/*
- *
- * 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 "typedefs.h"
-#include "smalloc.h"
-#include "grompp.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "grompp-impl.h"
+#include "gromacs/legacyheaders/macros.h"
#include "toputil.h"
#include "hackblock.h"
-#include "string2.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
static void clear_atom_list(int i0, atom_id a[])
{
- int i;
-
- for (i=i0; i < MAXATOMLIST; i++)
- a[i]=-1;
+ int i;
+
+ for (i = i0; i < MAXATOMLIST; i++)
+ {
+ a[i] = -1;
+ }
}
static void clear_force_param(int i0, real c[])
{
- int i;
-
- for (i=i0; i < MAXFORCEPARAM; i++)
- c[i]=NOTSET;
+ int i;
+
+ for (i = i0; i < MAXFORCEPARAM; i++)
+ {
+ c[i] = NOTSET;
+ }
}
-void add_param(t_params *ps,int ai,int aj, real *c, char *s)
+void add_param(t_params *ps, int ai, int aj, real *c, char *s)
{
- int i;
-
- if ((ai < 0) || (aj < 0))
- gmx_fatal(FARGS,"Trying to add impossible atoms: ai=%d, aj=%d",ai,aj);
- pr_alloc(1,ps);
- ps->param[ps->nr].AI=ai;
- ps->param[ps->nr].AJ=aj;
- clear_atom_list(2, ps->param[ps->nr].a);
- if (c==NULL)
- clear_force_param(0, ps->param[ps->nr].c);
- else
- for(i=0; (i < MAXFORCEPARAM); i++)
- ps->param[ps->nr].c[i]=c[i];
- set_p_string(&(ps->param[ps->nr]),s);
- ps->nr++;
+ int i;
+
+ if ((ai < 0) || (aj < 0))
+ {
+ gmx_fatal(FARGS, "Trying to add impossible atoms: ai=%d, aj=%d", ai, aj);
+ }
+ pr_alloc(1, ps);
+ ps->param[ps->nr].AI = ai;
+ ps->param[ps->nr].AJ = aj;
+ clear_atom_list(2, ps->param[ps->nr].a);
+ if (c == NULL)
+ {
+ clear_force_param(0, ps->param[ps->nr].c);
+ }
+ else
+ {
+ for (i = 0; (i < MAXFORCEPARAM); i++)
+ {
+ ps->param[ps->nr].c[i] = c[i];
+ }
+ }
+ set_p_string(&(ps->param[ps->nr]), s);
+ ps->nr++;
}
-void add_imp_param(t_params *ps,int ai,int aj,int ak,int al,real c0, real c1,
- char *s)
+void add_imp_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
+ char *s)
{
- pr_alloc(1,ps);
- ps->param[ps->nr].AI=ai;
- ps->param[ps->nr].AJ=aj;
- ps->param[ps->nr].AK=ak;
- ps->param[ps->nr].AL=al;
- clear_atom_list (4, ps->param[ps->nr].a);
- ps->param[ps->nr].C0=c0;
- ps->param[ps->nr].C1=c1;
- clear_force_param(2, ps->param[ps->nr].c);
- set_p_string(&(ps->param[ps->nr]),s);
- ps->nr++;
+ pr_alloc(1, ps);
+ ps->param[ps->nr].AI = ai;
+ ps->param[ps->nr].AJ = aj;
+ ps->param[ps->nr].AK = ak;
+ ps->param[ps->nr].AL = al;
+ clear_atom_list (4, ps->param[ps->nr].a);
+ ps->param[ps->nr].C0 = c0;
+ ps->param[ps->nr].C1 = c1;
+ clear_force_param(2, ps->param[ps->nr].c);
+ set_p_string(&(ps->param[ps->nr]), s);
+ ps->nr++;
}
-void add_dih_param(t_params *ps,int ai,int aj,int ak,int al,real c0, real c1,
- real c2,char *s)
