void constructFragmenterBondTypes(
std::istream *inStream,
const std::map<unsigned int, std::string> &atomTypes,
std::vector<FragmenterBondType> &defs, const std::string &comment,
bool validate, bool labelByConnector) {
PRECONDITION(inStream, "no stream");
defs.clear();
defs.resize(0);
unsigned int line = 0;
while (!inStream->eof()) {
++line;
std::string tempStr = getLine(inStream);
if (tempStr == "" || tempStr.find(comment) == 0) continue;
std::vector<std::string> tokens;
boost::split(tokens, tempStr, boost::is_any_of(" \t"),
boost::token_compress_on);
if (tokens.size() < 3) {
BOOST_LOG(rdWarningLog) << "line " << line << " is too short"
<< std::endl;
continue;
}
unsigned int idx1 = boost::lexical_cast<unsigned int>(tokens[0]);
if (atomTypes.find(idx1) == atomTypes.end()) {
BOOST_LOG(rdWarningLog) << "atom type #" << idx1 << " not recognized."
<< std::endl;
continue;
}
unsigned int idx2 = boost::lexical_cast<unsigned int>(tokens[1]);
if (atomTypes.find(idx2) == atomTypes.end()) {
BOOST_LOG(rdWarningLog) << "atom type #" << idx2 << " not recognized."
<< std::endl;
continue;
}
std::string sma1 = atomTypes.find(idx1)->second;
std::string sma2 = atomTypes.find(idx2)->second;
std::string smarts = "[$(" + sma1 + ")]" + tokens[2] + "[$(" + sma2 + ")]";
ROMol *p = SmartsToMol(smarts);
if (validate) {
if (!p) {
BOOST_LOG(rdWarningLog) << "cannot convert SMARTS " << smarts
<< " to molecule at line " << line << std::endl;
continue;
}
}
FragmenterBondType fbt;
fbt.atom1Type = idx1;
fbt.atom2Type = idx2;
if (labelByConnector) {
fbt.atom1Label = idx1;
fbt.atom2Label = idx2;
} else {
fbt.atom1Label = idx2;
fbt.atom2Label = idx1;
}
if (p) {
// for the purposes of replacing the bond, we'll use just the first
// character to set the bond type (if we recognize it):
switch (tokens[2][0]) {
case '-':
fbt.bondType = Bond::SINGLE;
break;
case '=':
fbt.bondType = Bond::DOUBLE;
break;
case '#':
fbt.bondType = Bond::TRIPLE;
break;
case ':':
fbt.bondType = Bond::AROMATIC;
break;
default:
fbt.bondType = p->getBondWithIdx(0)->getBondType();
}
fbt.query = ROMOL_SPTR(p);
} else {
fbt.bondType = Bond::UNSPECIFIED;
fbt.query = ROMOL_SPTR();
}
defs.push_back(fbt);
}
}
void logging_function2()
{
src::logger_mt& lg = my_logger::get();
BOOST_LOG(lg) << "Greetings from the global logger!";
}
void on_data_sent(std::size_t size)
{
BOOST_LOG(m_stat) << logging::add_value("SentSize", size) << "Some data sent";
}
void on_data_received(std::size_t size)
{
BOOST_LOG(m_stat) << logging::add_value("ReceivedSize", size) << "Some data received";
}
void logging_function()
{
src::logger lg;
BOOST_LOG(lg) << "Hello, world!";
}
void FPBReader::init() {
PRECONDITION(dp_istrm, "no stream");
dp_impl = new detail::FPBReader_impl;
dp_impl->istrm = dp_istrm;
dp_impl->df_lazy = df_lazyRead;
char magic[detail::magicSize];
dp_istrm->read(magic, detail::magicSize);
if (detail::FPB_MAGIC != std::string(magic, detail::magicSize)) {
throw BadFileException("Invalid FPB magic");
}
while (1) {
if (dp_istrm->eof()) throw BadFileException("EOF hit before FEND record");
std::string chunkNm;
boost::uint64_t chunkSz;
boost::uint8_t *chunk = NULL;
detail::readChunkDetails(*dp_istrm, chunkNm, chunkSz);
// std::cerr << " Chunk: " << chunkNm << " " << chunkSz << std::endl;
if (!df_lazyRead || (chunkNm != "AREN" && chunkNm != "FPID")) {
detail::readChunkData(*dp_istrm, chunkSz, chunk);
if (chunkNm == "FEND") {
break;
} else if (chunkNm == "POPC") {
detail::extractPopCounts(dp_impl, chunkSz, chunk);
} else if (chunkNm == "AREN") {
dp_impl->dp_arenaChunk.reset(chunk);
detail::extractArena(dp_impl, chunkSz, chunk);
chunk = NULL;
} else if (chunkNm == "FPID") {
dp_impl->dp_idChunk.reset(chunk);
detail::extractIds(dp_impl, chunkSz, chunk);
chunk = NULL;
} else if (chunkNm == "META") {
// currently ignored
} else if (chunkNm == "HASH") {
// currently ignored
} else {
BOOST_LOG(rdWarningLog) << "Unknown chunk: " << chunkNm << " ignored."
<< std::endl;
}
delete[] chunk;
} else {
// we are reading the AREN or FPID chunk in lazy mode, just get our
// position in
// the file.
if (chunkNm == "AREN") {
detail::extractArenaDetails(dp_impl, chunkSz);
} else if (chunkNm == "FPID") {
detail::extractIdsDetails(dp_impl, chunkSz);
}
}
}
if ((!df_lazyRead && !dp_impl->dp_arenaChunk) ||
(df_lazyRead && !dp_impl->fpDataOffset))
throw BadFileException("No AREN record found");
if ((!df_lazyRead && !dp_impl->dp_idChunk) ||
(df_lazyRead && !dp_impl->idDataOffset))
throw BadFileException("No FPID record found");
df_init = true;
};
