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// $Id$
//
// Copyright (C) 2001-2006 Rational Discovery LLC
//
// @@ 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 "PeriodicTable.h"
#include <string>
#include <boost/tokenizer.hpp>
typedef boost::tokenizer<boost::char_separator<char>> tokenizer;
#include <sstream>
#include <locale>
#ifdef RDK_BUILD_THREADSAFE_SSS
#include <mutex>
#endif
namespace RDKit {
class std::unique_ptr<PeriodicTable> PeriodicTable::ds_instance = nullptr;
PeriodicTable::PeriodicTable() {
// it is assumed that the atomic atomData string constains atoms
// in sequence and no atoms are missing in between
byanum.clear();
byname.clear();
boost::char_separator<char> eolSep("\n");
tokenizer tokens(periodicTableAtomData, eolSep);
for (tokenizer::iterator token = tokens.begin(); token != tokens.end();
++token) {
if (*token != " ") {
atomicData adata(*token);
std::string enam = adata.Symbol();
byname[enam] = adata.AtomicNum();
// there are, for backwards compatibility reasons, some duplicate rows for
// atomic numbers in the atomic_data data structure. It's ok to have
// multiple symbols map to the same atomic number (above), but we need to
// be sure that we only store one entry per atomic number.
// Note that this only works because the first atom in the adata list is
// the dummy atom (atomic number 0). This was #2784
if (rdcast<size_t>(adata.AtomicNum()) == byanum.size()) {
byanum.push_back(adata);
}
}
}
unsigned int lidx = 0;
std::istringstream istr;
istr.imbue(std::locale("C"));
while (isotopesAtomData[lidx] != "" && isotopesAtomData[lidx] != "EOS") {
tokenizer lines(isotopesAtomData[lidx++], eolSep);
boost::char_separator<char> spaceSep(" \t");
for (tokenizer::iterator line = lines.begin(); line != lines.end();
++line) {
if (*line != " ") {
tokenizer tokens(*line, spaceSep);
tokenizer::iterator token = tokens.begin();
int anum;
istr.clear();
istr.str(*token);
istr >> anum;
atomicData &adata = byanum[anum];
++token;
if (token == tokens.end()) {
continue;
}
++token;
if (token == tokens.end()) {
continue;
}
unsigned int isotope;
istr.clear();
istr.str(*token);
istr >> isotope;
++token;
if (token == tokens.end()) {
continue;
}
double mass;
istr.clear();
istr.str(*token);
istr >> mass;
++token;
if (token == tokens.end()) {
continue;
}
double abundance;
istr.clear();
istr.str(*token);
istr >> abundance;
adata.d_isotopeInfoMap[isotope] = std::make_pair(mass, abundance);
}
}
}
}
void PeriodicTable::initInstance() {
ds_instance = std::unique_ptr<PeriodicTable>(new PeriodicTable());
}
PeriodicTable *PeriodicTable::getTable() {
#ifdef RDK_BUILD_THREADSAFE_SSS
static std::once_flag pt_init_once;
std::call_once(pt_init_once, initInstance);
#else
if (!ds_instance) {
initInstance();
}
#endif
return ds_instance.get();
}
} // namespace RDKit
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