/*
- *
- * 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) 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
+ * 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.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "typedefs.h"
-#include "symtab.h"
-#include "futil.h"
+#include "gmxpre.h"
+
+#include <ctype.h>
+#include <string.h>
+
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/futil.h"
#include "resall.h"
#include "h_db.h"
-#include "string2.h"
-#include "strdb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "ter_db.h"
#include "toputil.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
#include "fflibutil.h"
+#include "gromacs/fileio/strdb.h"
/* use bonded types definitions in hackblock.h */
#define ekwRepl ebtsNR+1
#define ekwDel ebtsNR+3
#define ekwNR 3
const char *kw_names[ekwNR] = {
- "replace", "add", "delete"
+ "replace", "add", "delete"
};
int find_kw(char *keyw)
{
- int i;
-
- for(i=0; i<ebtsNR; i++)
- if (gmx_strcasecmp(btsNames[i],keyw) == 0)
- return i;
- for(i=0; i<ekwNR; i++)
- if (gmx_strcasecmp(kw_names[i],keyw) == 0)
- return ebtsNR + 1 + i;
-
- return NOTSET;
+ int i;
+
+ for (i = 0; i < ebtsNR; i++)
+ {
+ if (gmx_strcasecmp(btsNames[i], keyw) == 0)
+ {
+ return i;
+ }
+ }
+ for (i = 0; i < ekwNR; i++)
+ {
+ if (gmx_strcasecmp(kw_names[i], keyw) == 0)
+ {
+ return ebtsNR + 1 + i;
+ }
+ }
+
+ return NOTSET;
}
-#define FATAL() gmx_fatal(FARGS,"Reading Termini Database: not enough items on line\n%s",line)
+#define FATAL() gmx_fatal(FARGS, "Reading Termini Database: not enough items on line\n%s", line)
static void read_atom(char *line, gmx_bool bAdd,
- char **nname, t_atom *a, gpp_atomtype_t atype, int *cgnr)
+ char **nname, t_atom *a, gpp_atomtype_t atype, int *cgnr)
{
- int nr, i;
- char buf[5][30],type[12];
- double m, q;
-
- /* This code is messy, because of support for different formats:
- * for replace: [new name] <atom type> <m> <q> [cgnr (old format)]
- * for add: <atom type> <m> <q> [cgnr]
- */
- nr = sscanf(line,"%s %s %s %s %s",buf[0],buf[1],buf[2],buf[3],buf[4]);
-
- /* Here there an ambiguity due to the old replace format with cgnr,
- * which was read for years, but ignored in the rest of the code.
- * We have to assume that the atom type does not start with a digit
- * to make a line with 4 entries uniquely interpretable.
- */
- if (!bAdd && nr == 4 && isdigit(buf[1][0])) {
- nr = 3;
- }
-
- if (nr < 3 || nr > 4) {
- gmx_fatal(FARGS,"Reading Termini Database: expected %d or %d items of atom data in stead of %d on line\n%s", 3, 4, nr, line);
- }
- i = 0;
- if (!bAdd) {
- if (nr == 4) {
- *nname = strdup(buf[i++]);
- } else {
- *nname = NULL;
+ int nr, i;
+ char buf[5][30], type[12];
+ double m, q;
+
+ /* This code is messy, because of support for different formats:
+ * for replace: [new name] <atom type> <m> <q> [cgnr (old format)]
+ * for add: <atom type> <m> <q> [cgnr]
+ */
+ nr = sscanf(line, "%s %s %s %s %s", buf[0], buf[1], buf[2], buf[3], buf[4]);
+
+ /* Here there an ambiguity due to the old replace format with cgnr,
+ * which was read for years, but ignored in the rest of the code.
+ * We have to assume that the atom type does not start with a digit
+ * to make a line with 4 entries uniquely interpretable.
