rdkit/Code/GraphMol/FileParsers/PDBSupplier.cpp

//
//  Copyright (C) 2013 Greg Landrum and NextMove Software
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <iostream>
#include <fstream>
#include <RDGeneral/BadFileException.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>


namespace RDKit {

  PDBMolSupplier::PDBMolSupplier(std::istream *inStream, bool takeOwnership,
                                 bool sanitize, bool removeHs,
                                 unsigned int flavor)
  {
    dp_inStream = inStream;
    df_owner = takeOwnership;
    df_sanitize = sanitize;
    df_removeHs = removeHs;
    d_flavor = flavor;
  }

  PDBMolSupplier::PDBMolSupplier(const std::string &fileName,
                                 bool sanitize, bool removeHs,
                                 unsigned int flavor)
  {
    std::ifstream *ifs = new std::ifstream(fileName.c_str(),
                                           std::ios_base::binary);
    if (!ifs || !(*ifs) || ifs->bad()) {
      std::ostringstream errout;
      errout << "Bad input file " << fileName;
      throw BadFileException(errout.str());
    }
    dp_inStream = (std::istream*)ifs;
    df_owner = true;
    df_sanitize = sanitize;
    df_removeHs = removeHs;
    d_flavor = flavor;
  }

  void PDBMolSupplier::init() {}
  void PDBMolSupplier::reset() {}

  ROMol *PDBMolSupplier::next()
  {
    return (ROMol*)PDBDataStreamToMol(dp_inStream,df_sanitize,
                                      df_removeHs,d_flavor);
  }

  bool PDBMolSupplier::atEnd()
  {
    if (dp_inStream->eof())
      return true;
    int ch = dp_inStream->peek();
    return ch == -1;
  }
}