/*
- *
- * 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.
+ * 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.
-
- * 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) 2011,2014, 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
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
- *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but 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 www.gromacs.org.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * 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.
+ *
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * 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 <string.h>
#include "hackblock.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "string2.h"
-#include "macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/names.h"
/* these MUST correspond to the enum in hackblock.h */
const char *btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };
-const int btsNiatoms[ebtsNR] = { 2, 3, 4, 4, 2, 5 };
+const int btsNiatoms[ebtsNR] = { 2, 3, 4, 4, 2, 5 };
static void free_t_bonded(t_rbonded *rb)
{
- int i;
-
- for (i=0; i<MAXATOMLIST; i++)
- sfree(rb->a[i]);
- sfree(rb->s);
+ int i;
+
+ for (i = 0; i < MAXATOMLIST; i++)
+ {
+ sfree(rb->a[i]);
+ }
+ sfree(rb->s);
}
static void free_t_bondeds(t_rbondeds *rbs)
{
- int i;
-
- for(i=0; i<rbs->nb; i++)
- free_t_bonded(&rbs->b[i]);
- sfree(rbs->b);
- rbs->b=NULL;
- rbs->nb=0;
+ int i;
+
+ for (i = 0; i < rbs->nb; i++)
+ {
+ free_t_bonded(&rbs->b[i]);
+ }
+ sfree(rbs->b);
+ rbs->b = NULL;
+ rbs->nb = 0;
}
void free_t_restp(int nrtp, t_restp **rtp)
{
- int i,j;
-
- for(i=0; i<nrtp; i++) {
- sfree((*rtp)[i].resname);
- sfree((*rtp)[i].atom);
- for(j=0; j<(*rtp)[i].natom; j++) {
- sfree(*(*rtp)[i].atomname[j]);
- sfree((*rtp)[i].atomname[j]);
+ int i, j;
+
+ for (i = 0; i < nrtp; i++)
+ {
+ sfree((*rtp)[i].resname);
+ sfree((*rtp)[i].atom);
+ for (j = 0; j < (*rtp)[i].natom; j++)
+ {
+ sfree(*(*rtp)[i].atomname[j]);
+ sfree((*rtp)[i].atomname[j]);
+ }
+ sfree((*rtp)[i].atomname);
+ sfree((*rtp)[i].cgnr);
+ for (j = 0; j < ebtsNR; j++)
+ {
+ free_t_bondeds(&(*rtp)[i].rb[j]);
+ }
}
- sfree((*rtp)[i].atomname);
- sfree((*rtp)[i].cgnr);
- for(j=0; j<ebtsNR; j++)
- free_t_bondeds(&(*rtp)[i].rb[j]);
- }
- free(*rtp);
+ sfree(*rtp);
}
void free_t_hack(int nh, t_hack **h)
{
- int i, j;
-
- for(i=0; i<nh; i++) {
- sfree((*h)[i].oname);
- sfree((*h)[i].nname);
- sfree((*h)[i].atom);
- for(j=0; j<4; j++)
- sfree((*h)[i].a[j]);
- }
- sfree(*h);
- *h=NULL;
+ int i, j;
+
+ for (i = 0; i < nh; i++)
+ {
+ sfree((*h)[i].oname);
+ sfree((*h)[i].nname);
+ sfree((*h)[i].atom);
+ for (j = 0; j < 4; j++)
+ {
+ sfree((*h)[i].a[j]);
+ }
+ }
+ sfree(*h);
+ *h = NULL;
}
void free_t_hackblock(int nhb, t_hackblock **hb)
{
- int i, j;
-
- for(i=0; i<nhb; i++) {
- sfree((*hb)[i].name);
- free_t_hack((*hb)[i].nhack, &(*hb)[i].hack);
- for(j=0; j<ebtsNR; j++)
- free_t_bondeds(&(*hb)[i].rb[j]);
- }
- sfree(*hb);
+ int i, j;
+
+ for (i = 0; i < nhb; i++)
+ {
+ sfree((*hb)[i].name);
+ free_t_hack((*hb)[i].nhack, &(*hb)[i].hack);
+ for (j = 0; j < ebtsNR; j++)
+ {
+ free_t_bondeds(&(*hb)[i].rb[j]);
+ }
+ }
+ sfree(*hb);
}
void clear_t_hackblock(t_hackblock *hb)
{
- int i;
-
