/****************************************************************************
 * Copyright (C) 2009-2015 EPAM Systems
 * 
 * This file is part of Indigo toolkit.
 * 
 * This file may be distributed and/or modified under the terms of the
 * GNU General Public License version 3 as published by the Free Software
 * Foundation and appearing in the file LICENSE.GPL included in the
 * packaging of this file.
 * 
 * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
 * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
 ***************************************************************************/ 

//
// This is a command line utility for producing canonical SMILES
// or layered code for molecules in MOL or SDF format
//

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "indigo.h"

void onError (const char *message, void *context)
{
   fflush(stdout);
   fprintf(stderr, "%s\n", message);
   fflush(stderr);
   exit(-1);
}

void usage ()
{
   printf(
      "Usage:\n"
      "  indigo-cano filename.{mol,smi,cml,sdf,sdf.gz,rdf,rdf.gz} [parameters]\n"
      "  indigo-cano - SMILES [parameters]\n"
      "Parameters:\n"
      "  -smiles          Output canonical SMILES (default)\n"
      "  -layered         Output canonical layered code\n"
      "  -id <string>     ID field in SDF file\n"
      "  -no-arom         Do not aromatize molecules\n"
      "  -no-tetrahedral  Ignore tetrahedral stereocenters\n"
      "  -no-cistrans     Ignore cis-trans bonds information\n"
      "Examples:\n"
      "   indigo-cano infile.sdf\n"
      "   indigo-cano infile.sdf.gz -id molregno > results.txt\n"
      "   indigo-cano infile.smi -layered -no-cistrans\n"
      "   indigo-cano - 'NC1C=CC(O)=CC=1'\n"
      );
}

int processMolecule (int mol, int smiles, int no_arom, int no_cistrans, int no_tetra)
{
   if (no_cistrans)
      if (indigoClearCisTrans(mol) < 0)
         return -1;

   if (no_tetra)
      if (!indigoClearStereocenters(mol))
         return -1;

   if (smiles && !no_arom)
      if (indigoAromatize(mol) < 0)
         return -1;

   if (smiles)
   {
      const char *res = indigoCanonicalSmiles(mol);
      if (res == 0)
         return -1;
      printf("%s\n", res);
   }
   else
   {
      const char *res = indigoLayeredCode(mol);
      if (res == 0)
         return -1;
      printf("%s\n", res);
   }
   return 1;
}

int main (int argc, char *argv[])
{
   int smiles = 1;
   int no_cistrans = 0;
   int no_tetra = 0;
   int no_arom = 0;
   int i = 2;
   const char *idfield = 0;
   const char *filename = 0;
   const char *ext = 0;

   if (argc < 2)
   {
      usage();
      return -1;
   }

   if (strcmp(argv[1], "-") != 0)
      filename = argv[1];
   else if (argc >= 3 && strcmp(argv[1], "-") == 0)
      i = 3;
   else
   {
      usage();
      return -1;
   }

   while (i < argc)
   {
      if (strcmp(argv[i], "-smiles") == 0)
         smiles = 1;
      else if (strcmp(argv[i], "-layered") == 0)
         smiles = 0;
      else if (strcmp(argv[i], "-no-cistrans") == 0)
         no_cistrans = 1;
      else if (strcmp(argv[i], "-no-arom") == 0)
         no_arom = 1;
      else if (strcmp(argv[i], "-no-tetrahedral") == 0)
         no_tetra= 1;
      else if (strcmp(argv[i], "-id") == 0)
      {
         if (++i >= argc)
         {
            fprintf(stderr, "expecting an identifier after -id\n");
            return -1;
         }

         idfield = argv[i];
      }
      else
      {
         fprintf(stderr, "unknown parameter: %s\n", argv[i]);
         return -1;
      }
      i++;
   }

   indigoSetErrorHandler(onError, 0);

   if (filename == 0)
   {
      int mol = indigoLoadMoleculeFromString(argv[2]);
      processMolecule(mol, smiles, no_arom, no_cistrans, no_tetra);
      indigoFree(mol);
      return 0;
   }

   if (strlen(filename) > 4 && filename[strlen(filename) - 4] == '.')
      ext = filename + strlen(filename) - 3;
   else if (strlen(filename) > 7 && filename[strlen(filename) - 7] == '.')
      ext = filename + strlen(filename) - 6;
   else
   {
      fprintf(stderr, "input file format not recognized\n");
      return -1;
   }

   if (strcmp(ext, "mol") == 0)
   {
      int mol = indigoLoadMoleculeFromFile(filename);
      processMolecule(mol, smiles, no_arom, no_cistrans, no_tetra);
      indigoFree(mol);
      return 0;
   }
   else if (strcmp(ext, "cml") == 0 ||
            strcmp(ext, "sdf") == 0 || strcmp(ext, "sdf.gz") == 0 ||
            strcmp(ext, "rdf") == 0 || strcmp(ext, "rdf.gz") == 0 ||
            strcmp(ext, "smi") == 0 || strcmp(ext, "smi.gz") == 0)
   {
      int item, iter;

      if ((strstr(ext, "cml") != NULL))
         iter = indigoIterateCMLFile(filename);
      else if (strstr(ext, "sdf") != NULL)
         iter = indigoIterateSDFile(filename);
      else if (strstr(ext, "rdf") != NULL)
         iter = indigoIterateRDFile(filename);
      else
         iter = indigoIterateSmilesFile(filename);

      while ((item = indigoNext(iter)))
      {
         indigoSetErrorHandler(0, 0);
         if (processMolecule(item, smiles, no_arom, no_cistrans, no_tetra) == -1)
            printf("%s\n", indigoGetLastError());
         indigoSetErrorHandler(onError, 0);
         indigoFree(item);
      }
      indigoFree(iter);
   }
   else
   {
      fprintf(stderr, "input file format not recognized\n");
      return -1;
   }
   return 0;
}