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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 "FragmentCatalogUtils.h"
#include <RDGeneral/BadFileException.h>
#include <boost/tokenizer.hpp>
#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 {
ROMol *getMol(const std::string &name, const std::string &smarts) {
auto mol = SmartsToMol(smarts);
if (!mol) {
throw ValueErrorException("Failed parsing fragment SMARTS: " + smarts);
}
mol->setProp(common_properties::_Name, name);
mol->setProp(common_properties::_fragSMARTS, smarts);
return mol;
}
ROMol *getMol(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;
++token;
// There must be a SMARTS expression
if (token == tokens.end()) {
throw ValueErrorException("no SMARTS found in input: " + tmpStr);
}
// grab the smarts:
std::string smarts = *token;
boost::erase_all(smarts, " ");
++token;
return getMol(name, smarts);
}
} // namespace
namespace MolStandardize {
std::vector<std::shared_ptr<ROMol>> readFuncGroups(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<ROMol>> funcGroups;
funcGroups = readFuncGroups(inStream);
return funcGroups;
}
std::vector<std::shared_ptr<ROMol>> readFuncGroups(std::istream &inStream,
int nToRead) {
if (inStream.bad()) {
throw BadFileException("Bad stream contents.");
}
const int MAX_LINE_LEN = 512;
char inLine[MAX_LINE_LEN];
int nRead = 0;
std::vector<std::shared_ptr<ROMol>> funcGroups;
while (!inStream.eof() && !inStream.fail() &&
(nToRead < 0 || nRead < nToRead)) {
inStream.getline(inLine, MAX_LINE_LEN, '\n');
std::string tmpstr(inLine);
// parse the molecule on this line (if there is one)
std::shared_ptr<ROMol> mol(getMol(std::move(tmpstr)));
if (mol) {
funcGroups.push_back(mol);
nRead++;
}
}
return funcGroups;
}
std::vector<std::shared_ptr<ROMol>> readFuncGroups(
const std::vector<std::pair<std::string, std::string>> &data) {
std::vector<std::shared_ptr<ROMol>> funcGroups;
for (const auto &pr : data) {
auto mol = getMol(pr.first, pr.second);
if (mol) {
funcGroups.push_back(std::shared_ptr<ROMol>(mol));
}
}
return funcGroups;
}
} // namespace MolStandardize
} // namespace RDKit
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