- hb->name = NULL;
- hb->nhack = 0;
- hb->maxhack= 0;
- hb->hack = NULL;
- for(i=0; i<ebtsNR; i++) {
- hb->rb[i].nb=0;
- hb->rb[i].b=NULL;
- }
+ int i;
+
+ hb->name = NULL;
+ hb->nhack = 0;
+ hb->maxhack = 0;
+ hb->hack = NULL;
+ for (i = 0; i < ebtsNR; i++)
+ {
+ hb->rb[i].nb = 0;
+ hb->rb[i].b = NULL;
+ }
}
void clear_t_hack(t_hack *hack)
{
- int i;
-
- hack->nr = 0;
- hack->oname = NULL;
- hack->nname = NULL;
- hack->atom = NULL;
- hack->cgnr = NOTSET;
- hack->tp = 0;
- hack->nctl = 0;
- for(i=0; i<4; i++)
- hack->a[i] = NULL;
- for(i=0; i<DIM; i++)
- hack->newx[i] = NOTSET;
+ int i;
+
+ hack->nr = 0;
+ hack->oname = NULL;
+ hack->nname = NULL;
+ hack->atom = NULL;
+ hack->cgnr = NOTSET;
+ hack->tp = 0;
+ hack->nctl = 0;
+ for (i = 0; i < 4; i++)
+ {
+ hack->a[i] = NULL;
+ }
+ for (i = 0; i < DIM; i++)
+ {
+ hack->newx[i] = NOTSET;
+ }
}
-#define safe_strdup(str) ((str != NULL) ? strdup(str) : NULL)
+#define safe_strdup(str) ((str != NULL) ? gmx_strdup(str) : NULL)
static void copy_t_rbonded(t_rbonded *s, t_rbonded *d)
{
- int i;
-
- for(i=0; i<MAXATOMLIST; i++)
- d->a[i] = safe_strdup(s->a[i]);
- d->s = safe_strdup(s->s);
+ int i;
+
+ for (i = 0; i < MAXATOMLIST; i++)
+ {
+ d->a[i] = safe_strdup(s->a[i]);
+ }
+ d->s = safe_strdup(s->s);
+ d->match = s->match;
}
-static gmx_bool contains_char(t_rbonded *s,char c)
+static gmx_bool contains_char(t_rbonded *s, char c)
{
- int i;
- gmx_bool bRet;
-
- bRet = FALSE;
- for(i=0; i<MAXATOMLIST; i++)
- if (s->a[i] && s->a[i][0]==c)
- bRet = TRUE;
-
- return bRet;
+ int i;
+ gmx_bool bRet;
+
+ bRet = FALSE;
+ for (i = 0; i < MAXATOMLIST; i++)
+ {
+ if (s->a[i] && s->a[i][0] == c)
+ {
+ bRet = TRUE;
+ }
+ }
+
+ return bRet;
}
-gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],gmx_bool bMin,gmx_bool bPlus)
+gmx_bool rbonded_atoms_exist_in_list(t_rbonded *b, t_rbonded blist[], int nlist, int natoms)
{
- int i, j;
- gmx_bool bBondsRemoved;
-
- bBondsRemoved = FALSE;
- for(i=0; i < ebtsNR; i++) {
- if ( s[i].nb > 0 ) {
- /* make space */
- srenew(d[i].b, d[i].nb + s[i].nb);
- for(j=0; j < s[i].nb; j++)
- if (!(bMin && contains_char(&s[i].b[j],'-'))
- && !(bPlus && contains_char(&s[i].b[j],'+'))) {
- copy_t_rbonded(&s[i].b[j], &d[i].b[ d[i].nb ]);
- d[i].nb ++;
- } else if (i == ebtsBONDS) {
- bBondsRemoved = TRUE;
- }
+ int i, k;
+ gmx_bool matchFound = FALSE;
+ gmx_bool atomsMatch;
+
+ for (i = 0; i < nlist && !matchFound; i++)
+ {
+ atomsMatch = TRUE;
+ for (k = 0; k < natoms && atomsMatch; k++)
+ {
+ atomsMatch = atomsMatch && !strcmp(b->a[k], blist[i].a[k]);
+ }
+ /* Try reverse if forward match did not work */
+ if (!atomsMatch)
+ {
+ atomsMatch = TRUE;
+ for (k = 0; k < natoms && atomsMatch; k++)
+ {
+ atomsMatch = atomsMatch && !strcmp(b->a[k], blist[i].a[natoms-1-k]);
+ }
+ }
+ matchFound = atomsMatch;
}
- }
+ return matchFound;
+}
- return bBondsRemoved;
+gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[], gmx_bool bMin, gmx_bool bPlus)
+{
+ int i, j;
+ gmx_bool bBondsRemoved;
+
+ bBondsRemoved = FALSE;
+ for (i = 0; i < ebtsNR; i++)
+ {
+ if (s[i].nb > 0)
+ {
+ /* make space */
+ srenew(d[i].b, d[i].nb + s[i].nb);
+ for (j = 0; j < s[i].nb; j++)
+ {
+ /* Check if this bonded string already exists before adding.
