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da6cd73168
* run clang-format-18 across Code/*.cpp and Code/*.h * run clang-format-18 across External
126 lines
3.8 KiB
C++
126 lines
3.8 KiB
C++
//
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// Copyright (C) 2018-2021 Susan H. Leung and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "AcidBaseCatalogUtils.h"
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#include <RDGeneral/BadFileException.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <boost/algorithm/string.hpp>
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#include <boost/tokenizer.hpp>
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typedef boost::tokenizer<boost::char_separator<char>> tokenizer;
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#include <fstream>
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#include <string>
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namespace RDKit {
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namespace {
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std::pair<ROMol *, ROMol *> *getPair(const std::string &name,
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const std::string &acid_smarts,
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const std::string &base_smarts) {
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ROMol *acid(SmartsToMol(acid_smarts));
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if (!acid) {
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throw ValueErrorException("Failed parsing acid SMARTS: " + acid_smarts);
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}
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ROMol *base(SmartsToMol(base_smarts));
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if (!base) {
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delete acid;
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throw ValueErrorException("Failed parsing base SMARTS: " + base_smarts);
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}
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acid->setProp(common_properties::_Name, name);
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base->setProp(common_properties::_Name, name);
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return new std::pair<ROMol *, ROMol *>(acid, base);
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}
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std::pair<ROMol *, ROMol *> *getPair(std::string tmpStr) {
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// Remove whitespace
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boost::trim(tmpStr);
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if (tmpStr.length() == 0 || tmpStr.substr(0, 2) == "//") {
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// empty or comment line
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return nullptr;
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}
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boost::char_separator<char> tabSep("\t");
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tokenizer tokens(tmpStr, tabSep);
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tokenizer::iterator token = tokens.begin();
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// name of the functional groups
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std::string name = *token;
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boost::erase_all(name, " ");
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++token;
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// grab the acid:
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std::string acid_smarts = *token;
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boost::erase_all(acid_smarts, " ");
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++token;
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// grab the base:
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std::string base_smarts = *token;
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boost::erase_all(base_smarts, " ");
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++token;
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return getPair(name, acid_smarts, base_smarts);
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}
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} // namespace
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namespace MolStandardize {
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std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> readPairs(std::string fileName) {
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std::ifstream inStream(fileName.c_str());
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if ((!inStream) || (inStream.bad())) {
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std::ostringstream errout;
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errout << "Bad input file " << fileName;
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throw BadFileException(errout.str());
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}
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std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> mol_pairs =
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readPairs(inStream);
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return mol_pairs;
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}
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std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> readPairs(std::istream &inStream,
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int nToRead) {
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std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> pairs;
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pairs.clear();
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if (inStream.bad()) {
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throw BadFileException("Bad stream contents.");
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}
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const int MAX_LINE_LEN = 512;
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char inLine[MAX_LINE_LEN];
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std::string tmpstr;
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int nRead = 0;
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while (!inStream.eof() && !inStream.fail() &&
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(nToRead < 0 || nRead < nToRead)) {
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inStream.getline(inLine, MAX_LINE_LEN, '\n');
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tmpstr = inLine;
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// parse the molpair on this line (if there is one)
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std::shared_ptr<std::pair<ROMol *, ROMol *>> mol_pair(getPair(tmpstr));
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if (mol_pair != nullptr) {
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pairs.emplace_back(ROMOL_SPTR(mol_pair->first),
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ROMOL_SPTR(mol_pair->second));
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nRead++;
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}
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}
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return pairs;
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}
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std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> readPairs(
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const std::vector<std::tuple<std::string, std::string, std::string>>
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&data) {
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std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> pairs;
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for (const auto &tpl : data) {
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std::shared_ptr<std::pair<ROMol *, ROMol *>> mol_pair(
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getPair(std::get<0>(tpl), std::get<1>(tpl), std::get<2>(tpl)));
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pairs.emplace_back(ROMOL_SPTR(mol_pair->first),
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ROMOL_SPTR(mol_pair->second));
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}
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return pairs;
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}
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} // namespace MolStandardize
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} // namespace RDKit
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