+void add_dih_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
+ real c2, char *s)
{
- pr_alloc(1,ps);
- ps->param[ps->nr].AI=ai;
- ps->param[ps->nr].AJ=aj;
- ps->param[ps->nr].AK=ak;
- ps->param[ps->nr].AL=al;
- clear_atom_list (4, ps->param[ps->nr].a);
- ps->param[ps->nr].C0=c0;
- ps->param[ps->nr].C1=c1;
- ps->param[ps->nr].C2=c2;
- clear_force_param(3, ps->param[ps->nr].c);
- set_p_string(&(ps->param[ps->nr]),s);
- ps->nr++;
+ pr_alloc(1, ps);
+ ps->param[ps->nr].AI = ai;
+ ps->param[ps->nr].AJ = aj;
+ ps->param[ps->nr].AK = ak;
+ ps->param[ps->nr].AL = al;
+ clear_atom_list (4, ps->param[ps->nr].a);
+ ps->param[ps->nr].C0 = c0;
+ ps->param[ps->nr].C1 = c1;
+ ps->param[ps->nr].C2 = c2;
+ clear_force_param(3, ps->param[ps->nr].c);
+ set_p_string(&(ps->param[ps->nr]), s);
+ ps->nr++;
}
void add_cmap_param(t_params *ps, int ai, int aj, int ak, int al, int am, char *s)
{
- pr_alloc(1,ps);
- ps->param[ps->nr].AI=ai;
- ps->param[ps->nr].AJ=aj;
- ps->param[ps->nr].AK=ak;
- ps->param[ps->nr].AL=al;
- ps->param[ps->nr].AM=am;
- clear_atom_list(5,ps->param[ps->nr].a);
- clear_force_param(0,ps->param[ps->nr].c);
- set_p_string(&(ps->param[ps->nr]),s);
- ps->nr++;
+ pr_alloc(1, ps);
+ ps->param[ps->nr].AI = ai;
+ ps->param[ps->nr].AJ = aj;
+ ps->param[ps->nr].AK = ak;
+ ps->param[ps->nr].AL = al;
+ ps->param[ps->nr].AM = am;
+ clear_atom_list(5, ps->param[ps->nr].a);
+ clear_force_param(0, ps->param[ps->nr].c);
+ set_p_string(&(ps->param[ps->nr]), s);
+ ps->nr++;
}
-void add_vsite2_atoms(t_params *ps,int ai,int aj,int ak)
+void add_vsite2_atoms(t_params *ps, int ai, int aj, int ak)
{
- pr_alloc(1,ps);
- ps->param[ps->nr].AI=ai;
- ps->param[ps->nr].AJ=aj;
- ps->param[ps->nr].AK=ak;
- clear_atom_list (3, ps->param[ps->nr].a);
- clear_force_param(0, ps->param[ps->nr].c);
- set_p_string(&(ps->param[ps->nr]),"");
- ps->nr++;
+ pr_alloc(1, ps);
+ ps->param[ps->nr].AI = ai;
+ ps->param[ps->nr].AJ = aj;
+ ps->param[ps->nr].AK = ak;
+ clear_atom_list (3, ps->param[ps->nr].a);
+ clear_force_param(0, ps->param[ps->nr].c);
+ set_p_string(&(ps->param[ps->nr]), "");
+ ps->nr++;
}
-void add_vsite2_param(t_params *ps,int ai,int aj,int ak,real c0)
+void add_vsite2_param(t_params *ps, int ai, int aj, int ak, real c0)
{
- pr_alloc(1,ps);
- ps->param[ps->nr].AI=ai;
- ps->param[ps->nr].AJ=aj;
- ps->param[ps->nr].AK=ak;
- clear_atom_list (3, ps->param[ps->nr].a);
- ps->param[ps->nr].C0=c0;
- clear_force_param(1, ps->param[ps->nr].c);
- set_p_string(&(ps->param[ps->nr]),"");
- ps->nr++;
+ pr_alloc(1, ps);
+ ps->param[ps->nr].AI = ai;
+ ps->param[ps->nr].AJ = aj;
+ ps->param[ps->nr].AK = ak;
+ clear_atom_list (3, ps->param[ps->nr].a);