+ * We are merging from the main rtp to the hackblocks, so this
+ * will mean the hackblocks overwrite the man rtp, as intended.
+ */
+ if (!rbonded_atoms_exist_in_list(&s[i].b[j], d[i].b, d[i].nb, btsNiatoms[i]))
+ {
+ if (!(bMin && contains_char(&s[i].b[j], '-'))
+ && !(bPlus && contains_char(&s[i].b[j], '+')))
+ {
+ copy_t_rbonded(&s[i].b[j], &d[i].b[ d[i].nb ]);
+ d[i].nb++;
+ }
+ else if (i == ebtsBONDS)
+ {
+ bBondsRemoved = TRUE;
+ }
+ }
+ }
+ }
+ }
+ return bBondsRemoved;
}
void copy_t_restp(t_restp *s, t_restp *d)
{
- int i;
-
- *d = *s;
- d->resname = safe_strdup(s->resname);
- snew(d->atom, s->natom);
- for(i=0; i < s->natom; i++)
- d->atom[i] = s->atom[i];
- snew(d->atomname, s->natom);
- for(i=0; i < s->natom; i++) {
- snew(d->atomname[i],1);
- *d->atomname[i] = safe_strdup(*s->atomname[i]);
- }
- snew(d->cgnr, s->natom);
- for(i=0; i < s->natom; i++)
- d->cgnr[i] = s->cgnr[i];
- for(i=0; i < ebtsNR; i++) {
- d->rb[i].type = s->rb[i].type;
- d->rb[i].nb = 0;
- d->rb[i].b = NULL;
- }
- merge_t_bondeds(s->rb, d->rb,FALSE,FALSE);
+ int i;
+
+ *d = *s;
+ d->resname = safe_strdup(s->resname);
+ snew(d->atom, s->natom);
+ for (i = 0; i < s->natom; i++)
+ {
+ d->atom[i] = s->atom[i];
+ }
+ snew(d->atomname, s->natom);
+ for (i = 0; i < s->natom; i++)
+ {
+ snew(d->atomname[i], 1);
+ *d->atomname[i] = safe_strdup(*s->atomname[i]);
+ }
+ snew(d->cgnr, s->natom);
+ for (i = 0; i < s->natom; i++)
+ {
+ d->cgnr[i] = s->cgnr[i];
+ }
+ for (i = 0; i < ebtsNR; i++)
+ {
+ d->rb[i].type = s->rb[i].type;
+ d->rb[i].nb = 0;
+ d->rb[i].b = NULL;
+ }
+ merge_t_bondeds(s->rb, d->rb, FALSE, FALSE);
}
void copy_t_hack(t_hack *s, t_hack *d)
{
- int i;
-
- *d = *s;
- d->oname = safe_strdup(s->oname);
- d->nname = safe_strdup(s->nname);
- if (s->atom) {
- snew(d->atom, 1);
- *(d->atom) = *(s->atom);
- } else
- d->atom = NULL;
- for(i=0; i<4; i++)
- d->a[i] = safe_strdup(s->a[i]);
- copy_rvec(s->newx, d->newx);
+ int i;
+
+ *d = *s;
+ d->oname = safe_strdup(s->oname);
+ d->nname = safe_strdup(s->nname);
+ if (s->atom)
+ {
+ snew(d->atom, 1);
+ *(d->atom) = *(s->atom);
+ }
+ else
+ {
+ d->atom = NULL;
+ }
+ for (i = 0; i < 4; i++)
+ {
+ d->a[i] = safe_strdup(s->a[i]);
+ }
+ copy_rvec(s->newx, d->newx);
}
void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d)
{
- int i;
-
- if (ns) {
- srenew(*d, *nd + ns);
- for(i=0; i < ns; i++)
- copy_t_hack(&s[i], &(*d)[*nd + i]);
- (*nd) += ns;
- }
+ int i;
+
+ if (ns)
+ {
+ srenew(*d, *nd + ns);
+ for (i = 0; i < ns; i++)
+ {
+ copy_t_hack(&s[i], &(*d)[*nd + i]);
+ }
+ (*nd) += ns;
+ }
}
void merge_hacks(t_hackblock *s, t_hackblock *d)
{
- merge_hacks_lo(s->nhack, s->hack, &d->nhack, &d->hack);
+ merge_hacks_lo(s->nhack, s->hack, &d->nhack, &d->hack);
}
void merge_t_hackblock(t_hackblock *s, t_hackblock *d)
{
- merge_hacks(s, d);
- merge_t_bondeds(s->rb, d->rb,FALSE,FALSE);
+ merge_hacks(s, d);
+ merge_t_bondeds(s->rb, d->rb, FALSE, FALSE);
}
void copy_t_hackblock(t_hackblock *s, t_hackblock *d)
{
- int i;
-
- *d = *s;
- d->name = safe_strdup(s->name);
- d->nhack = 0;
- d->hack = NULL;
- for(i=0; i<ebtsNR; i++) {
- d->rb[i].nb=0;
- d->rb[i].b=NULL;
- }
- merge_t_hackblock(s, d);
+ int i;
+
+ *d = *s;
+ d->name = safe_strdup(s->name);
+ d->nhack = 0;
+ d->hack = NULL;
+ for (i = 0; i < ebtsNR; i++)
+ {
+ d->rb[i].nb = 0;
+ d->rb[i].b = NULL;
+ }
+ merge_t_hackblock(s, d);
}
#undef safe_strdup
void dump_hb(FILE *out, int nres, t_hackblock hb[])
{
- int i,j,k,l;
-
+ int i, j, k, l;
+
#define SS(s) (s) ? (s) : "-"
#define SA(s) (s) ? "+" : ""
- fprintf(out,"t_hackblock\n");
- for(i=0; i<nres; i++) {
- fprintf(out, "%3d %4s %2d %2d\n",
- i, SS(hb[i].name), hb[i].nhack, hb[i].maxhack);
- if (hb[i].nhack)
- for(j=0; j<hb[i].nhack; j++) {
- fprintf(out, "%d: %d %4s %4s %1s %2d %d %4s %4s %4s %4s\n",
- j, hb[i].hack[j].nr,
- SS(hb[i].hack[j].oname), SS(hb[i].hack[j].nname),
- SA(hb[i].hack[j].atom), hb[i].hack[j].tp, hb[i].hack[j].cgnr,
- SS(hb[i].hack[j].AI), SS(hb[i].hack[j].AJ),
- SS(hb[i].hack[j].AK), SS(hb[i].hack[j].AL) );
- }
- for(j=0; j<ebtsNR; j++)
- if (hb[i].rb[j].nb) {
- fprintf(out, " %c %d:", btsNames[j][0], hb[i].rb[j].nb);
- for(k=0; k<hb[i].rb[j].nb; k++) {
- fprintf(out, " [");
- for(l=0; l<btsNiatoms[j]; l++)
- fprintf(out, " %s",hb[i].rb[j].b[k].a[l]);
- fprintf(out, " %s]",SS(hb[i].rb[j].b[k].s));
- }
- fprintf(out,"\n");
- }
- fprintf(out,"\n");
- }
+ fprintf(out, "t_hackblock\n");
+ for (i = 0; i < nres; i++)
+ {
+ fprintf(out, "%3d %4s %2d %2d\n",
+ i, SS(hb[i].name), hb[i].nhack, hb[i].maxhack);
+ if (hb[i].nhack)
+ {
+ for (j = 0; j < hb[i].nhack; j++)
+ {
+ fprintf(out, "%d: %d %4s %4s %1s %2d %d %4s %4s %4s %4s\n",
+ j, hb[i].hack[j].nr,
+ SS(hb[i].hack[j].oname), SS(hb[i].hack[j].nname),
+ SA(hb[i].hack[j].atom), hb[i].hack[j].tp, hb[i].hack[j].cgnr,
+ SS(hb[i].hack[j].AI), SS(hb[i].hack[j].AJ),
+ SS(hb[i].hack[j].AK), SS(hb[i].hack[j].AL) );
+ }
+ }
+ for (j = 0; j < ebtsNR; j++)
+ {
+ if (hb[i].rb[j].nb)
+ {
+ fprintf(out, " %c %d:", btsNames[j][0], hb[i].rb[j].nb);
+ for (k = 0; k < hb[i].rb[j].nb; k++)
+ {
+ fprintf(out, " [");
+ for (l = 0; l < btsNiatoms[j]; l++)
+ {
+ fprintf(out, " %s", hb[i].rb[j].b[k].a[l]);
+ }
+ fprintf(out, " %s]", SS(hb[i].rb[j].b[k].s));
+ }
+ fprintf(out, " Entry matched: %s\n", yesno_names[hb[i].rb[j].b[k].match]);
+ }
+ }
+ fprintf(out, "\n");
+ }
#undef SS
#undef SA
}
void init_t_protonate(t_protonate *protonate)
{
- protonate->bInit=FALSE;
+ protonate->bInit = FALSE;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff