src/kernel/pgutil.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  34  */
  35 /* This file is completely threadsafe - keep it that way! */
  36
  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40 #include "string2.h"
  41 #include "pgutil.h"
  42 #include "string.h"
  43 #include "gmx_fatal.h"
  44
  45 static void atom_not_found(int fatal_errno,const char *file,int line,
  46                            const char *atomname,int resind,
  47                            const char *bondtype,bool bDontQuit)
  48 {
  49   if (strcmp(bondtype,"check") != 0) {
  50     if (bDontQuit) {
  51       fprintf(stderr,
  52               "WARNING: atom %s not found in residue seq.nr. %d while adding %s\n",
  53               atomname,resind+1,bondtype);
  54     } else {
  55       gmx_fatal(fatal_errno,file,line,
  56                 "Atom %s not found in residue seq.nr. %d while adding %s\n",
  57                 atomname,resind+1,bondtype);
  58     }
  59   }
  60 }
  61
  62 atom_id search_atom(const char *type,int start,int natoms,t_atom at[],
  63                     char ** const * anm,
  64                     const char *bondtype,bool bDontQuit)
  65 {
  66   int     i,resind=-1;
  67   bool    bPrevious,bNext;
  68
  69   bPrevious = (strchr(type,'-') != NULL);
  70   bNext     = (strchr(type,'+') != NULL);
  71
  72   if (!bPrevious) {
  73     resind = at[start].resind;
  74     if (bNext) {
  75       /* The next residue */
  76       type++;
  77       while ((start<natoms) && (at[start].resind == resind))
  78         start++;
  79       if (start < natoms)
  80         resind = at[start].resind;
  81     }
  82
  83     for(i=start; (i<natoms) && (bNext || (at[i].resind == resind)); i++) {
  84       if (anm[i] && strcasecmp(type,*(anm[i]))==0)
  85         return (atom_id) i;
  86     }
  87     if (!(bNext && at[start].resind==at[natoms-1].resind))
  88       atom_not_found(FARGS,type,at[start].resind,bondtype,bDontQuit);
  89   }
  90   else {
  91     /* The previous residue */
  92     type++;
  93     if (start > 0)
  94       resind = at[start-1].resind;
  95     for(i=start-1; (i>=0) /*&& (at[i].resind == resind)*/; i--)
  96       if (strcasecmp(type,*(anm[i]))==0)
  97         return (atom_id) i;
  98     if (start > 0)
  99       atom_not_found(FARGS,type,at[start].resind,bondtype,bDontQuit);
 100   }
 101   return NO_ATID;
 102 }
 103
 104 void set_at(t_atom *at,real m,real q,int type,int resind)
 105 {
 106   at->m=m;
 107   at->q=q;
 108   at->type=type;
 109   at->resind=resind;
 110 }