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https://github.com/rdkit/rdkit.git
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ec366c1ab7
* a round of cleanups courtesy of PVS studio * add a test to make sure that a warning is a false alarm * bug fix * Fix a UFF bug * more PVS studio cleanups * next round of PVS studio cleanups * completely remove the chances for that bug * changes in response to review * add an additional test + a bit of reformatting that snuck in
102 lines
2.6 KiB
C++
102 lines
2.6 KiB
C++
//
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// Copyright (C) 2018 Susan H. Leung
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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 "FragmentCatalogUtils.h"
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#include <RDGeneral/BadFileException.h>
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#include <boost/tokenizer.hpp>
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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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ROMol *getSmarts(std::string &&tmpStr) {
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ROMol *mol = nullptr;
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// Remove whitespace
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boost::trim(tmpStr);
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if (tmpStr.length() == 0) {
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// empty line
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return mol;
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}
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if (tmpStr.substr(0, 2) == "//") {
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// comment line
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return mol;
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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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++token;
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// There must be a SMARTS expression
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CHECK_INVARIANT(token != tokens.end(), tmpStr);
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// grab the smarts:
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std::string smarts = *token;
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boost::erase_all(smarts, " ");
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++token;
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mol = SmartsToMol(smarts);
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CHECK_INVARIANT(mol, smarts);
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mol->setProp(common_properties::_Name, name);
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mol->setProp(common_properties::_fragSMARTS, smarts);
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return mol;
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}
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} // namespace
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namespace MolStandardize {
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std::vector<std::shared_ptr<ROMol>> readFuncGroups(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::shared_ptr<ROMol>> funcGroups;
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funcGroups = readFuncGroups(inStream);
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return funcGroups;
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}
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std::vector<std::shared_ptr<ROMol>> readFuncGroups(std::istream &inStream,
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int nToRead) {
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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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int nRead = 0;
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std::vector<std::shared_ptr<ROMol>> funcGroups;
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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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std::string tmpstr(inLine);
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// parse the molecule on this line (if there is one)
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std::shared_ptr<ROMol> mol(getSmarts(std::move(tmpstr)));
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if (mol) {
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funcGroups.push_back(mol);
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nRead++;
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}
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}
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return funcGroups;
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}
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} // namespace MolStandardize
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} // namespace RDKit
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