src/kernel/rtp2xml.c

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.1
  11  * Copyright (c) 1991-2001, University of Groningen, The Netherlands
  12  * This program is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU General Public License
  14  * as published by the Free Software Foundation; either version 2
  15  * of the License, or (at your option) any later version.
  16  *
  17  * If you want to redistribute modifications, please consider that
  18  * scientific software is very special. Version control is crucial -
  19  * bugs must be traceable. We will be happy to consider code for
  20  * inclusion in the official distribution, but derived work must not
  21  * be called official GROMACS. Details are found in the README & COPYING
  22  * files - if they are missing, get the official version at www.gromacs.org.
  23  *
  24  * To help us fund GROMACS development, we humbly ask that you cite
  25  * the papers on the package - you can find them in the top README file.
  26  *
  27  * For more info, check our website at http://www.gromacs.org
  28  *
  29  * And Hey:
  30  * GROningen Mixture of Alchemy and Childrens' Stories
  31  */
  32 static char *SRCID_pdb2gmx_c = "$Id$";
  33 #include <time.h>
  34 #include <ctype.h>
  35 #include "assert.h"
  36 #include "sysstuff.h"
  37 #include "typedefs.h"
  38 #include "smalloc.h"
  39 #include "copyrite.h"
  40 #include "string2.h"
  41 #include "confio.h"
  42 #include "symtab.h"
  43 #include "vec.h"
  44 #include "statutil.h"
  45 #include "futil.h"
  46 #include "fatal.h"
  47 #include "pdbio.h"
  48 #include "toputil.h"
  49 #include "h_db.h"
  50 #include "physics.h"
  51 #include "pgutil.h"
  52 #include "calch.h"
  53 #include "resall.h"
  54 #include "pdb2top.h"
  55 #include "ter_db.h"
  56 #include "strdb.h"
  57 #include "txtdump.h"
  58 #include "gbutil.h"
  59 #include "genhydro.h"
  60 #include "readinp.h"
  61 #include "xlate.h"
  62 #include "specbond.h"
  63 #include "index.h"
  64 #include "hizzie.h"
  65
  66 static void dump_res(FILE *fp,int indent,t_restp *restp,int nah,
  67                      t_hackblock *ah,int nres_long,char **res_long)
  68 {
  69   char *rtype[ebtsNR] = { "rbond", "rangle", "rdihedral", "rimproper" };
  70   int ntype[ebtsNR] = { 2, 3, 4, 4 };
  71   int  i,j,k,nn;
  72   char *tmp,descr[128];
  73
  74   descr[0] = '\0';
  75   for(nn=0; (nn < nres_long) && (strstr(res_long[nn],restp->resname) == NULL); nn++)
  76     ;
  77   if (nn < nres_long) {
  78     tmp = res_long[nn] + strlen(restp->resname);
  79     while (*tmp && isspace(*tmp)) {
  80       tmp++;
  81     }
  82     if (strlen(tmp) > 0)
  83       strcpy(descr,tmp);
  84   }
  85
  86   pr_indent(fp,indent);
  87   fprintf(fp,"<residue restype=\"%s\" longname=\"%s\">\n",restp->resname,descr);
  88   indent += 2;
  89
  90   for(i=0; (i<restp->natom); i++) {
  91     pr_indent(fp,indent);
  92     fprintf(fp,"<ratom name=\"%s\">\n",*restp->atomname[i]);
  93   }
  94   for(i=0; (i<ebtsNR); i++) {
  95     for(j=0; (j<restp->rb[i].nb); j++) {
  96       pr_indent(fp,indent);
  97       fprintf(fp,"<%s",rtype[i]);
  98       for(k=0; (k<ntype[i]); k++)
  99         fprintf(fp," a%d=\"%s\"",k+1,restp->rb[i].b[j].a[k]);
 100       fprintf(fp,"/>\n");
 101     }
 102   }
 103   for(i=0; (i<nah); i++) {
 104     if (strcmp(restp->resname,ah[i].name) == 0) {
 105       for(j=0; (j<ah[i].nhack); j++) {
 106         pr_indent(fp,indent);
 107         if ((ah[i].hack[j].a[0][0] == 'O') || (ah[i].hack[j].a[0][0] == 'N'))
 108           fprintf(fp,"<raddh hclass=\"polar\"    ");
 109         else
 110           fprintf(fp,"<raddh hclass=\"aliphatic\"");
 111         fprintf(fp," addgeom=\"%d\" addnum=\"%d\"",
 112                 ah[i].hack[j].tp,ah[i].hack[j].nr);
 113         fprintf(fp," addto=\"%s",ah[i].hack[j].a[0]);
 114         for(k=1; ((k <= 3) && (ah[i].hack[j].a[k] > 0)); k++)
 115           fprintf(fp," %s",ah[i].hack[j].a[k]);
 116         fprintf(fp,"\"/>\n");
 117       }
 118       break;
 119     }
 120   }
 121   indent -= 2;
 122   pr_indent(fp,indent);
 123   fprintf(fp,"</residue>\n\n");
 124 }
 125
 126 static void dump_hack_add(FILE *fp,int indent,t_hack *hack)
 127 {
 128   pr_indent(fp,indent);
 129   fprintf(fp,"<modadd addname=\"%s\" addgeom=\"%d\" addto=\"%s %s %s\"/>\n",
 130           hack->nname,hack->tp,hack->a[0],hack->a[1],hack->a[2]);
 131 }
 132
 133 static void dump_hack_del(FILE *fp,int indent,t_hack *hack)
 134 {
 135   pr_indent(fp,indent);
 136   fprintf(fp,"<moddelete delname=\"%s\"/>\n",hack->oname);
 137 }
 138
 139 static void dump_hack_rep(FILE *fp,int indent,t_hack *hack)
 140 {
 141   pr_indent(fp,indent);
 142   fprintf(fp,"<modreplace oldname=\"%s\" newname=\"%s\"/>\n",hack->oname,hack->nname);
 143 }
 144
 145 static void dump_mod(FILE *fp,int indent,t_hackblock *tdb,t_atomtype *atype)
 146 {
 147   int i,j,k;
 148
 149   pr_indent(fp,indent);
 150   fprintf(fp,"<moddef modtype=\"%s\"\n",tdb->name);
 151   indent += 2;
 152   for(j=0; (j<tdb->nhack); j++) {
 153     if (tdb->hack[j].oname == NULL)
 154       dump_hack_add(fp,indent,&(tdb->hack[j]));
 155     else if (tdb->hack[j].nname == NULL)
 156       dump_hack_del(fp,indent,&(tdb->hack[j]));
 157     else
 158       dump_hack_rep(fp,indent,&(tdb->hack[j]));
 159   }
 160   indent -= 2;
 161   pr_indent(fp,indent);
 162   fprintf(fp,"</moddef>\n\n");
 163 }
 164
 165 static void dump_mods(FILE *fp,int indent,
 166                       int n,t_hackblock tdb[],t_atomtype *atype)
 167 {
 168   int i,j;
 169
 170   for(i=0; (i<n); i++)
 171     dump_mod(fp,indent,&(tdb[i]),atype);
 172 }
 173
 174 static void do_specbonds(FILE *fp,int indent)
 175 {
 176   t_specbond *sb;
 177   int i,nsb;
 178
 179   pr_indent(fp,indent);
 180   fprintf(fp,"<linkdef linktype=\"peptide\" restype=\"* *\" atomprev=\"C\" atomnext=\"N\" refdist=\"0.133\"/>\n");
 181   sb = get_specbonds(&nsb);
 182   for(i=0; (i<nsb); i++) {
 183     pr_indent(fp,indent);
 184     fprintf(fp,"<linkdef linktype=\"unknown\" restype=\"%s %s\" atomprev=\"%s\" atomnext=\"%s\" refdist=\"%g\"/>\n",
 185             sb[i].res1,sb[i].res2,sb[i].atom1,sb[i].atom2,sb[i].length);
 186   }
 187   done_specbonds(nsb,sb);
 188   sfree(sb);
 189   fprintf(fp,"\n");
 190 }
 191
 192 int main(int argc, char *argv[])
 193 {
 194   static char *desc[] = {
 195     "This program reads an rtp file and dumps an xml file."
 196   };
 197
 198   typedef struct {
 199     char chain;
 200     int  start;
 201     int  natom;
 202     bool bAllWat;
 203     int  nterpairs;
 204     int  *chainstart;
 205   } t_pdbchain;
 206
 207   typedef struct {
 208     char chain;
 209     bool bAllWat;
 210     int nterpairs;
 211     int *chainstart;
 212     t_hackblock **ntdb;
 213     t_hackblock **ctdb;
 214     int *rN;
 215     int *rC;
 216     t_atoms *pdba;
 217     rvec *x;
 218   } t_chain;
 219
 220   FILE       *fp;
 221   int        natom,nres;
 222   t_atoms    pdba_all,*pdba;
 223   t_atoms    *atoms;
 224   t_block    *block;
 225   int        chain,nch,maxch,nwaterchain;
 226   t_pdbchain *pdb_ch;
 227   t_chain    *chains,*cc;
 228   char       **res_long;
 229   int        nres_long;
 230   char       *ff;
 231   int        i,j,k,l,nrtp;
 232   int        *swap_index,si;
 233   int        bts[ebtsNR];
 234   t_restp    *restp;
 235   t_hackblock *ah;
 236   t_symtab   symtab;
 237   t_atomtype *atype;
 238   char       fn[256],*top_fn,itp_fn[STRLEN],posre_fn[STRLEN],buf_fn[STRLEN];
 239   char       molname[STRLEN],title[STRLEN];
 240   char       *c;
 241   int        nah,nNtdb,nCtdb;
 242   t_hackblock *ntdb,*ctdb;
 243   int        nssbonds;
 244   t_ssbond   *ssbonds;
 245   rvec       *pdbx,*x;
 246   bool       bUsed,bDummies=FALSE,bWat,bPrevWat=FALSE,bITP,bDummyAromatics=FALSE;
 247   real       mHmult=0;
 248   int        nrexcl;
 249   bool       bAlldih;
 250
 251   CopyRight(stderr,argv[0]);
 252
 253   ff = strdup("ffgmx2");
 254
 255   /* Read long residue names */
 256   nres_long = get_file("res-long.dat",&res_long);
 257
 258   /* Read atomtypes... */
 259   atype=read_atype(ff,&symtab);
 260
 261   /* read residue database */
 262   printf("Reading residue database... (%s)\n",ff);
 263   nrtp=read_resall(ff,bts,&restp,atype,&symtab,&bAlldih,&nrexcl);
 264
 265   /* read hydrogen database */
 266   nah=read_h_db(ff,&ah);
 267
 268   /* Read Termini database... */
 269   nNtdb=read_ter_db(ff,'n',&ntdb,atype);
 270   nCtdb=read_ter_db(ff,'c',&ctdb,atype);
 271
 272   fp=fopen("residues.xml","w");
 273   /* fprintf(fp,"<?xml version=\"1.0\"?>\n");
 274      fprintf(fp,"<!DOCTYPE residues SYSTEM \"residues.dtd\">\n"); */
 275   fprintf(fp,"\n<residues>\n");
 276   for(i=0; (i<nrtp); i++) {
 277     dump_res(fp,2,&(restp[i]),nah,ah,nres_long,res_long);
 278   }
 279   do_specbonds(fp,2);
 280   dump_mods(fp,2,nNtdb,ntdb,atype);
 281   dump_mods(fp,2,nCtdb,ctdb,atype);
 282   fprintf(fp,"</residues>\n");
 283   fclose(fp);
 284
 285   thanx(stderr);
 286
 287   return 0;
 288 }