src/kernel/rtp2xml.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 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <time.h>
  40 #include <ctype.h>
  41 #include "sysstuff.h"
  42 #include "typedefs.h"
  43 #include "smalloc.h"
  44 #include "copyrite.h"
  45 #include "string2.h"
  46 #include "confio.h"
  47 #include "symtab.h"
  48 #include "vec.h"
  49 #include "statutil.h"
  50 #include "futil.h"
  51 #include "gmx_fatal.h"
  52 #include "pdbio.h"
  53 #include "toputil.h"
  54 #include "h_db.h"
  55 #include "physics.h"
  56 #include "pgutil.h"
  57 #include "calch.h"
  58 #include "resall.h"
  59 #include "pdb2top.h"
  60 #include "ter_db.h"
  61 #include "strdb.h"
  62 #include "txtdump.h"
  63 #include "gbutil.h"
  64 #include "genhydro.h"
  65 #include "readinp.h"
  66 #include "xlate.h"
  67 #include "specbond.h"
  68 #include "index.h"
  69 #include "hizzie.h"
  70
  71 static void dump_res(FILE *fp,int indent,t_restp *restp,int nah,
  72                      t_hackblock *ah,int nres_long,char **res_long)
  73 {
  74   char *rtype[ebtsNR] = { "rbond", "rangle", "rdihedral", "rimproper" };
  75   int ntype[ebtsNR] = { 2, 3, 4, 4 };
  76   int  i,j,k,nn;
  77   char *tmp,descr[128];
  78
  79   descr[0] = '\0';
  80   for(nn=0; (nn < nres_long) && (strstr(res_long[nn],restp->resname) == NULL); nn++)
  81     ;
  82   if (nn < nres_long) {
  83     tmp = res_long[nn] + strlen(restp->resname);
  84     while (*tmp && isspace(*tmp)) {
  85       tmp++;
  86     }
  87     if (strlen(tmp) > 0)
  88       strcpy(descr,tmp);
  89   }
  90
  91   pr_indent(fp,indent);
  92   fprintf(fp,"<residue restype=\"%s\" longname=\"%s\">\n",restp->resname,descr);
  93   indent += 2;
  94
  95   for(i=0; (i<restp->natom); i++) {
  96     pr_indent(fp,indent);
  97     fprintf(fp,"<ratom name=\"%s\">\n",*restp->atomname[i]);
  98   }
  99   for(i=0; (i<ebtsNR); i++) {
 100     for(j=0; (j<restp->rb[i].nb); j++) {
 101       pr_indent(fp,indent);
 102       fprintf(fp,"<%s",rtype[i]);
 103       for(k=0; (k<ntype[i]); k++)
 104         fprintf(fp," a%d=\"%s\"",k+1,restp->rb[i].b[j].a[k]);
 105       fprintf(fp,"/>\n");
 106     }
 107   }
 108   for(i=0; (i<nah); i++) {
 109     if (strcmp(restp->resname,ah[i].name) == 0) {
 110       for(j=0; (j<ah[i].nhack); j++) {
 111         pr_indent(fp,indent);
 112         if ((ah[i].hack[j].a[0][0] == 'O') || (ah[i].hack[j].a[0][0] == 'N'))
 113           fprintf(fp,"<raddh hclass=\"polar\"    ");
 114         else
 115           fprintf(fp,"<raddh hclass=\"aliphatic\"");
 116         fprintf(fp," addgeom=\"%d\" addnum=\"%d\"",
 117                 ah[i].hack[j].tp,ah[i].hack[j].nr);
 118         fprintf(fp," addto=\"%s",ah[i].hack[j].a[0]);
 119         for(k=1; ((k <= 3) && (ah[i].hack[j].a[k] > 0)); k++)
 120           fprintf(fp," %s",ah[i].hack[j].a[k]);
 121         fprintf(fp,"\"/>\n");
 122       }
 123       break;
 124     }
 125   }
 126   indent -= 2;
 127   pr_indent(fp,indent);
 128   fprintf(fp,"</residue>\n\n");
 129 }
 130
 131 static void dump_hack_add(FILE *fp,int indent,t_hack *hack)
 132 {
 133   pr_indent(fp,indent);
 134   fprintf(fp,"<modadd addname=\"%s\" addgeom=\"%d\" addto=\"%s %s %s\"/>\n",
 135           hack->nname,hack->tp,hack->a[0],hack->a[1],hack->a[2]);
 136 }
 137
 138 static void dump_hack_del(FILE *fp,int indent,t_hack *hack)
 139 {
 140   pr_indent(fp,indent);
 141   fprintf(fp,"<moddelete delname=\"%s\"/>\n",hack->oname);
 142 }
 143
 144 static void dump_hack_rep(FILE *fp,int indent,t_hack *hack)
 145 {
 146   pr_indent(fp,indent);
 147   fprintf(fp,"<modreplace oldname=\"%s\" newname=\"%s\"/>\n",hack->oname,hack->nname);
 148 }
 149
 150 static void dump_mod(FILE *fp,int indent,t_hackblock *tdb,t_atomtype *atype)
 151 {
 152   int i,j,k;
 153
 154   pr_indent(fp,indent);
 155   fprintf(fp,"<moddef modtype=\"%s\"\n",tdb->name);
 156   indent += 2;
 157   for(j=0; (j<tdb->nhack); j++) {
 158     if (tdb->hack[j].oname == NULL)
