/*
- *
- * 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,
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+ * 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 "string2.h"
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "futil.h"
-#include "symtab.h"
#include "h_db.h"
-#include "gmxfio.h"
-#include "fflibutil.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-
-/* There are 11 types of adding hydrogens, numbered from
- * 1 thru 11. Each of these has a specific number of
- * control atoms, that determine how the hydrogens are added.
- * Here these number are given. Because arrays start at 0 an
- * extra dummy for index 0 is added
+
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+/* Number of control atoms for each 'add' type.
+ *
+ * There are 11 types of adding hydrogens, numbered from 1 thru
+ * 11. Each of these has a specific number of control atoms, that
+ * determine how the hydrogens are added. Here these number are
+ * given. Because arrays start at 0, an extra dummy for index 0 is
+ * added.
*/
const int ncontrol[] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3, 1, 1 };
#define maxcontrol asize(ncontrol)
-int compaddh(const void *a,const void *b)
+int compaddh(const void *a, const void *b)
{
- t_hackblock *ah,*bh;
+ t_hackblock *ah, *bh;
- ah=(t_hackblock *)a;
- bh=(t_hackblock *)b;
- return gmx_strcasecmp(ah->name,bh->name);
+ ah = (t_hackblock *)a;
+ bh = (t_hackblock *)b;
+ return gmx_strcasecmp(ah->name, bh->name);
}
-void print_ab(FILE *out,t_hack *hack,char *nname)
+void print_ab(FILE *out, t_hack *hack, char *nname)
{
- int i;
+ int i;
- fprintf(out,"%d\t%d\t%s",hack->nr,hack->tp,nname);
- for(i=0; (i < hack->nctl); i++)
- fprintf(out,"\t%s",hack->a[i]);
- fprintf(out,"\n");
+ fprintf(out, "%d\t%d\t%s", hack->nr, hack->tp, nname);
+ for (i = 0; (i < hack->nctl); i++)
+ {
+ fprintf(out, "\t%s", hack->a[i]);
+ }
+ fprintf(out, "\n");
}
-void read_ab(char *line,const char *fn,t_hack *hack)
+void read_ab(char *line, const char *fn, t_hack *hack)
{
- int i,nh,tp,ns;
- char a[4][12];
- char hn[32];
-
- ns = sscanf(line,"%d%d%s%s%s%s%s",&nh,&tp,hn,a[0],a[1],a[2],a[3]);
- if (ns < 4)
- gmx_fatal(FARGS,"wrong format in input file %s on line\n%s\n",fn,line);
-
- hack->nr=nh;
- hack->tp=tp;
- if ((tp < 1) || (tp >= maxcontrol))
- gmx_fatal(FARGS,"Error in hdb file %s:\nH-type should be in 1-%d. Offending line:\n%s",fn,maxcontrol-1,line);
-
- hack->nctl = ns - 3;
- if ((hack->nctl != ncontrol[hack->tp]) && (ncontrol[hack->tp] != -1))
- gmx_fatal(FARGS,"Error in hdb file %s:\nWrong number of control atoms (%d iso %d) on line:\n%s\n",fn,hack->nctl,ncontrol[hack->tp],line);
- for(i=0; (i<hack->nctl); i++) {
- hack->a[i]=strdup(a[i]);
- }
- for( ; i<4; i++) {
- hack->a[i]=NULL;
- }