+ */
+ if (!bAdd && nr == 4 && isdigit(buf[1][0]))
+ {
+ nr = 3;
+ }
+
+ if (nr < 3 || nr > 4)
+ {
+ gmx_fatal(FARGS, "Reading Termini Database: expected %d or %d items of atom data in stead of %d on line\n%s", 3, 4, nr, line);
+ }
+ i = 0;
+ if (!bAdd)
+ {
+ if (nr == 4)
+ {
+ *nname = gmx_strdup(buf[i++]);
+ }
+ else
+ {
+ *nname = NULL;
+ }
+ }
+ a->type = get_atomtype_type(buf[i++], atype);
+ sscanf(buf[i++], "%lf", &m);
+ a->m = m;
+ sscanf(buf[i++], "%lf", &q);
+ a->q = q;
+ if (bAdd && nr == 4)
+ {
+ sscanf(buf[i++], "%d", cgnr);
+ }
+ else
+ {
+ *cgnr = NOTSET;
}
- }
- a->type = get_atomtype_type(buf[i++],atype);
- sscanf(buf[i++],"%lf",&m);
- a->m = m;
- sscanf(buf[i++],"%lf",&q);
- a->q = q;
- if (bAdd && nr == 4) {
- sscanf(buf[i++],"%d", cgnr);
- } else {
- *cgnr = NOTSET;
- }
}
-static void print_atom(FILE *out,t_atom *a,gpp_atomtype_t atype,char *newnm)
+static void print_atom(FILE *out, t_atom *a, gpp_atomtype_t atype)
{
- fprintf(out,"\t%s\t%g\t%g\n",
- get_atomtype_name(a->type,atype),a->m,a->q);
+ fprintf(out, "\t%s\t%g\t%g\n",
+ get_atomtype_name(a->type, atype), a->m, a->q);
}
-static void print_ter_db(const char *ff,char C,int nb,t_hackblock tb[],
- gpp_atomtype_t atype)
+static void print_ter_db(const char *ff, char C, int nb, t_hackblock tb[],
+ gpp_atomtype_t atype)
{
- FILE *out;
- int i,j,k,bt,nrepl,nadd,ndel;
- char buf[STRLEN],nname[STRLEN];
-
- sprintf(buf,"%s-%c.tdb",ff,C);
- out = gmx_fio_fopen(buf,"w");
-
- for(i=0; (i<nb); i++) {
- fprintf(out,"[ %s ]\n",tb[i].name);
-
- /* first count: */
- nrepl=0;
- nadd=0;
- ndel=0;
- for(j=0; j<tb[i].nhack; j++)
- if ( tb[i].hack[j].oname!=NULL && tb[i].hack[j].nname!=NULL )
- nrepl++;
- else if ( tb[i].hack[j].oname==NULL && tb[i].hack[j].nname!=NULL )
- nadd++;
- else if ( tb[i].hack[j].oname!=NULL && tb[i].hack[j].nname==NULL )
- ndel++;
- else if ( tb[i].hack[j].oname==NULL && tb[i].hack[j].nname==NULL )
- gmx_fatal(FARGS,"invalid hack (%s) in termini database",tb[i].name);
- if (nrepl) {
- fprintf(out,"[ %s ]\n",kw_names[ekwRepl-ebtsNR-1]);
- for(j=0; j<tb[i].nhack; j++)
- if ( tb[i].hack[j].oname!=NULL && tb[i].hack[j].nname!=NULL ) {
- fprintf(out,"%s\t",tb[i].hack[j].oname);
- print_atom(out,tb[i].hack[j].atom,atype,tb[i].hack[j].nname);
- }
- }
- if (nadd) {
- fprintf(out,"[ %s ]\n",kw_names[ekwAdd-ebtsNR-1]);
- for(j=0; j<tb[i].nhack; j++)
- if ( tb[i].hack[j].oname==NULL && tb[i].hack[j].nname!=NULL ) {
- print_ab(out,&(tb[i].hack[j]),tb[i].hack[j].nname);
- print_atom(out,tb[i].hack[j].atom,atype,tb[i].hack[j].nname);
- }
- }
- if (ndel) {
- fprintf(out,"[ %s ]\n",kw_names[ekwDel-ebtsNR-1]);
- for(j=0; j<tb[i].nhack; j++)
- if ( tb[i].hack[j].oname!=NULL && tb[i].hack[j].nname==NULL )
- fprintf(out,"%s\n",tb[i].hack[j].oname);
+ FILE *out;
+ int i, j, k, bt, nrepl, nadd, ndel;
+ char buf[STRLEN], nname[STRLEN];
+
+ sprintf(buf, "%s-%c.tdb", ff, C);
+ out = gmx_fio_fopen(buf, "w");
+
+ for (i = 0; (i < nb); i++)
+ {
+ fprintf(out, "[ %s ]\n", tb[i].name);
+
+ /* first count: */
+ nrepl = 0;
+ nadd = 0;
+ ndel = 0;
+ for (j = 0; j < tb[i].nhack; j++)
+ {
+ if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname != NULL)
+ {
+ nrepl++;
+ }
+ else if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname != NULL)
+ {
+ nadd++;
+ }
+ else if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname == NULL)
+ {
+ ndel++;
+ }
+ else if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname == NULL)
+ {
+ gmx_fatal(FARGS, "invalid hack (%s) in termini database", tb[i].name);
+ }
+ }
+ if (nrepl)
+ {
+ fprintf(out, "[ %s ]\n", kw_names[ekwRepl-ebtsNR-1]);
+ for (j = 0; j < tb[i].nhack; j++)
+ {
+ if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname != NULL)
+ {
+ fprintf(out, "%s\t", tb[i].hack[j].oname);
+ print_atom(out, tb[i].hack[j].atom, atype);
+ }
+ }
+ }
+ if (nadd)
+ {
+ fprintf(out, "[ %s ]\n", kw_names[ekwAdd-ebtsNR-1]);
+ for (j = 0; j < tb[i].nhack; j++)
+ {
+ if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname != NULL)
+ {
+ print_ab(out, &(tb[i].hack[j]), tb[i].hack[j].nname);
+ print_atom(out, tb[i].hack[j].atom, atype);
+ }
+ }
+ }
+ if (ndel)
+ {
+ fprintf(out, "[ %s ]\n", kw_names[ekwDel-ebtsNR-1]);
+ for (j = 0; j < tb[i].nhack; j++)
+ {
+ if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname == NULL)
+ {
+ fprintf(out, "%s\n", tb[i].hack[j].oname);
+ }
+ }
+ }
+ for (bt = 0; bt < ebtsNR; bt++)
+ {
+ if (tb[i].rb[bt].nb)
+ {
+ fprintf(out, "[ %s ]\n", btsNames[bt]);
+ for (j = 0; j < tb[i].rb[bt].nb; j++)
+ {
+ for (k = 0; k < btsNiatoms[bt]; k++)
+ {
+ fprintf(out, "%s%s", k ? "\t" : "", tb[i].rb[bt].b[j].a[k]);
+ }
+ if (tb[i].rb[bt].b[j].s)
+ {
+ fprintf(out, "\t%s", tb[i].rb[bt].b[j].s);
+ }
+ fprintf(out, "\n");
+ }
+ }
+ }
+ fprintf(out, "\n");
}
- for(bt=0; bt<ebtsNR; bt++)
- if (tb[i].rb[bt].nb) {
- fprintf(out,"[ %s ]\n", btsNames[bt]);
- for(j=0; j<tb[i].rb[bt].nb; j++) {
- for(k=0; k<btsNiatoms[bt]; k++)
- fprintf(out,"%s%s",k?"\t":"",tb[i].rb[bt].b[j].a[k]);
- if ( tb[i].rb[bt].b[j].s )
- fprintf(out,"\t%s",tb[i].rb[bt].b[j].s);
- fprintf(out,"\n");
- }
- }
- fprintf(out,"\n");
- }
- gmx_fio_fclose(out);
+ gmx_fio_fclose(out);
}
static void read_ter_db_file(char *fn,
- int *ntbptr,t_hackblock **tbptr,
- gpp_atomtype_t atype)
+ int *ntbptr, t_hackblock **tbptr,
+ gpp_atomtype_t atype)
{
- char filebase[STRLEN],*ptr;
- FILE *in;
- char header[STRLEN],buf[STRLEN],line[STRLEN];
- t_hackblock *tb;
- int i,j,n,ni,kwnr,nb,maxnb,nh;
-
- fflib_filename_base(fn,filebase,STRLEN);
- /* Remove the C/N termini extension */
- ptr = strrchr(filebase,'.');
- if (ptr != NULL) {
- ptr[0] = '\0';
- }
-
- in = fflib_open(fn);
- if (debug)
- fprintf(debug,"Opened %s\n",fn);
-
- tb = *tbptr;
- nb = *ntbptr - 1;
- maxnb=0;
- kwnr=NOTSET;
- get_a_line(in,line,STRLEN);
- while (!feof(in)) {
- if (get_header(line,header)) {
- /* this is a new block, or a new keyword */
- kwnr=find_kw(header);
-
- if (kwnr == NOTSET) {
- nb++;
- /* here starts a new block */
- if ( nb >= maxnb ) {
- maxnb = nb + 100;
- srenew(tb,maxnb);
- }
- clear_t_hackblock(&tb[nb]);
- tb[nb].name = strdup(header);
- tb[nb].filebase = strdup(filebase);
- }
- } else {
- if (nb < 0)
- gmx_fatal(FARGS,"reading termini database: "
- "directive expected before line:\n%s\n"
- "This might be a file in an old format.",line);
- /* this is not a header, so it must be data */
- if (kwnr >= ebtsNR) {
- /* this is a hack: add/rename/delete atoms */
- /* make space for hacks */
- if (tb[nb].nhack >= tb[nb].maxhack) {
- tb[nb].maxhack+=10;
- srenew(tb[nb].hack, tb[nb].maxhack);
- }
- nh=tb[nb].nhack;
- clear_t_hack(&(tb[nb].hack[nh]));
- for(i=0; i<4; i++)
- tb[nb].hack[nh].a[i]=NULL;
- tb[nb].nhack++;
-
- /* get data */
- n=0;
- if ( kwnr==ekwRepl || kwnr==ekwDel ) {
- if (sscanf(line, "%s%n", buf, &n) != 1)
- gmx_fatal(FARGS,"Reading Termini Database '%s': "
- "expected atom name on line\n%s",fn,line);
- tb[nb].hack[nh].oname = strdup(buf);
- /* we only replace or delete one atom at a time */
- tb[nb].hack[nh].nr = 1;
- } else if ( kwnr==ekwAdd ) {
- read_ab(line, fn, &(tb[nb].hack[nh]));
- get_a_line(in, line, STRLEN);
- } else
- gmx_fatal(FARGS,"unimplemented keyword number %d (%s:%d)",
- kwnr,__FILE__,__LINE__);
- if ( kwnr==ekwRepl || kwnr==ekwAdd ) {
- snew(tb[nb].hack[nh].atom, 1);
- read_atom(line+n,kwnr==ekwAdd,
- &tb[nb].hack[nh].nname, tb[nb].hack[nh].atom, atype,
- &tb[nb].hack[nh].cgnr);
- if (tb[nb].hack[nh].nname == NULL) {
- if (tb[nb].hack[nh].oname != NULL) {
- tb[nb].hack[nh].nname = strdup(tb[nb].hack[nh].oname);
- } else {
- gmx_fatal(FARGS,"Reading Termini Database '%s': don't know which name the new atom should have on line\n%s",fn,line);
- }
- }
- }
- } else if (kwnr >= 0 && kwnr < ebtsNR) {
- /* this is bonded data: bonds, angles, dihedrals or impropers */
- srenew(tb[nb].rb[kwnr].b,tb[nb].rb[kwnr].nb+1);
- n=0;
- for(j=0; j<btsNiatoms[kwnr]; j++) {
- if ( sscanf(line+n, "%s%n", buf, &ni) == 1 )
- tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = strdup(buf);
- else
- gmx_fatal(FARGS,"Reading Termini Database '%s': expected %d atom names (found %d) on line\n%s", fn, btsNiatoms[kwnr], j-1, line);
- n+=ni;
- }
- for( ; j<MAXATOMLIST; j++)
- tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = NULL;
- strcpy(buf, "");
- sscanf(line+n, "%s", buf);
- tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = strdup(buf);
- tb[nb].rb[kwnr].nb++;
- } else
- gmx_fatal(FARGS,"Reading Termini Database: Expecting a header at line\n"
- "%s",line);
+ char filebase[STRLEN], *ptr;
+ FILE *in;
+ char header[STRLEN], buf[STRLEN], line[STRLEN];
+ t_hackblock *tb;
+ int i, j, n, ni, kwnr, nb, maxnb, nh;
+
+ fflib_filename_base(fn, filebase, STRLEN);
+ /* Remove the C/N termini extension */
+ ptr = strrchr(filebase, '.');
+ if (ptr != NULL)
+ {
+ ptr[0] = '\0';
}
- get_a_line(in,line,STRLEN);
- }
- nb++;
- srenew(tb,nb);
-
- ffclose(in);
-
- *ntbptr = nb;
- *tbptr = tb;
+
+ in = fflib_open(fn);
+ if (debug)
+ {
+ fprintf(debug, "Opened %s\n", fn);
+ }
+
+ tb = *tbptr;
+ nb = *ntbptr - 1;
+ maxnb = 0;
+ kwnr = NOTSET;
+ get_a_line(in, line, STRLEN);
+ while (!feof(in))
+ {
+ if (get_header(line, header))
+ {
+ /* this is a new block, or a new keyword */
+ kwnr = find_kw(header);
+
+ if (kwnr == NOTSET)
+ {
+ nb++;
+ /* here starts a new block */
+ if (nb >= maxnb)
+ {
+ maxnb = nb + 100;
+ srenew(tb, maxnb);
+ }
+ clear_t_hackblock(&tb[nb]);
+ tb[nb].name = gmx_strdup(header);
+ tb[nb].filebase = gmx_strdup(filebase);
+ }
+ }
+ else
+ {
+ if (nb < 0)
+ {
+ gmx_fatal(FARGS, "reading termini database: "
+ "directive expected before line:\n%s\n"
+ "This might be a file in an old format.", line);
+ }
+ /* this is not a header, so it must be data */
+ if (kwnr >= ebtsNR)
+ {
+ /* this is a hack: add/rename/delete atoms */
+ /* make space for hacks */
+ if (tb[nb].nhack >= tb[nb].maxhack)
+ {
+ tb[nb].maxhack += 10;
+ srenew(tb[nb].hack, tb[nb].maxhack);
+ }
+ nh = tb[nb].nhack;
+ clear_t_hack(&(tb[nb].hack[nh]));
+ for (i = 0; i < 4; i++)
+ {
+ tb[nb].hack[nh].a[i] = NULL;
+ }
+ tb[nb].nhack++;
+
+ /* get data */
+ n = 0;
+ if (kwnr == ekwRepl || kwnr == ekwDel)
+ {
+ if (sscanf(line, "%s%n", buf, &n) != 1)
+ {
+ gmx_fatal(FARGS, "Reading Termini Database '%s': "
+ "expected atom name on line\n%s", fn, line);
+ }
+ tb[nb].hack[nh].oname = gmx_strdup(buf);
+ /* we only replace or delete one atom at a time */
+ tb[nb].hack[nh].nr = 1;
+ }
+ else if (kwnr == ekwAdd)
+ {
+ read_ab(line, fn, &(tb[nb].hack[nh]));
+ get_a_line(in, line, STRLEN);
+ }
+ else
+ {
+ gmx_fatal(FARGS, "unimplemented keyword number %d (%s:%d)",
+ kwnr, __FILE__, __LINE__);
+ }
+ if (kwnr == ekwRepl || kwnr == ekwAdd)
+ {
+ snew(tb[nb].hack[nh].atom, 1);
+ read_atom(line+n, kwnr == ekwAdd,
+ &tb[nb].hack[nh].nname, tb[nb].hack[nh].atom, atype,
+ &tb[nb].hack[nh].cgnr);
+ if (tb[nb].hack[nh].nname == NULL)
+ {
+ if (tb[nb].hack[nh].oname != NULL)
+ {
+ tb[nb].hack[nh].nname = gmx_strdup(tb[nb].hack[nh].oname);
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Reading Termini Database '%s': don't know which name the new atom should have on line\n%s", fn, line);
+ }
+ }
+ }
+ }
+ else if (kwnr >= 0 && kwnr < ebtsNR)
+ {
+ /* this is bonded data: bonds, angles, dihedrals or impropers */
+ srenew(tb[nb].rb[kwnr].b, tb[nb].rb[kwnr].nb+1);
+ n = 0;
+ for (j = 0; j < btsNiatoms[kwnr]; j++)
+ {
+ if (sscanf(line+n, "%s%n", buf, &ni) == 1)
+ {
+ tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = gmx_strdup(buf);
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Reading Termini Database '%s': expected %d atom names (found %d) on line\n%s", fn, btsNiatoms[kwnr], j-1, line);
+ }
+ n += ni;
+ }
+ for (; j < MAXATOMLIST; j++)
+ {
+ tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = NULL;
+ }
+ strcpy(buf, "");
+ sscanf(line+n, "%s", buf);
+ tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = gmx_strdup(buf);
+ tb[nb].rb[kwnr].nb++;
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Reading Termini Database: Expecting a header at line\n"
+ "%s", line);
+ }
+ }
+ get_a_line(in, line, STRLEN);
+ }
+ nb++;
+ srenew(tb, nb);
+
+ gmx_ffclose(in);
+
+ *ntbptr = nb;
+ *tbptr = tb;
}
-int read_ter_db(const char *ffdir,char ter,
- t_hackblock **tbptr,gpp_atomtype_t atype)
+int read_ter_db(const char *ffdir, char ter,
+ t_hackblock **tbptr, gpp_atomtype_t atype)
{
- char ext[STRLEN];
- int ntdbf,f;
- char **tdbf;
- int ntb;
-
- sprintf(ext,".%c.tdb",ter);
-
- /* Search for termini database files.
- * Do not generate an error when none are found.
- */
- ntdbf = fflib_search_file_end(ffdir,ext,FALSE,&tdbf);
- ntb = 0;
- *tbptr = NULL;
- for(f=0; f<ntdbf; f++) {
- read_ter_db_file(tdbf[f],&ntb,tbptr,atype);
- sfree(tdbf[f]);
- }
- sfree(tdbf);
-
- if (debug) {
- print_ter_db("new",ter,ntb,*tbptr,atype);
- }
-
- return ntb;
+ char ext[STRLEN];
+ int ntdbf, f;
+ char **tdbf;
+ int ntb;
+
+ sprintf(ext, ".%c.tdb", ter);
+
+ /* Search for termini database files.
+ * Do not generate an error when none are found.
+ */
+ ntdbf = fflib_search_file_end(ffdir, ext, FALSE, &tdbf);
+ ntb = 0;
+ *tbptr = NULL;
+ for (f = 0; f < ntdbf; f++)
+ {
+ read_ter_db_file(tdbf[f], &ntb, tbptr, atype);
+ sfree(tdbf[f]);
+ }
+ sfree(tdbf);
+
+ if (debug)
+ {
+ print_ter_db("new", ter, ntb, *tbptr, atype);
+ }
+
+ return ntb;
}
-t_hackblock **filter_ter(int nrtp,t_restp rtp[],
- int nb,t_hackblock tb[],
+t_hackblock **filter_ter(int nrtp, t_restp rtp[],
+ int nb, t_hackblock tb[],
const char *resname,
const char *rtpname,
int *nret)
* atomtypes for different residues there could be a lot
* of entries in the databases for specific residues
* (e.g. GLY-NH3+, SER-NH3+, ALA-NH3+).
- *
+ *
* To reduce the database size, we assume that a terminus specifier liker
*
* [ GLY|SER|ALA-NH3+ ]
*
- * would cover all of the three residue types above.
- * Wildcards (*,?) are not OK. Don't worry about e.g. GLU vs. GLUH since
+ * would cover all of the three residue types above.
+ * Wildcards (*,?) are not OK. Don't worry about e.g. GLU vs. GLUH since
* pdb2gmx only uses the first 3 letters when calling this routine.
- *
- * To automate this, this routines scans a list of termini
- * for the residue name "resname" and returns an allocated list of
- * pointers to the termini that could be applied to the
+ *
+ * To automate this, this routines scans a list of termini
+ * for the residue name "resname" and returns an allocated list of
+ * pointers to the termini that could be applied to the
* residue in question. The variable pointed to by nret will
* contain the number of valid pointers in the list.
* Remember to free the list when you are done with it...
- */
+ */
- t_restp * restp;
- int i,j,n,len,none_idx;
+ t_restp * restp;
+ int i, j, n, len, none_idx;
gmx_bool found;
- char *rtpname_match,*s,*s2,*c;
- t_hackblock **list;
-
- rtpname_match = search_rtp(rtpname,nrtp,rtp);
- restp = get_restp(rtpname_match,nrtp,rtp);
-
- n=0;
- list=NULL;
-
- for(i=0;i<nb;i++)
+ char *rtpname_match, *s, *s2, *c;
+ t_hackblock **list;
+
+ rtpname_match = search_rtp(rtpname, nrtp, rtp);
+ restp = get_restp(rtpname_match, nrtp, rtp);
+
+ n = 0;
+ list = NULL;
+
+ for (i = 0; i < nb; i++)
{
- s=tb[i].name;
- found=FALSE;
- do
+ s = tb[i].name;
+ found = FALSE;
+ do
{
/* The residue name should appear in a tdb file with the same base name
* as the file containing the rtp entry.