 159       dump_hack_add(fp,indent,&(tdb->hack[j]));
 160     else if (tdb->hack[j].nname == NULL)
 161       dump_hack_del(fp,indent,&(tdb->hack[j]));
 162     else
 163       dump_hack_rep(fp,indent,&(tdb->hack[j]));
 164   }
 165   indent -= 2;
 166   pr_indent(fp,indent);
 167   fprintf(fp,"</moddef>\n\n");
 168 }
 169
 170 static void dump_mods(FILE *fp,int indent,
 171                       int n,t_hackblock tdb[],t_atomtype *atype)
 172 {
 173   int i,j;
 174
 175   for(i=0; (i<n); i++)
 176     dump_mod(fp,indent,&(tdb[i]),atype);
 177 }
 178
 179 static void do_specbonds(FILE *fp,int indent)
 180 {
 181   t_specbond *sb;
 182   int i,nsb;
 183
 184   pr_indent(fp,indent);
 185   fprintf(fp,"<linkdef linktype=\"peptide\" restype=\"* *\" atomprev=\"C\" atomnext=\"N\" refdist=\"0.133\"/>\n");
 186   sb = get_specbonds(&nsb);
 187   for(i=0; (i<nsb); i++) {
 188     pr_indent(fp,indent);
 189     fprintf(fp,"<linkdef linktype=\"unknown\" restype=\"%s %s\" atomprev=\"%s\" atomnext=\"%s\" refdist=\"%g\"/>\n",
 190             sb[i].res1,sb[i].res2,sb[i].atom1,sb[i].atom2,sb[i].length);
 191   }
 192   done_specbonds(nsb,sb);
 193   sfree(sb);
 194   fprintf(fp,"\n");
 195 }
 196
 197 int main(int argc, char *argv[])
 198 {
 199   static char *desc[] = {
 200     "This program reads an rtp file and dumps an xml file."
 201   };
 202
 203   typedef struct {
 204     char chain;
 205     int  start;
 206     int  natom;
 207     gmx_bool bAllWat;
 208     int  nterpairs;
 209     int  *chainstart;
 210   } t_pdbchain;
 211
 212   typedef struct {
 213     char chain;
 214     gmx_bool bAllWat;
 215     int nterpairs;
 216     int *chainstart;
 217     t_hackblock **ntdb;
 218     t_hackblock **ctdb;
 219     int *rN;
 220     int *rC;
 221     t_atoms *pdba;
 222     rvec *x;
 223   } t_chain;
 224
 225   FILE       *fp;
 226   int        natom,nres;
 227   t_atoms    pdba_all,*pdba;
 228   t_atoms    *atoms;
 229   t_block    *block;
 230   int        chain,nch,maxch,nwaterchain;
 231   t_pdbchain *pdb_ch;
 232   t_chain    *chains,*cc;
 233   char       **res_long;
 234   int        nres_long;
 235   char       *ff;
 236   int        i,j,k,l,nrtp;
 237   int        *swap_index,si;
 238   int        bts[ebtsNR];
 239   t_restp    *restp;
 240   t_hackblock *ah;
 241   t_symtab   symtab;
 242   t_atomtype *atype;
 243   char       fn[256],*top_fn,itp_fn[STRLEN],posre_fn[STRLEN],buf_fn[STRLEN];
 244   char       molname[STRLEN],title[STRLEN];
 245   char       *c;
 246   int        nah,nNtdb,nCtdb;
 247   t_hackblock *ntdb,*ctdb;
 248   int        nssbonds;
 249   t_ssbond   *ssbonds;
 250   rvec       *pdbx,*x;
 251   gmx_bool       bUsed,bDummies=FALSE,bWat,bPrevWat=FALSE,bITP,bDummyAromatics=FALSE;
 252   real       mHmult=0;
 253   int        nrexcl;
 254   gmx_bool       bAlldih,bH14,bRemoveDih;
 255
 256   CopyRight(stderr,argv[0]);
 257
 258   ff = strdup("ffgmx2");
 259
 260   /* Read long residue names */
 261   nres_long = get_file("res-long.dat",&res_long);
 262
 263   /* Read atomtypes... */
 264   atype=read_atype(ff,&symtab);
 265
 266   /* read residue database */
 267   printf("Reading residue database... (%s)\n",ff);
 268   nrtp=read_resall(ff,bts,&restp,atype,&symtab,&bAlldih,&nrexcl,&bH14,&bRemoveDih);
 269
 270   /* read hydrogen database */
 271   nah=read_h_db(ff,&ah);
 272
 273   /* Read Termini database... */
 274   nNtdb=read_ter_db(ff,'n',&ntdb,atype);
 275   nCtdb=read_ter_db(ff,'c',&ctdb,atype);
 276
 277   fp=gmx_fio_fopen("residues.xml","w");
 278   /* fprintf(fp,"<?xml version=\"1.0\"?>\n");
 279      fprintf(fp,"<!DOCTYPE residues SYSTEM \"residues.dtd\">\n"); */
 280   fprintf(fp,"\n<residues>\n");
 281   for(i=0; (i<nrtp); i++) {
 282     dump_res(fp,2,&(restp[i]),nah,ah,nres_long,res_long);
 283   }
 284   do_specbonds(fp,2);
 285   dump_mods(fp,2,nNtdb,ntdb,atype);
 286   dump_mods(fp,2,nCtdb,ctdb,atype);
 287   fprintf(fp,"</residues>\n");
 288   gmx_fio_fclose(fp);
 289
 290   thanx(stderr);
 291
 292   return 0;
 293 }