- hack->oname=NULL;
- hack->nname=strdup(hn);
- hack->atom=NULL;
- hack->cgnr=NOTSET;
- hack->bXSet=FALSE;
- for(i=0; i<DIM; i++)
- hack->newx[i]=NOTSET;
+ int i, nh, tp, ns;
+ char a[4][12];
+ char hn[32];
+
+ ns = sscanf(line, "%d%d%s%s%s%s%s", &nh, &tp, hn, a[0], a[1], a[2], a[3]);
+ if (ns < 4)
+ {
+ gmx_fatal(FARGS, "wrong format in input file %s on line\n%s\n", fn, line);
+ }
+
+ hack->nr = nh;
+ hack->tp = tp;
+ if ((tp < 1) || (tp >= maxcontrol))
+ {
+ gmx_fatal(FARGS, "Error in hdb file %s:\nH-type should be in 1-%d. Offending line:\n%s", fn, maxcontrol-1, line);
+ }
+
+ hack->nctl = ns - 3;
+ if ((hack->nctl != ncontrol[hack->tp]) && (ncontrol[hack->tp] != -1))
+ {
+ gmx_fatal(FARGS, "Error in hdb file %s:\nWrong number of control atoms (%d iso %d) on line:\n%s\n", fn, hack->nctl, ncontrol[hack->tp], line);
+ }
+ for (i = 0; (i < hack->nctl); i++)
+ {
+ hack->a[i] = gmx_strdup(a[i]);
+ }
+ for (; i < 4; i++)
+ {
+ hack->a[i] = NULL;
+ }
+ hack->oname = NULL;
+ hack->nname = gmx_strdup(hn);
+ hack->atom = NULL;
+ hack->cgnr = NOTSET;
+ hack->bXSet = FALSE;
+ for (i = 0; i < DIM; i++)
+ {
+ hack->newx[i] = NOTSET;
+ }
}
-static void read_h_db_file(const char *hfn,int *nahptr,t_hackblock **ah)
-{
- FILE *in;
- char filebase[STRLEN],line[STRLEN], buf[STRLEN];
- int i, n, nab, nah;
- t_hackblock *aah;
-
- if (debug) fprintf(debug,"Hydrogen Database (%s):\n",hfn);
-
- fflib_filename_base(hfn,filebase,STRLEN);
- /* Currently filebase is read and set, but not used.
- * hdb entries from any hdb file and be applied to rtp entries
- * in any rtp file.
- */
-
- in = fflib_open(hfn);
-
- nah = *nahptr;
- aah = *ah;
- while (fgets2(line,STRLEN-1,in)) {
- if (sscanf(line,"%s%n",buf,&n) != 1) {
- fprintf(stderr,"Error in hdb file: nah = %d\nline = '%s'\n",
- nah,line);
- break;
+static void read_h_db_file(const char *hfn, int *nahptr, t_hackblock **ah)
+{
+ FILE *in;
+ char filebase[STRLEN], line[STRLEN], buf[STRLEN];
+ int i, n, nab, nah;
+ t_hackblock *aah;
+
+ if (debug)
+ {
+ fprintf(debug, "Hydrogen Database (%s):\n", hfn);
}
- if (debug) fprintf(debug,"%s",buf);
- srenew(aah,nah+1);
- clear_t_hackblock(&aah[nah]);
- aah[nah].name = strdup(buf);
- aah[nah].filebase = strdup(filebase);
-
- if (sscanf(line+n,"%d",&nab) == 1) {
- if (debug) fprintf(debug," %d\n",nab);
- snew(aah[nah].hack,nab);
- aah[nah].nhack = nab;
- for(i=0; (i<nab); i++) {
- if (feof(in))
- gmx_fatal(FARGS, "Expected %d lines of hydrogens, found only %d "
- "while reading Hydrogen Database %s residue %s",
- nab, i-1, aah[nah].name, hfn);
- if(NULL==fgets(buf, STRLEN, in))
+
+ fflib_filename_base(hfn, filebase, STRLEN);
+ /* Currently filebase is read and set, but not used.
+ * hdb entries from any hdb file and be applied to rtp entries
+ * in any rtp file.