* This makes termini selection for different molecule types
* much cleaner.
*/
- if (gmx_strcasecmp(restp->filebase,tb[i].filebase) == 0 &&
- gmx_strncasecmp(resname,s,3) == 0)
+ if (gmx_strcasecmp(restp->filebase, tb[i].filebase) == 0 &&
+ gmx_strncasecmp(resname, s, 3) == 0)
{
- found=TRUE;
- srenew(list,n+1);
- list[n]=&(tb[i]);
+ found = TRUE;
+ srenew(list, n+1);
+ list[n] = &(tb[i]);
n++;
}
- else
+ else
{
/* advance to next |-separated field */
- s=strchr(s,'|');
- if(s!=NULL)
+ s = strchr(s, '|');
+ if (s != NULL)
{
s++;
}
}
}
- while(!found && s!=NULL);
+ while (!found && s != NULL);
}
-
+
/* All residue-specific termini have been added. See if there
* are some generic ones by searching for the occurence of
* '-' in the name prior to the last position (which indicates charge).
* The [ None ] alternative is special since we don't want that
* to be the default, so we put it last in the list we return.
*/
- none_idx=-1;
- for(i=0;i<nb;i++)
+ none_idx = -1;
+ for (i = 0; i < nb; i++)
{
- s=tb[i].name;
+ s = tb[i].name;
/* The residue name should appear in a tdb file with the same base name
* as the file containing the rtp entry.
* This makes termini selection for different molecule types
* much cleaner.
*/
- if(gmx_strcasecmp(restp->filebase,tb[i].filebase) == 0)
+ if (gmx_strcasecmp(restp->filebase, tb[i].filebase) == 0)
{
- if(!gmx_strcasecmp("None",s))
+ if (!gmx_strcasecmp("None", s))
{
- none_idx=i;
+ none_idx = i;
}
- else
+ else
{
- c=strchr(s,'-');
- if(c==NULL || ((c-s+1)==strlen(s)))
+ c = strchr(s, '-');
+ if (c == NULL || ((c-s+1) == strlen(s)))
{
- /* Check that we haven't already added a residue-specific version
+ /* Check that we haven't already added a residue-specific version
* of this terminus.
*/
- for(j=0;j<n && strstr((*list[j]).name,s)==NULL;j++);
- if(j==n)
+ for (j = 0; j < n && strstr((*list[j]).name, s) == NULL; j++)
{
- srenew(list,n+1);
- list[n]=&(tb[i]);
+ ;
+ }
+ if (j == n)
+ {
+ srenew(list, n+1);
+ list[n] = &(tb[i]);
n++;
}
}
}
- }
+ }
}
- if(none_idx>=0)
+ if (none_idx >= 0)
{
- srenew(list,n+1);
- list[n]=&(tb[none_idx]);
+ srenew(list, n+1);
+ list[n] = &(tb[none_idx]);
n++;
- }
-
- *nret=n;
+ }
+
+ *nret = n;
return list;
}
-t_hackblock *choose_ter(int nb,t_hackblock **tb,const char *title)
+t_hackblock *choose_ter(int nb, t_hackblock **tb, const char *title)
{
- int i,sel,ret;
-
- printf("%s\n",title);
- for(i=0; (i<nb); i++)
- {
- char *advice_string = "";
- if (0 == gmx_wcmatch("*ZWITTERION*", (*tb[i]).name))
+ int i, sel, ret;
+
+ printf("%s\n", title);
+ for (i = 0; (i < nb); i++)
{
- advice_string = " (only use with zwitterions containing exactly one residue)";
+ char *advice_string = "";
+ if (0 == gmx_wcmatch("*ZWITTERION*", (*tb[i]).name))
+ {
+ advice_string = " (only use with zwitterions containing exactly one residue)";
+ }
+ printf("%2d: %s%s\n", i, (*tb[i]).name, advice_string);
}
- printf("%2d: %s%s\n",i,(*tb[i]).name, advice_string);
- }
- do {
- ret=fscanf(stdin,"%d",&sel);
- } while ((ret != 1) || (sel < 0) || (sel >= nb));
-
- return tb[sel];
-}
+ do
+ {
+ ret = fscanf(stdin, "%d", &sel);
+ }
+ while ((ret != 1) || (sel < 0) || (sel >= nb));
+ return tb[sel];
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff