src/mdlib/gmx_qhop_xml.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39
  40 #include <string.h>
  41 #include "gmx_fatal.h"
  42 #include "smalloc.h"
  43 #include "macros.h"
  44 #include "futil.h"
  45 #include "gmx_qhop_parm.h"
  46
  47 #ifdef HAVE_LIBXML2
  48 #include <libxml/parser.h>
  49 #include <libxml/tree.h>
  50
  51 extern int xmlDoValidityCheckingDefaultValue;
  52
  53 #define NN(x) (NULL != (x))
  54
  55 static const char *xmltypes[] = {
  56   NULL,
  57   "XML_ELEMENT_NODE",
  58   "XML_ATTRIBUTE_NODE",
  59   "XML_TEXT_NODE",
  60   "XML_CDATA_SECTION_NODE",
  61   "XML_ENTITY_REF_NODE",
  62   "XML_ENTITY_NODE",
  63   "XML_PI_NODE",
  64   "XML_COMMENT_NODE",
  65   "XML_DOCUMENT_NODE",
  66   "XML_DOCUMENT_TYPE_NODE",
  67   "XML_DOCUMENT_FRAG_NODE",
  68   "XML_NOTATION_NODE",
  69   "XML_HTML_DOCUMENT_NODE",
  70   "XML_DTD_NODE",
  71   "XML_ELEMENT_DECL",
  72   "XML_ATTRIBUTE_DECL",
  73   "XML_ENTITY_DECL",
  74   "XML_NAMESPACE_DECL",
  75   "XML_XINCLUDE_START",
  76   "XML_XINCLUDE_END"
  77 };
  78 #define NXMLTYPES asize(xmltypes)
  79
  80 enum {
  81   exmlQHOPS,
  82   exmlQHOP, exmlDONOR, exmlACCEPTOR,
  83   exmlPARAM, exmlNAME, exmlVALUE,
  84   exmlUNIT,
  85   exmlNR
  86 };
  87
  88 static const char *exml_names[exmlNR] = {
  89   "qhops",
  90   "qhop", "donor", "acceptor", "parameter",
  91   "name", "value", "unit"
  92 };
  93
  94 typedef struct {
  95   int        nqh;
  96   gmx_qhop_t *gqh;
  97 } t_xmlrec;
  98
  99 static int find_elem(char *name,int nr,const char *names[])
 100 {
 101   int i;
 102
 103   for(i=0; (i<nr); i++)
 104     if (strcmp(name,names[i]) == 0)
 105       break;
 106   if (i == nr)
 107     gmx_fatal(FARGS,"Unknown element name %s",name);
 108
 109   return i;
 110 }
 111
 112 void add_xml_int(xmlNodePtr ptr,const char *name,int val)
 113 {
 114   xmlChar buf[32];
 115
 116   sprintf((char *)buf,"%d",val);
 117   if (xmlSetProp(ptr,(xmlChar *)name,buf) == 0)
 118     gmx_fatal(FARGS,"Setting",(char *)name);
 119 }
 120
 121 void add_xml_double(xmlNodePtr ptr,const char *name,double val)
 122 {
 123   xmlChar buf[32];
 124
 125   sprintf((char *)buf,"%g",val);
 126   if (xmlSetProp(ptr,(xmlChar *)name,buf) == 0)
 127     gmx_fatal(FARGS,"Setting",(char *)name);
 128 }
 129
 130 void add_xml_char(xmlNodePtr ptr,const char *name,char *val)
 131 {
 132   if (xmlSetProp(ptr,(xmlChar *)name,(xmlChar *)val) == 0)
 133     gmx_fatal(FARGS,"Setting",(char *)name);
 134 }
 135
 136 xmlNodePtr add_xml_child(xmlNodePtr parent,const char *type)
 137 {
 138   xmlNodePtr child;
 139
 140   if ((child = xmlNewChild(parent,NULL,(xmlChar *)type,NULL)) == NULL)
 141     gmx_fatal(FARGS,"Creating element",(char *)type);
 142
 143   return child;
 144 }
 145
 146 xmlNodePtr add_xml_comment(xmlDocPtr doc,
 147                            xmlNodePtr prev,char *comment)
 148 {
 149   xmlNodePtr comm,ptr;
 150
 151   if ((comm = xmlNewComment((xmlChar *)comment)) == NULL)
 152     gmx_fatal(FARGS,"Creating doc comment element","");
 153   ptr = prev;
 154   while (ptr->next != NULL)
 155     ptr=ptr->next;
 156   ptr->next    = comm;
 157   comm->prev   = ptr;
 158   comm->doc    = doc;
 159
 160   return comm;
 161 }
 162
 163 static char *sp(int n, char buf[], int maxindent)
 164 {
 165   int i;
 166   if(n>=maxindent)
 167     n=maxindent-1;
 168
 169   /* Don't indent more than maxindent characters */
 170   for(i=0; (i<n); i++)
 171     buf[i] = ' ';
 172   buf[i] = '\0';
 173
 174   return buf;
 175 }
 176
 177 static void qhop_process_attr(FILE *fp,xmlAttrPtr attr,int parent,
 178                               int elem,int indent,gmx_qhop_t qht)
 179 {
 180   char *attrname,*attrval;
 181   char buf[100];
 182   int  i,kkk,eprop;
 183   char *xbuf[exmlNR];
 184
 185   for(i=0; (i<exmlNR); i++)
 186     xbuf[i] = NULL;
 187   while (attr != NULL) {
 188     attrname = (char *)attr->name;
 189     attrval  = (char *)attr->children->content;
 190
 191 #define atest(s) ((gmx_strcasecmp(attrname,s) == 0) && (attrval != NULL))
 192     kkk = find_elem(attrname,exmlNR,exml_names);
 193     if (attrval != NULL)
 194       xbuf[kkk] = strdup(attrval);
 195
 196     if (fp)
 197       fprintf(fp,"%sProperty: '%s' Value: '%s'\n",sp(indent,buf,99),
 198               attrname,attrval);
 199     attr = attr->next;
 200 #undef atest
 201   }
 202
 203   switch (elem) {
 204   case exmlQHOP:
 205     if (NN(xbuf[exmlDONOR]) && NN(xbuf[exmlACCEPTOR])) {
 206       gmx_qhop_set_donor(qht,xbuf[exmlDONOR]);
 207       gmx_qhop_set_acceptor(qht,xbuf[exmlACCEPTOR]);
 208     }
 209     break;
 210   case exmlPARAM:
 211     if (NN(xbuf[exmlNAME]) && NN(xbuf[exmlUNIT]) && NN(xbuf[exmlVALUE])) {
 212       gmx_qhop_add_param(qht,xbuf[exmlNAME],xbuf[exmlVALUE],
 213                          xbuf[exmlUNIT]);
 214     }
 215     break;
 216   default:
 217     break;
 218   }
 219   for(i=0; (i<exmlNR); i++)
 220     if (NN(xbuf[i]))
 221       sfree(xbuf[i]);
 222 }
 223
 224 static void qhop_process_element(FILE *fp,xmlNodePtr tree,int parent,
 225                                  int indent,t_xmlrec *xml)
 226 {
 227   int elem;
 228   char buf[100];
 229
 230   elem = find_elem((char *)tree->name,exmlNR,exml_names);
 231   if (fp)
 232     fprintf(fp,"%sElement node name %s\n",sp(indent,buf,99),
 233             (char *)tree->name);
 234   if (elem == exmlQHOP) {
 235     xml->nqh++;
 236     srenew(xml->gqh,xml->nqh);
 237     xml->gqh[xml->nqh-1] = gmx_qhop_init();
 238   }
 239   if (elem != exmlQHOPS)
 240     qhop_process_attr(fp,tree->properties,parent,
 241                       elem,indent+2,xml->gqh[xml->nqh-1]);
 242 }
 243
 244 static void qhop_process_tree(FILE *fp,xmlNodePtr tree,int parent,
 245                               int indent,t_xmlrec *xml)
 246 {
 247   char buf[100];
 248   int  elem;
 249
 250   while (tree != NULL) {
 251     if (fp) {
 252       if ((tree->type > 0) && (tree->type < NXMLTYPES))
 253         fprintf(fp,"Node type %s encountered with name %s\n",
 254                 xmltypes[tree->type],(char *)tree->name);
 255       else
 256         fprintf(fp,"Node type %d encountered\n",tree->type);
 257     }
 258
 259     switch (tree->type) {
 260     case XML_ELEMENT_NODE:
 261       qhop_process_element(fp,tree,parent,indent+2,xml);
 262
 263       if (tree->children) {
 264         elem = find_elem((char *)tree->name,exmlNR,exml_names);
 265         qhop_process_tree(fp,tree->children,elem,indent+2,xml);
 266       }
 267       break;
 268     default:
 269       break;
 270     }
 271     tree = tree->next;
 272   }
 273 }
 274
 275 gmx_qhop_t *
 276 gmx_qhops_read(char *fn,int *nqhop)
 277 {
 278   xmlDocPtr     doc;
 279   int           i,npd;
 280   t_xmlrec      *xml;
 281   const char *db="qhops.dat";
 282   gmx_bool fna=FALSE;
 283
 284   xmlDoValidityCheckingDefaultValue = 0;
 285   if (NULL == fn)
 286   {
 287     fn = (char *)gmxlibfn(db);
 288     fna=TRUE;
 289   }
 290   if ((doc = xmlParseFile(fn)) == NULL) {
 291                 fprintf(stderr,"Reading XML file %s. Run a syntax checker such as nsgmls.",
 292                                 fn);
 293     exit(1);
 294   }
 295
 296   snew(xml,1);
 297   qhop_process_tree(NULL,doc->children,0,0,xml);
 298
 299   xmlFreeDoc(doc);
 300   if (fna)
 301       sfree(fn);
 302
 303   *nqhop = xml->nqh;
 304
 305   return xml->gqh;
 306 }
 307
 308 static void add_xml_qhop(xmlNodePtr parent,gmx_qhop_t qht)
 309 {
 310   xmlNodePtr ptr,child,grandchild,comp;
 311   char   *name,*type,*value,*unit;
 312
 313   ptr = add_xml_child(parent,exml_names[exmlQHOP]);
 314   add_xml_char(ptr,exml_names[exmlDONOR],gmx_qhop_get_donor(qht));
 315   add_xml_char(ptr,exml_names[exmlACCEPTOR],gmx_qhop_get_acceptor(qht));
 316
 317   while (gmx_qhop_get_param(qht,&name,&value,&unit) == 1) {
 318     child = add_xml_child(ptr,exml_names[exmlPARAM]);
 319     add_xml_char(child,exml_names[exmlNAME],name);
 320     add_xml_char(child,exml_names[exmlVALUE],value);
 321     add_xml_char(child,exml_names[exmlUNIT],unit);
 322     sfree(name);
 323     sfree(value);
 324     sfree(unit);
 325   }
 326 }
 327
 328 void gmx_qhops_write(char *fn,int nqhop,gmx_qhop_t qht[])
 329 {
 330   xmlDocPtr  doc;
 331   xmlDtdPtr  dtd;
 332   xmlNodePtr myroot;
 333   int        i,nmt;
 334   xmlChar    *libdtdname,*dtdname,*gmx;
 335
 336   gmx        = (xmlChar *) "qhops";
 337   dtdname    = (xmlChar *) "qhops.dtd";
 338   libdtdname = dtdname;
 339
 340   if ((doc = xmlNewDoc((xmlChar *)"1.0")) == NULL)
 341     gmx_fatal(FARGS,"Creating XML document","");
 342
 343   if ((dtd = xmlCreateIntSubset(doc,dtdname,libdtdname,dtdname)) == NULL)
 344     gmx_fatal(FARGS,"Creating XML DTD","");
 345
 346   if ((myroot = xmlNewDocNode(doc,NULL,gmx,NULL)) == NULL)
 347     gmx_fatal(FARGS,"Creating root element","");
 348   dtd->next = myroot;
 349   myroot->prev = (xmlNodePtr) dtd;
 350
 351   /* Add molecule definitions */
 352   for(i=0; (i<nqhop); i++)
 353     add_xml_qhop(myroot,qht[i]);
 354
 355   xmlSetDocCompressMode(doc,0);
 356   xmlIndentTreeOutput = 1;
 357   if (xmlSaveFormatFileEnc(fn,doc,"ISO-8859-1",2) == 0)
 358     gmx_fatal(FARGS,"Saving file",fn);
 359   xmlFreeDoc(doc);
 360 }
 361
 362
 363
 364 #else
 365
 366 gmx_qhop_t gmx_qhops_read(char *fn,int *nqhop)
 367 {
 368   gmx_fatal(FARGS,"You need to configure the software with --with-xml for function gmx_qhops_read to work");
 369   return NULL;
 370 }
 371
 372 void gmx_qhops_write(char *fn,int nqhop,gmx_qhop_t qht)
 373 {
 374   gmx_fatal(FARGS,"You need to configure the software with --with-xml for function gmx_qhops_write to work");
 375 }
 376
 377 #endif