+ ps->param[ps->nr].C0 = c0;
+ clear_force_param(1, ps->param[ps->nr].c);
+ set_p_string(&(ps->param[ps->nr]), "");
+ ps->nr++;
}
-void add_vsite3_param(t_params *ps,int ai,int aj,int ak,int al,
- real c0, real c1)
+void add_vsite3_param(t_params *ps, int ai, int aj, int ak, int al,
+ real c0, real c1)
{
- pr_alloc(1,ps);
- ps->param[ps->nr].AI=ai;
- ps->param[ps->nr].AJ=aj;
- ps->param[ps->nr].AK=ak;
- ps->param[ps->nr].AL=al;
- clear_atom_list (4, ps->param[ps->nr].a);
- ps->param[ps->nr].C0=c0;
- ps->param[ps->nr].C1=c1;
- clear_force_param(2, ps->param[ps->nr].c);
- set_p_string(&(ps->param[ps->nr]),"");
- ps->nr++;
+ pr_alloc(1, ps);
+ ps->param[ps->nr].AI = ai;
+ ps->param[ps->nr].AJ = aj;
+ ps->param[ps->nr].AK = ak;
+ ps->param[ps->nr].AL = al;
+ clear_atom_list (4, ps->param[ps->nr].a);
+ ps->param[ps->nr].C0 = c0;
+ ps->param[ps->nr].C1 = c1;
+ clear_force_param(2, ps->param[ps->nr].c);
+ set_p_string(&(ps->param[ps->nr]), "");
+ ps->nr++;
}
-void add_vsite3_atoms(t_params *ps,int ai,int aj,int ak,int al, gmx_bool bSwapParity)
+void add_vsite3_atoms(t_params *ps, int ai, int aj, int ak, int al, gmx_bool bSwapParity)
{
- pr_alloc(1,ps);
- ps->param[ps->nr].AI=ai;
- ps->param[ps->nr].AJ=aj;
- ps->param[ps->nr].AK=ak;
- ps->param[ps->nr].AL=al;
- clear_atom_list (4, ps->param[ps->nr].a);
- clear_force_param(0, ps->param[ps->nr].c);
- if (bSwapParity)
- ps->param[ps->nr].C1=-1;
- set_p_string(&(ps->param[ps->nr]),"");
- ps->nr++;
+ pr_alloc(1, ps);
+ ps->param[ps->nr].AI = ai;
+ ps->param[ps->nr].AJ = aj;
+ ps->param[ps->nr].AK = ak;
+ ps->param[ps->nr].AL = al;
+ clear_atom_list (4, ps->param[ps->nr].a);
+ clear_force_param(0, ps->param[ps->nr].c);
+ if (bSwapParity)
+ {
+ ps->param[ps->nr].C1 = -1;
+ }
+ set_p_string(&(ps->param[ps->nr]), "");
+ ps->nr++;
}
-void add_vsite4_atoms(t_params *ps,int ai,int aj,int ak,int al,int am)
+void add_vsite4_atoms(t_params *ps, int ai, int aj, int ak, int al, int am)
{
- pr_alloc(1,ps);
- ps->param[ps->nr].AI=ai;
- ps->param[ps->nr].AJ=aj;
- ps->param[ps->nr].AK=ak;
- ps->param[ps->nr].AL=al;
- ps->param[ps->nr].AM=am;
- clear_atom_list (5, ps->param[ps->nr].a);
- clear_force_param(0, ps->param[ps->nr].c);
- set_p_string(&(ps->param[ps->nr]),"");
- ps->nr++;
+ pr_alloc(1, ps);
+ ps->param[ps->nr].AI = ai;
+ ps->param[ps->nr].AJ = aj;
+ ps->param[ps->nr].AK = ak;
+ ps->param[ps->nr].AL = al;
+ ps->param[ps->nr].AM = am;
+ clear_atom_list (5, ps->param[ps->nr].a);
+ clear_force_param(0, ps->param[ps->nr].c);
+ set_p_string(&(ps->param[ps->nr]), "");
+ ps->nr++;
}
-int search_jtype(t_restp *rtp,char *name,gmx_bool bNterm)
+int search_jtype(t_restp *rtp, char *name, gmx_bool bNterm)
{
