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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 "AcidBaseCatalogUtils.h"
#include <RDGeneral/BadFileException.h>
#include <GraphMol/SmilesParse/SmilesParse.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 {
std::pair<ROMol*, ROMol*>* getPair(const std::string& name,
const std::string& acid_smarts,
const std::string& base_smarts) {
ROMol* acid(SmartsToMol(acid_smarts));
if (!acid) {
throw ValueErrorException("Failed parsing acid SMARTS: " + acid_smarts);
}
ROMol* base(SmartsToMol(base_smarts));
if (!base) {
delete acid;
throw ValueErrorException("Failed parsing base SMARTS: " + base_smarts);
}
acid->setProp(common_properties::_Name, name);
base->setProp(common_properties::_Name, name);
return new std::pair<ROMol*, ROMol*>(acid, base);
}
std::pair<ROMol*, ROMol*>* getPair(std::string tmpStr) {
// Remove whitespace
boost::trim(tmpStr);
if (tmpStr.length() == 0 || tmpStr.substr(0, 2) == "//") {
// empty or comment line
return nullptr;
}
boost::char_separator<char> tabSep("\t");
tokenizer tokens(tmpStr, tabSep);
tokenizer::iterator token = tokens.begin();
// name of the functional groups
std::string name = *token;
boost::erase_all(name, " ");
++token;
// grab the acid:
std::string acid_smarts = *token;
boost::erase_all(acid_smarts, " ");
++token;
// grab the base:
std::string base_smarts = *token;
boost::erase_all(base_smarts, " ");
++token;
return getPair(name, acid_smarts, base_smarts);
}
} // namespace
namespace MolStandardize {
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> readPairs(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::pair<ROMOL_SPTR, ROMOL_SPTR>> mol_pairs =
readPairs(inStream);
return mol_pairs;
}
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> readPairs(std::istream& inStream,
int nToRead) {
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> pairs;
pairs.clear();
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 molpair on this line (if there is one)
std::shared_ptr<std::pair<ROMol*, ROMol*>> mol_pair(getPair(tmpstr));
if (mol_pair != nullptr) {
pairs.emplace_back(ROMOL_SPTR(mol_pair->first),
ROMOL_SPTR(mol_pair->second));
nRead++;
}
}
return pairs;
}
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> readPairs(
const std::vector<std::tuple<std::string, std::string, std::string>>&
data) {
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> pairs;
for (const auto& tpl : data) {
std::shared_ptr<std::pair<ROMol*, ROMol*>> mol_pair(
getPair(std::get<0>(tpl), std::get<1>(tpl), std::get<2>(tpl)));
pairs.emplace_back(ROMOL_SPTR(mol_pair->first),
ROMOL_SPTR(mol_pair->second));
}
return pairs;
}
} // namespace MolStandardize
} // namespace RDKit
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