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https://github.com/rdkit/rdkit.git
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0147cd8201
* revert duplicate chunk in release notes * replace deprecated ifdefs This one gets rid of USE_BUILTIN_POPCNT and RDK_THREADSAFE_SS use RDK_OPTIMIZE_POPCNT or RDK_BUILD_THREADSAFE_SSS instead * get rid of BUILD_COORDGEN_SUPPORT from ROMol.i * fix a stupid typo * update release notes
119 lines
3.3 KiB
C++
119 lines
3.3 KiB
C++
// $Id$
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//
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// Copyright (C) 2001-2006 Rational Discovery LLC
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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 "PeriodicTable.h"
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#include <string>
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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 <sstream>
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#include <locale>
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#ifdef RDK_BUILD_THREADSAFE_SSS
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#include <mutex>
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#endif
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namespace RDKit {
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class std::unique_ptr<PeriodicTable> PeriodicTable::ds_instance = nullptr;
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PeriodicTable::PeriodicTable() {
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// it is assumed that the atomic atomData string constains atoms
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// in sequence and no atoms are missing in between
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byanum.clear();
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byname.clear();
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boost::char_separator<char> eolSep("\n");
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tokenizer tokens(periodicTableAtomData, eolSep);
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for (tokenizer::iterator token = tokens.begin(); token != tokens.end();
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++token) {
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if (*token != " ") {
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atomicData adata(*token);
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std::string enam = adata.Symbol();
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byname[enam] = adata.AtomicNum();
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// there are, for backwards compatibility reasons, some duplicate rows for
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// atomic numbers in the atomic_data data structure. It's ok to have
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// multiple symbols map to the same atomic number (above), but we need to
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// be sure that we only store one entry per atomic number.
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// Note that this only works because the first atom in the adata list is
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// the dummy atom (atomic number 0). This was #2784
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if (rdcast<size_t>(adata.AtomicNum()) == byanum.size()) {
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byanum.push_back(adata);
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}
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}
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}
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unsigned int lidx = 0;
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std::istringstream istr;
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istr.imbue(std::locale("C"));
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while (isotopesAtomData[lidx] != "" && isotopesAtomData[lidx] != "EOS") {
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tokenizer lines(isotopesAtomData[lidx++], eolSep);
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boost::char_separator<char> spaceSep(" \t");
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for (tokenizer::iterator line = lines.begin(); line != lines.end();
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++line) {
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if (*line != " ") {
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tokenizer tokens(*line, spaceSep);
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tokenizer::iterator token = tokens.begin();
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int anum;
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istr.clear();
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istr.str(*token);
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istr >> anum;
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atomicData &adata = byanum[anum];
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++token;
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if (token == tokens.end()) {
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continue;
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}
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++token;
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if (token == tokens.end()) {
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continue;
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}
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unsigned int isotope;
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istr.clear();
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istr.str(*token);
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istr >> isotope;
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++token;
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if (token == tokens.end()) {
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continue;
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}
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double mass;
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istr.clear();
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istr.str(*token);
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istr >> mass;
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++token;
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if (token == tokens.end()) {
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continue;
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}
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double abundance;
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istr.clear();
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istr.str(*token);
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istr >> abundance;
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adata.d_isotopeInfoMap[isotope] = std::make_pair(mass, abundance);
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}
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}
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}
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}
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void PeriodicTable::initInstance() {
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ds_instance = std::unique_ptr<PeriodicTable>(new PeriodicTable());
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}
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PeriodicTable *PeriodicTable::getTable() {
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#ifdef RDK_BUILD_THREADSAFE_SSS
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static std::once_flag pt_init_once;
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std::call_once(pt_init_once, initInstance);
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#else
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if (!ds_instance) {
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initInstance();
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}
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#endif
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return ds_instance.get();
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}
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} // namespace RDKit
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