- int niter,iter,j,k,kmax,jmax,minstrlen;
- char *rtpname,searchname[12];
-
- strcpy(searchname,name);
-
- /* Do a best match comparison */
- /* for protein N-terminus, allow renaming of H1, H2 and H3 to H */
- if ( bNterm && (strlen(searchname)==2) && (searchname[0] == 'H') &&
- ( (searchname[1] == '1') || (searchname[1] == '2') ||
- (searchname[1] == '3') ) ) {
- niter = 2;
- } else {
- niter = 1;
- }
- kmax=0;
- jmax=-1;
- for(iter=0; (iter<niter && jmax==-1); iter++) {
- if (iter == 1) {
- /* Try without the hydrogen number in the N-terminus */
- searchname[1] = '\0';
+ int niter, iter, j, k, kmax, jmax, minstrlen;
+ char *rtpname, searchname[12];
+
+ strcpy(searchname, name);
+
+ /* Do a best match comparison */
+ /* for protein N-terminus, allow renaming of H1, H2 and H3 to H */
+ if (bNterm && (strlen(searchname) == 2) && (searchname[0] == 'H') &&
+ ( (searchname[1] == '1') || (searchname[1] == '2') ||
+ (searchname[1] == '3') ) )
+ {
+ niter = 2;
+ }
+ else
+ {
+ niter = 1;
+ }
+ kmax = 0;
+ jmax = -1;
+ for (iter = 0; (iter < niter && jmax == -1); iter++)
+ {
+ if (iter == 1)
+ {
+ /* Try without the hydrogen number in the N-terminus */
+ searchname[1] = '\0';
+ }
+ for (j = 0; (j < rtp->natom); j++)
+ {
+ rtpname = *(rtp->atomname[j]);
+ if (gmx_strcasecmp(searchname, rtpname) == 0)
+ {
+ jmax = j;
+ kmax = strlen(searchname);
+ break;
+ }
+ if (iter == niter - 1)
+ {
+ minstrlen = min(strlen(searchname), strlen(rtpname));
+ for (k = 0; k < minstrlen; k++)
+ {
+ if (searchname[k] != rtpname[k])
+ {
+ break;
+ }
+ }
+ if (k > kmax)
+ {
+ kmax = k;
+ jmax = j;
+ }
+ }
+ }
}
- for(j=0; (j<rtp->natom); j++) {
- rtpname=*(rtp->atomname[j]);
- if (gmx_strcasecmp(searchname,rtpname) == 0) {
- jmax=j;
- kmax=strlen(searchname);
- break;
- }
- if (iter == niter - 1) {
- minstrlen = min(strlen(searchname), strlen(rtpname));
- for(k=0; k < minstrlen; k++)
- if (searchname[k] != rtpname[k])
- break;
- if (k > kmax) {
- kmax=k;
- jmax=j;
- }
- }
+ if (jmax == -1)
+ {
+ gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s",
+ searchname, rtp->resname);
}
- }
- if (jmax == -1)
- gmx_fatal(FARGS,"Atom %s not found in rtp database in residue %s",
- searchname,rtp->resname);
- if (kmax != strlen(searchname))
- gmx_fatal(FARGS,"Atom %s not found in rtp database in residue %s, "
- "it looks a bit like %s",
- searchname,rtp->resname,*(rtp->atomname[jmax]));
- return jmax;
+ if (kmax != strlen(searchname))
+ {
+ gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s, "
+ "it looks a bit like %s",
+ searchname, rtp->resname, *(rtp->atomname[jmax]));
+ }
+ return jmax;
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff