rdkit/Code/GraphMol/FileParsers/SDMolSupplier.cpp

// $Id$
//
//  Copyright (C) 2002-2012 Greg Landrum and Rational Discovery LLC
//
//   @@ 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 <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/SanitException.h>

#include <boost/algorithm/string.hpp>
#include "MolSupplier.h"
#include "FileParsers.h"

#include <fstream>
#include <iostream>
#include <sstream>
#include <string>

namespace RDKit {

SDMolSupplier::SDMolSupplier(const std::string &fileName, bool sanitize,
                             bool removeHs, bool strictParsing) {
  init();
  // FIX: this binary mode of opening file is here because of a bug in VC++ 6.0
  // the function "tellg" does not work correctly if we do not open it this way
  //   Jan 2009: Confirmed that this is still the case in visual studio 2008
  std::istream *tmpStream = nullptr;
  tmpStream = static_cast<std::istream *>(
      new std::ifstream(fileName.c_str(), std::ios_base::binary));
  if (!tmpStream || (!(*tmpStream)) || (tmpStream->bad())) {
    std::ostringstream errout;
    errout << "Bad input file " << fileName;
    if (tmpStream) { delete tmpStream; }
    throw BadFileException(errout.str());
  }

  // dp_inStream = static_cast<std::istream *>(tmpStream);
  dp_inStream = tmpStream;
  df_owner = true;
  d_molpos.push_back(dp_inStream->tellg());
  df_sanitize = sanitize;
  df_removeHs = removeHs;
  df_strictParsing = strictParsing;
  this->checkForEnd();
  if (df_end) {
    // checkForEnd() sets d_len if we're at EOF. undo that (was GitHub issue
    // 19):
    d_len = 0;
  }
  POSTCONDITION(dp_inStream, "bad instream");
}

SDMolSupplier::SDMolSupplier(std::istream *inStream, bool takeOwnership,
                             bool sanitize, bool removeHs, bool strictParsing) {
  PRECONDITION(inStream, "bad stream");
  init();
  dp_inStream = inStream;
  df_owner = takeOwnership;
  d_molpos.push_back(dp_inStream->tellg());
  df_sanitize = sanitize;
  df_removeHs = removeHs;
  df_strictParsing = strictParsing;
  this->checkForEnd();
  if (df_end) {
    // checkForEnd() sets d_len if we're at EOF. undo that (was GitHub issue
    // 19):
    d_len = 0;
  }
  POSTCONDITION(dp_inStream, "bad instream");
}

void SDMolSupplier::init() {
  ForwardSDMolSupplier::init();
  d_len = -1;
  d_last = 0;
}

void SDMolSupplier::setDataCommon(const std::string &text, bool sanitize,
                                  bool removeHs) {
  if (dp_inStream && df_owner) delete dp_inStream;
  init();
  std::istream *tmpStream = nullptr;
  tmpStream = static_cast<std::istream *>(
      new std::istringstream(text, std::ios_base::binary));
  dp_inStream = tmpStream;
  df_owner = true;
  d_molpos.push_back(dp_inStream->tellg());
  df_sanitize = sanitize;
  df_removeHs = removeHs;
  this->checkForEnd();
  if (df_end) {
    // checkForEnd() sets d_len if we're at EOF. undo that (was GitHub issue
    // 19):
    d_len = 0;
  }
  POSTCONDITION(dp_inStream, "bad instream");
}

void SDMolSupplier::setData(const std::string &text, bool sanitize,
                            bool removeHs) {
  df_strictParsing = true;
  setDataCommon(text, sanitize, removeHs);
}

void SDMolSupplier::setData(const std::string &text, bool sanitize,
                            bool removeHs, bool strictParsing) {
  df_strictParsing = strictParsing;
  setDataCommon(text, sanitize, removeHs);
}

void SDMolSupplier::checkForEnd() {
  PRECONDITION(dp_inStream, "no stream");
  // we will call it end of file if we have more than 4 contiguous empty lines
  // or we reach end of file in the meantime
  if (dp_inStream->eof()) {
    df_end = true;
    d_len = rdcast<int>(d_molpos.size());
    return;
  }
  // we are not at the end of file, check for blank lines
  unsigned int nempty = 0;
  std::string tempStr, stmp;
  for (unsigned int i = 0; i < 4; i++) {
    tempStr = getLine(dp_inStream);
    if (dp_inStream->eof()) {
      df_end = true;
      d_len = rdcast<int>(d_molpos.size());
      return;
    }
    if (tempStr.find_first_not_of(" \t\r\n") == std::string::npos) {
      ++nempty;
    }
  }
  if (nempty == 4) {
    df_end = true;
    d_len = rdcast<int>(d_molpos.size());
  }
}

void SDMolSupplier::reset() {
  PRECONDITION(dp_inStream, "no stream");
  dp_inStream->clear();
  dp_inStream->seekg(0, std::ios::beg);
  df_end = false;
  d_last = 0;
  d_line = 0;
}

ROMol *SDMolSupplier::next() {
  PRECONDITION(dp_inStream, "no stream");
  if (df_end && d_last >= d_len) {
    throw FileParseException("EOF hit.");
  }

  // set the stream to the current position
  dp_inStream->seekg(d_molpos[d_last]);

  std::string tempStr;
  ROMol *res = nullptr;
  // finally if we reached the end of the file set end to be true
  if (dp_inStream->eof()) {
    // FIX: we should probably be throwing an exception here
    df_end = true;
    d_len = rdcast<int>(d_molpos.size());
    return res;
  }

  res = _next();

  ++d_last;
  std::streampos posHold = dp_inStream->tellg();
  this->checkForEnd();
  if (!this->df_end && d_last >= static_cast<int>(d_molpos.size())) {
    d_molpos.push_back(posHold);
  }

  return res;
}

std::string SDMolSupplier::getItemText(unsigned int idx) {
  PRECONDITION(dp_inStream, "no stream");
  unsigned int holder = d_last;
  moveTo(idx);
  std::streampos begP = d_molpos[idx];
  std::streampos endP;
  try {
    moveTo(idx + 1);
    endP = d_molpos[idx + 1];
  } catch (FileParseException &) {
    dp_inStream->clear();
    dp_inStream->seekg(0, std::ios_base::end);
    endP = dp_inStream->tellg();
  }
  d_last = holder;
  auto *buff = new char[endP - begP];
  dp_inStream->seekg(begP);
  dp_inStream->read(buff, endP - begP);
  std::string res(buff, endP - begP);
  delete[] buff;
  return res;
}

void SDMolSupplier::moveTo(unsigned int idx) {
  PRECONDITION(dp_inStream, "no stream");

  // dp_inStream->seekg() is called for all idx values
  // and earlier calls to next() may have put the stream into a bad state
  dp_inStream->clear();

  // move until we hit the desired idx
  if (idx < d_molpos.size()) {
    dp_inStream->seekg(d_molpos[idx]);
    d_last = idx;
  } else {
    std::string tempStr;
    dp_inStream->seekg(d_molpos.back());
    d_last = rdcast<int>(d_molpos.size()) - 1;
    while ((d_last < static_cast<int>(idx)) && (!dp_inStream->eof())) {
      d_line++;
      tempStr = getLine(dp_inStream);

      if (tempStr[0] == '$' && tempStr.substr(0, 4) == "$$$$") {
        std::streampos posHold = dp_inStream->tellg();
        this->checkForEnd();
        if (!this->df_end) {
          d_molpos.push_back(posHold);
          d_last++;
        }
      }
    }
    // if we reached end of file without reaching "idx" we have an index error
    if (dp_inStream->eof()) {
      d_len = rdcast<int>(d_molpos.size());
      std::ostringstream errout;
      errout << "ERROR: Index error (idx = " << idx << ") : "
             << " we do no have enough mol blocks";
      throw FileParseException(errout.str());
    }
  }
}

ROMol *SDMolSupplier::operator[](unsigned int idx) {
  PRECONDITION(dp_inStream, "no stream");
  // get the molecule with index idx
  moveTo(idx);
  return next();
}

unsigned int SDMolSupplier::length() {
  PRECONDITION(dp_inStream, "no stream");
  // return the number of mol blocks in the sdfile
  if (d_len > 0 || (df_end && d_len == 0)) {
    return d_len;
  } else {
    std::string tempStr;
    d_len = rdcast<int>(d_molpos.size());
    dp_inStream->seekg(d_molpos.back());
    while (!dp_inStream->eof()) {
      std::getline(*dp_inStream, tempStr);
      if (tempStr.length() >= 4 && tempStr[0] == '$' && tempStr[1] == '$' &&
          tempStr[2] == '$' && tempStr[3] == '$') {
        std::streampos posHold = dp_inStream->tellg();
        // don't worry about the last molecule:
        this->checkForEnd();
        if (!this->df_end) {
          d_molpos.push_back(posHold);
          ++d_len;
        }
      }
    }
    // now remember to set the stream to the last postion we want to read
    dp_inStream->clear();
    dp_inStream->seekg(d_molpos[d_last]);
    return d_len;
  }
}

bool SDMolSupplier::atEnd() {
  PRECONDITION(dp_inStream, "no stream");
  return df_end;
}

void SDMolSupplier::setStreamIndices(const std::vector<std::streampos> &locs) {
  d_molpos.clear();
  d_molpos.resize(locs.size());
  std::copy(locs.begin(), locs.end(), d_molpos.begin());
  this->reset();
  d_len = rdcast<int>(d_molpos.size());
}
}