones that are already there from the rtp file
* will be retained.
if (hb)
{
gen_excls(atoms, excls, hb, bAllowMissing);
+ /* mark all entries as not matched yet */
+ for (i = 0; i < atoms->nres; i++)
+ {
+ for (j = 0; j < ebtsNR; j++)
+ {
+ for (k = 0; k < hb[i].rb[j].nb; k++)
+ {
+ hb[i].rb[j].b[k].match = FALSE;
+ }
+ }
+ }
}
/* Extract all i-j-k-l neighbours from nnb struct to generate all
if (bFound)
{
set_p_string(&(ang[nang]), hbang->b[l].s);
+ /* Mark that we found a match for this entry */
+ hbang->b[l].match = TRUE;
}
}
}
if (bFound)
{
set_p_string(&dih[ndih], hbdih->b[n].s);
+ /* Mark that we found a match for this entry */
+ hbdih->b[n].match = TRUE;
/* Set the last parameter to be able to see
if the dihedral was in the rtp list.
}
}
+ /* The above approach is great in that we double-check that e.g. an angle
+ * really corresponds to three atoms connected by bonds, but this is not
+ * generally true. Go through the angle and dihedral hackblocks to add
+ * entries that we have not yet marked as matched when going through bonds.
+ */
+ for (i = 0; i < atoms->nres; i++)
+ {
+ /* Add remaining angles from hackblock */
+ hbang = &hb[i].rb[ebtsANGLES];
+ for (j = 0; j < hbang->nb; j++)
+ {
+ if (hbang->b[j].match == TRUE)
+ {
+ /* We already used this entry, continue to the next */
+ continue;
+ }
+ /* Hm - entry not used, let's see if we can find all atoms */
+ if (nang == maxang)
+ {
+ maxang += ninc;
+ srenew(ang, maxang);
+ }
+ bFound = TRUE;
+ for (k = 0; k < 3 && bFound; k++)
+ {
+ p = hbang->b[j].a[k];
+ res = i;
+ if (p[0] == '-')
+ {
+ p++;
+ res--;
+ }
+ else if (p[0] == '+')
+ {
+ p++;
+ res++;
+ }
+ ang[nang].a[k] = search_res_atom(p, res, atoms, "angle", TRUE);
+ bFound = (ang[nang].a[k] != NO_ATID);
+ }
+ ang[nang].C0 = NOTSET;
+ ang[nang].C1 = NOTSET;
+
+ if (bFound)
+ {
+ set_p_string(&(ang[nang]), hbang->b[j].s);
+ hbang->b[j].match = TRUE;
+ /* Incrementing nang means we save this angle */
+ nang++;
+ }
+ }
+
+ /* Add remaining dihedrals from hackblock */
+ hbdih = &hb[i].rb[ebtsPDIHS];
+ for (j = 0; j < hbdih->nb; j++)
+ {
+ if (hbdih->b[j].match == TRUE)
+ {
+ /* We already used this entry, continue to the next */
+ continue;
+ }
+ /* Hm - entry not used, let's see if we can find all atoms */
+ if (ndih == maxdih)
+ {
+ maxdih += ninc;
+ srenew(dih, maxdih);
+ }
+ bFound = TRUE;
+ for (k = 0; k < 4 && bFound; k++)
+ {
+ p = hbdih->b[j].a[k];
+ res = i;
+ if (p[0] == '-')
+ {
+ p++;
+ res--;
+ }
+ else if (p[0] == '+')
+ {
+ p++;
+ res++;
+ }
+ dih[ndih].a[k] = search_res_atom(p, res, atoms, "dihedral", TRUE);
+ bFound = (dih[ndih].a[k] != NO_ATID);
+ }
+ for (m = 0; m < MAXFORCEPARAM; m++)
+ {
+ dih[ndih].c[m] = NOTSET;
+ }
+
+ if (bFound)
+ {
+ set_p_string(&(dih[ndih]), hbdih->b[j].s);
+ hbdih->b[j].match = TRUE;
+ /* Incrementing ndih means we save this dihedral */
+ ndih++;
+ }
+ }
+ }
+
/* Sort angles with respect to j-i-k (middle atom first) */
if (nang > 1)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff