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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 "TautomerCatalogUtils.h"
#include <RDGeneral/BadFileException.h>
#include <boost/tokenizer.hpp>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.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::unique_ptr<MolStandardize::TautomerTransform> getTautomer(
const std::string& name, const std::string& smarts,
const std::string& bond_str, const std::string& charge_str) {
std::vector<Bond::BondType> bond_types =
MolStandardize::stringToBondType(bond_str);
std::vector<int> charges = MolStandardize::stringToCharge(charge_str);
ROMol* tautomer = SmartsToMol(smarts);
if (!tautomer) {
throw ValueErrorException("cannot parse tautomer SMARTS: " + smarts);
}
tautomer->setProp(common_properties::_Name, name);
return std::make_unique<MolStandardize::TautomerTransform>(
tautomer, bond_types, charges);
}
std::unique_ptr<MolStandardize::TautomerTransform> getTautomer(
const std::string& 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);
std::vector<std::string> result(tokens.begin(), tokens.end());
// tautomer information to collect from each line
std::string name;
std::string smarts;
std::string bond_str;
std::string charge_str;
// line must have at least two tab separated values
if (result.size() < 2) {
BOOST_LOG(rdWarningLog) << "Invalid line: " << tmpStr << std::endl;
return nullptr;
}
// line only has name and smarts
if (result.size() == 2) {
name = result[0];
smarts = result[1];
}
// line has name, smarts, bonds
if (result.size() == 3) {
name = result[0];
smarts = result[1];
bond_str = result[2];
}
// line has name, smarts, bonds, charges
if (result.size() == 4) {
name = result[0];
smarts = result[1];
bond_str = result[2];
charge_str = result[3];
}
boost::erase_all(smarts, " ");
boost::erase_all(name, " ");
boost::erase_all(bond_str, " ");
boost::erase_all(charge_str, " ");
return getTautomer(name, smarts, bond_str, charge_str);
}
} // namespace
namespace MolStandardize {
std::vector<Bond::BondType> stringToBondType(std::string bond_str) {
std::vector<Bond::BondType> bonds;
for (const auto& c : bond_str) {
switch (c) {
case '-':
bonds.push_back(Bond::SINGLE);
break;
case '=':
bonds.push_back(Bond::DOUBLE);
break;
case '#':
bonds.push_back(Bond::TRIPLE);
break;
case ':':
bonds.push_back(Bond::AROMATIC);
break;
}
}
return bonds;
}
std::vector<int> stringToCharge(std::string charge_str) {
std::vector<int> charges;
for (const auto& c : charge_str) {
switch (c) {
case '+':
charges.push_back(1);
break;
case '0':
charges.push_back(0);
break;
case '-':
charges.push_back(-1);
break;
default:
throw ValueErrorException("Charge symbol not recognised.");
}
}
return charges;
}
std::vector<TautomerTransform> readTautomers(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<TautomerTransform> tautomers = readTautomers(inStream);
return tautomers;
}
std::vector<TautomerTransform> readTautomers(std::istream& inStream,
int nToRead) {
if (inStream.bad()) {
throw BadFileException("Bad stream contents.");
}
std::vector<TautomerTransform> tautomers;
if (nToRead > 0) {
tautomers.reserve(nToRead);
}
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 tautomer on this line (if there is one)
auto transform = getTautomer(tmpstr);
if (transform) {
tautomers.emplace_back(*transform);
nRead++;
}
}
return tautomers;
}
std::vector<TautomerTransform> readTautomers(
const TautomerTransformDefs& data) {
std::vector<TautomerTransform> tautomers;
for (const auto& tpl : data) {
auto transform = getTautomer(std::get<0>(tpl), std::get<1>(tpl),
std::get<2>(tpl), std::get<3>(tpl));
if (transform) {
tautomers.emplace_back(*transform);
}
}
return tautomers;
}
} // namespace MolStandardize
} // namespace RDKit
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