NCBI C Toolkit Cross Reference

   /* $Id: mmdbFF.c,v 6.4 2000/06/20 20:47:03 lewisg Exp $
   * ===========================================================================
   *
   *                            PUBLIC DOMAIN NOTICE
   *            National Center for Biotechnology Information (NCBI)
   *
   *  This software/database is a "United States Government Work" under the
   *  terms of the United States Copyright Act.  It was written as part of
   *  the author's official duties as a United States Government employee and
  *  thus cannot be copyrighted.  This software/database is freely available
  *  to the public for use. The National Library of Medicine and the U.S.
  *  Government do not place any restriction on its use or reproduction.
  *  We would, however, appreciate having the NCBI and the author cited in
  *  any work or product based on this material
  *
  *  Although all reasonable efforts have been taken to ensure the accuracy
  *  and reliability of the software and data, the NLM and the U.S.
  *  Government do not and cannot warrant the performance or results that
  *  may be obtained by using this software or data. The NLM and the U.S.
  *  Government disclaim all warranties, express or implied, including
  *  warranties of performance, merchantability or fitness for any particular
  *  purpose.
  *
  * ===========================================================================
  *
  * File Name:  mmdbFF.c - file based retrieval interface
  * 
  * Modifications:  
  * --------------------------------------------------------------------------
  * Date     Name        Description of modification
  * -------  ----------  -----------------------------------------------------
  *
  * $Log: mmdbFF.c,v $
  * Revision 6.4  2000/06/20 20:47:03  lewisg
  * use gzip
  *
  * Revision 6.3  1999/09/08 18:43:54  zimmerma
  * Modified HashPDBCode with calls to "toupper" to ensure case-insensitivity
  *
  * Revision 6.2  1999/06/22 22:35:02  kimelman
  * function names were changed to original names
  * so we have now 3 version of access files again
  *
  * Revision 6.1  1999/05/11 21:31:07  kimelman
  * file based retrival funciton extracted here from mmdblocl.c
  * (function names slightly changed)
  *
  *
  */
  
  /* LoadMMDBIdx reads the local MMDB index "mmdb.idx" into memory */
  /* index format is
  3\n
  1 1ABC\n
  3 3INS\n
  234567 4GWA\n
  eof
  */
  
  #include <ncbi.h>
  #include <mmdbapi1.h>
  #include <mmdbdata.h>
  #include <mmdblocl.h>
  #include <assert.h>
  
  static Int4Ptr pI4Mmdbidx = NULL;
  static Uint4Ptr pU4Pdbidx = NULL;
  static long iMMDBSize = 0;
  static Char indexname[PATH_MAX];
  static Char database[PATH_MAX];
  static Int4Ptr pI4position = NULL;
  static Char gunzip[PATH_MAX];
  
  
  /* These functions are only required when working with flat files:
   * - Load/Remove the mmbd.idx file for cross referencing MMDBids with PDBids
   * - Define the hash function for PDB strings                                   */
  
  static Uint4 HashPDBCode(CharPtr pcPdb) {
    Uint4 iPdbhash;
    Uint4 c1, c2, c3, c4;
  
    if (!pcPdb) return 0;
    if (StringLen(pcPdb) != 4) return 0;
    c1 =  toupper(pcPdb[3]);
    c2 =  toupper(pcPdb[2]);
    c3 =  toupper(pcPdb[1]);
    c4 =  toupper(pcPdb[0]);
    iPdbhash =  c1 + (c2 << 8) + (c3 << 16) + (c4 << 24);
    
    return iPdbhash;
  }
  
  /* The index file is loaded as a list of (long) mmdbids correlated with a 
     list of unsigned long HASHED PDB codes                                       */
  
  static Boolean LoadMMDBIdx(CharPtr db,  CharPtr idx) {
    FILE *f;
    Char fullpath [PATH_MAX];
   CharPtr ptr;
   Char pcBuf[100];
   CharPtr pcTest;
   Char  pcMmdb[20];
   Char  pcPdb[20];
   Uint4Ptr     pU4Pdb;
   Int4Ptr      pI4Mmdb;
   long count = 0;
   long mmdbid = 0;
   int status;
   char *msg;
 
 #define ERROR(err_msg) { msg = err_msg; goto errexit; }
 
   StringCpy(fullpath, db);
   StringCat(fullpath, idx);
   if ((f = FileOpen (fullpath, "r")) == NULL) 
     ERROR("MMDBInit: Couldn't load MMDB index.");
    
   fscanf(f, "%ld", &iMMDBSize);
   if ((iMMDBSize == 0) || (iMMDBSize > 100000))
     ERROR ("Internal - LoadMMDBIdx() Failure 2;");
 
   pI4Mmdbidx = (Int4Ptr) MemNew((size_t) ((iMMDBSize)*sizeof(Int4)));
   pU4Pdbidx = (Uint4Ptr) MemNew((size_t) ((iMMDBSize)*sizeof(Uint4)));
 
   if ((!pI4Mmdbidx) || (!pU4Pdbidx))
     ERROR ("Internal - LoadMMDBIdx() Out of Memory;");
    
   pI4Mmdb = pI4Mmdbidx;
   pU4Pdb = pU4Pdbidx;
    
   while ((status = fscanf(f, "%ld%s",  &mmdbid,  pcPdb)) != EOF) {
 
     StrUpper(pcPdb);
     if ((mmdbid == 0) ||  (StringLen(pcPdb) > 4)) {
       MMDBFini();
       ERROR ("Internal - LoadMMDBIdx() Bad Index Values");
     }
     
     *pI4Mmdb = mmdbid;
     *pU4Pdb =  HashPDBCode(pcPdb);
     pI4Mmdb++;
     pU4Pdb++;
     count++;
     if (count > (iMMDBSize)) {
       MMDBFini();
       ERROR ("Internal - LoadMMDBIdx() Index count is wrong at top of file;");
     }
   }
   FileClose(f);
   return TRUE;
 
 #undef ERROR
 errexit:
   ErrPostEx(SEV_FATAL,0,0, msg);
   return FALSE;
 }
 
 static void CloseMMDBIdx() {
   if (pI4Mmdbidx) MemFree(pI4Mmdbidx);
   if (pU4Pdbidx) MemFree(pU4Pdbidx);
   return;
 }
 
 /* Given a Char PDBid, hash-encode it and retrieve the corresponding long MMDBid */
 
 DocUid MMDBEvalPDB (CharPtr str) 
 {
   register Uint4Ptr pU4Pdb = NULL;
   register Int4Ptr pI4Mmdb = NULL;
   register Uint4   iHash = 0;
   long i = 0;
   
   ASSERT ((pI4Mmdbidx != NULL) && (pU4Pdbidx != NULL));
   pI4Mmdb = pI4Mmdbidx;
   pU4Pdb = pU4Pdbidx;
   iHash = HashPDBCode(str);
 
   while (i++ < iMMDBSize && iHash != *pU4Pdb) {
     pU4Pdb++;
     pI4Mmdb++;
   } 
   if (iHash == *pU4Pdb)
     return (DocUid) *pI4Mmdb;
   return (DocUid) 0;
 }
 
 /*****************************FF_BiostrucGet******************************/
 BiostrucPtr MMDBBiostrucGet (DocUid uid, Int4 mdlLvl, Int4 maxModels)
 {
   Char path[PATH_MAX], compath[PATH_MAX];
   AsnIoPtr    aip = NULL;
   FILE *pipe;
   BiostrucPtr pbs = NULL;
 
   sprintf(path, "%s%ld.val", database, (long) uid);
   if (FileLength(path) >0)
     aip = AsnIoOpen(path, "rb");
   else
     {
       if (gunzip[0] == 0) {
         ErrPostEx(SEV_FATAL,0,0, "MMDBBiostrucGet_files failed: gunzip path missing.");
         return NULL;
       }
       sprintf(path, "%s%ld.val.gz", database, (long) uid);
       if (FileLength(path) <=0)
         return NULL;
       
       sprintf(compath,"%s -c -d %s ", gunzip, path);
       pipe=popen(compath,"rb");
       if (pipe == 0)
         {
           ErrPostEx(SEV_FATAL,0,0, "MMDBBiostrucGet failed: Can't find gunzip in path");
           return NULL;
         }
       aip = AsnIoNew(ASNIO_BIN_IN, pipe , NULL, NULL, NULL);
     }
   if (!aip)
     return NULL;
 
   pbs = BiostrucAsnGet(aip, NULL,  mdlLvl,  maxModels);
   AsnIoClose (aip);
   return pbs;
 }
 
 Boolean MMDBInit (void) 
 {
   char *msg;
   char ndxPath[PATH_MAX];
   FILE *f;
   
 #define ERROR(err_msg) { msg = err_msg; goto errexit; }
 
   GetAppParam("mmdb", "MMDB", "Index"   , "", indexname, sizeof(indexname));
   GetAppParam("mmdb", "MMDB", "Database", "", database, sizeof(database));
   if (!(database[0] && indexname[0]))
     return FALSE ;
   
   /* let's check if index file really there */
     
   assert(sizeof(ndxPath) > strlen(database) + strlen(indexname));
   sprintf(ndxPath,"%s%s",database,indexname);
   
   if ((f = fopen(ndxPath,"r")) == NULL)
     ERROR("MMDBInit failed: incorrect mmdb.idx path.");
   fclose(f);
   if(FALSE==LoadMMDBIdx(database,  indexname))
     return FALSE;
   GetAppParam("mmdb", "MMDBSRV", "Gunzip", "", gunzip, sizeof(gunzip));
   if(gunzip[0])
     {
       f = fopen(gunzip,"r");
       if(f)
         fclose(f);
       else
         gunzip[0]=0;
     }
   return TRUE;
   
 #undef ERROR
 
 errexit:
   ErrPostEx(SEV_ERROR,0,0, msg);
   return FALSE;
 }
 
 void LIBCALL
 MMDBFini (void)
 {
   CloseMMDBIdx();
 }
 
 CharPtr LIBCALL
 MMDB_configuration(void)
 {
   return "Version:\t$Id: mmdbFF.c,v 6.4 2000/06/20 20:47:03 lewisg Exp $\nConfiguration: Flat Files" ;
 }