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//
// Copyright (C) 2018-2021 Susan H. Leung and other RDKit contributors
//
// @@ 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 "TransformCatalogUtils.h"
#include <RDGeneral/BadFileException.h>
#include <boost/tokenizer.hpp>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <boost/algorithm/string.hpp>
#include <boost/tokenizer.hpp>
typedef boost::tokenizer<boost::char_separator<char>> tokenizer;
#include <fstream>
#include <string>
namespace RDKit {
namespace {
ChemicalReaction *getReaction(const std::string &name,
const std::string &smarts) {
auto transformation = RxnSmartsToChemicalReaction(smarts);
if (!transformation) {
throw ValueErrorException("Failed parsing reaction SMARTS: " + smarts);
}
transformation->setProp(common_properties::_Name, name);
return transformation;
}
ChemicalReaction *getReaction(const std::string &tmpStr) {
if (tmpStr.length() == 0 || tmpStr.substr(0, 2) == "//") {
// empty line or comment
return nullptr;
}
boost::char_separator<char> tabSep("\t");
tokenizer tokens(tmpStr, tabSep);
tokenizer::iterator token = tokens.begin();
// name of the functional groups
auto name = *token;
boost::erase_all(name, " ");
++token;
// grab the smirks:
auto smirks = *token;
boost::erase_all(smirks, " ");
++token;
return getReaction(name, smirks);
}
} // namespace
namespace MolStandardize {
std::vector<std::shared_ptr<ChemicalReaction>> readTransformations(
std::string fileName) {
std::ifstream inStream(fileName.c_str());
if ((!inStream) || (inStream.bad())) {
std::ostringstream errout;
errout << "Bad input file " << fileName;
throw BadFileException(errout.str());
}
std::vector<std::shared_ptr<ChemicalReaction>> transformations;
transformations = readTransformations(inStream);
return transformations;
}
std::vector<std::shared_ptr<ChemicalReaction>> readTransformations(
std::istream &inStream, int nToRead) {
std::vector<std::shared_ptr<ChemicalReaction>> transformations;
if (inStream.bad()) {
throw BadFileException("Bad stream contents.");
}
const int MAX_LINE_LEN = 512;
char inLine[MAX_LINE_LEN];
std::string tmpstr;
int nRead = 0;
while (!inStream.eof() && !inStream.fail() &&
(nToRead < 0 || nRead < nToRead)) {
inStream.getline(inLine, MAX_LINE_LEN, '\n');
tmpstr = inLine;
// parse the reaction on this line (if there is one)
auto transformation = getReaction(tmpstr);
if (transformation) {
transformations.push_back(
std::shared_ptr<ChemicalReaction>(transformation));
nRead++;
}
}
return transformations;
}
std::vector<std::shared_ptr<ChemicalReaction>> readTransformations(
const std::vector<std::pair<std::string, std::string>> &data) {
std::vector<std::shared_ptr<ChemicalReaction>> transformations;
for (const auto &pr : data) {
auto transformation = getReaction(pr.first, pr.second);
if (transformation) {
transformations.push_back(
std::shared_ptr<ChemicalReaction>(transformation));
}
}
return transformations;
}
} // namespace MolStandardize
} // namespace RDKit
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