+ */
+
+ in = fflib_open(hfn);
+
+ nah = *nahptr;
+ aah = *ah;
+ while (fgets2(line, STRLEN-1, in))
+ {
+ if (sscanf(line, "%s%n", buf, &n) != 1)
{
- gmx_fatal(FARGS,"Error reading from file %s",hfn);
- }
- read_ab(buf,hfn,&(aah[nah].hack[i]));
- }
+ fprintf(stderr, "Error in hdb file: nah = %d\nline = '%s'\n",
+ nah, line);
+ break;
+ }
+ if (debug)
+ {
+ fprintf(debug, "%s", buf);
+ }
+ srenew(aah, nah+1);
+ clear_t_hackblock(&aah[nah]);
+ aah[nah].name = gmx_strdup(buf);
+ aah[nah].filebase = gmx_strdup(filebase);
+
+ if (sscanf(line+n, "%d", &nab) == 1)
+ {
+ if (debug)
+ {
+ fprintf(debug, " %d\n", nab);
+ }
+ snew(aah[nah].hack, nab);
+ aah[nah].nhack = nab;
+ for (i = 0; (i < nab); i++)
+ {
+ if (feof(in))
+ {
+ gmx_fatal(FARGS, "Expected %d lines of hydrogens, found only %d "
+ "while reading Hydrogen Database %s residue %s",
+ nab, i-1, aah[nah].name, hfn);
+ }
+ if (NULL == fgets(buf, STRLEN, in))
+ {
+ gmx_fatal(FARGS, "Error reading from file %s", hfn);
+ }
+ read_ab(buf, hfn, &(aah[nah].hack[i]));
+ }
+ }
+ nah++;
}
- nah++;
- }
- ffclose(in);
-
- /* Sort the list (necessary to be able to use bsearch */
- qsort(aah,nah,(size_t)sizeof(**ah),compaddh);
-
- /*
- if (debug)
- dump_h_db(hfn,nah,aah);
- */
-
- *nahptr = nah;
- *ah = aah;
+ gmx_ffclose(in);
+
+ /* Sort the list (necessary to be able to use bsearch */
+ qsort(aah, nah, (size_t)sizeof(**ah), compaddh);
+
+ /*
+ if (debug)
+ dump_h_db(hfn,nah,aah);
+ */
+
+ *nahptr = nah;
+ *ah = aah;
}
-int read_h_db(const char *ffdir,t_hackblock **ah)
+int read_h_db(const char *ffdir, t_hackblock **ah)
{
- int nhdbf,f;
- char **hdbf;
- int nah;
- FILE *fp;
-
- /* Read the hydrogen database file(s).
- * Do not generate an error when no files are found.
- */
- nhdbf = fflib_search_file_end(ffdir,".hdb",FALSE,&hdbf);
- nah = 0;
- *ah = NULL;
- for(f=0; f<nhdbf; f++) {
- read_h_db_file(hdbf[f],&nah,ah);
- sfree(hdbf[f]);
- }
- sfree(hdbf);
-
- return nah;
+ int nhdbf, f;
+ char **hdbf;
+ int nah;
+ FILE *fp;
+
+ /* Read the hydrogen database file(s).
+ * Do not generate an error when no files are found.
+ */
+ nhdbf = fflib_search_file_end(ffdir, ".hdb", FALSE, &hdbf);
+ nah = 0;
+ *ah = NULL;
+ for (f = 0; f < nhdbf; f++)
+ {
+ read_h_db_file(hdbf[f], &nah, ah);
+ sfree(hdbf[f]);
+ }
+ sfree(hdbf);
+
+ return nah;
}
-t_hackblock *search_h_db(int nh,t_hackblock ah[],char *key)
+t_hackblock *search_h_db(int nh, t_hackblock ah[], char *key)
{
- t_hackblock ahkey,*result;
+ t_hackblock ahkey, *result;
+
+ if (nh <= 0)
+ {
+ return NULL;
+ }
+
+ ahkey.name = key;
- if (nh <= 0)
- return NULL;
-
- ahkey.name=key;
+ result = (t_hackblock *)bsearch(&ahkey, ah, nh, (size_t)sizeof(ah[0]), compaddh);
- result=(t_hackblock *)bsearch(&ahkey,ah,nh,(size_t)sizeof(ah[0]),compaddh);
-
- return result;
+ return result;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff