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// $Id$
//
// Copyright (C) 2003-2006 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 <boost/tokenizer.hpp>
typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
#include "GasteigerParams.h"
#include <RDGeneral/BoostStartInclude.h>
#include <boost/flyweight.hpp>
#include <boost/flyweight/key_value.hpp>
#include <boost/flyweight/no_tracking.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <sstream>
#include <locale>
namespace RDKit {
/*! \brief Gasteiger partial charge parameters
*/
std::string defaultParamData =
"H * 7.17 6.24 -0.56 \n \
C sp3 7.98 9.18 1.88 \n \
C sp2 8.79 9.32 1.51 \n \
C sp 10.39 9.45 0.73 \n \
N sp3 11.54 10.82 1.36 \n \
N sp2 12.87 11.15 0.85 \n \
N sp 15.68 11.7 -0.27 \n \
O sp3 14.18 12.92 1.39 \n \
O sp2 17.07 13.79 0.47 \n \
F sp3 14.66 13.85 2.31 \n \
Cl sp3 11.00 9.69 1.35 \n \
Br sp3 10.08 8.47 1.16 \n \
I sp3 9.9 7.96 0.96 \n \
S sp3 10.14 9.13 1.38 \n \
S so 10.14 9.13 1.38 \n \
S so2 12.00 10.81 1.20 \n \
S sp2 10.88 9.49 1.33 \n \
P sp3 8.90 8.24 0.96 \n \
X * 0.00 0.00 0.00 \n \
";
/*! \brief additional Gasteiger partial charge parameters
generated using the calculation in PyBabel:
http://mgltools.scripps.edu/api/PyBabel/PyBabel.gasteiger-pysrc.html
*/
std::string additionalParamData =
"P sp2 9.665 8.530 0.735 \n \
Si sp3 7.300 6.567 0.657 \n \
Si sp2 7.905 6.748 0.443 \n \
Si sp 9.065 7.027 -0.002 \n \
B sp3 5.980 6.820 1.605 \n \
B sp2 6.420 6.807 1.322 \n \
Be sp3 3.845 6.755 3.165 \n \
Be sp2 4.005 6.725 3.035 \n \
Mg sp2 3.565 5.572 2.197 \n \
Mg sp3 3.300 5.587 2.447 \n \
Mg sp 4.040 5.472 1.823 \n \
Al sp3 5.375 4.953 0.867 \n \
Al sp2 5.795 5.020 0.695 \n \
";
typedef boost::flyweight<
boost::flyweights::key_value<std::string, GasteigerParams>,
boost::flyweights::no_tracking> gparam_flyweight;
GasteigerParams::GasteigerParams(std::string paramData) {
boost::char_separator<char> eolSep("\n");
boost::char_separator<char> spaceSep(" \t");
if (paramData == "") paramData = defaultParamData + additionalParamData;
tokenizer lines(paramData, eolSep);
d_paramMap.clear();
std::istringstream istr;
istr.imbue(std::locale("C"));
for (tokenizer::iterator lineIter = lines.begin(); lineIter != lines.end();
++lineIter) {
std::string dataLine = *lineIter;
tokenizer tokens(dataLine, spaceSep);
if (tokens.begin() != tokens.end()) {
tokenizer::iterator tokIter = tokens.begin();
// read the element and the mode
std::string elem = *tokIter;
++tokIter;
std::string mode = *tokIter;
++tokIter;
// read in the parameters
DOUBLE_VECT params(3);
istr.clear();
istr.str(*tokIter);
istr >> params[0];
++tokIter;
istr.clear();
istr.str(*tokIter);
istr >> params[1];
++tokIter;
istr.clear();
istr.str(*tokIter);
istr >> params[2];
++tokIter;
std::pair<std::string, std::string> key(elem, mode);
d_paramMap[key] = params;
}
}
}
const GasteigerParams *GasteigerParams::getParams(
const std::string ¶mData) {
const GasteigerParams *res = &(gparam_flyweight(paramData).get());
return res;
}
}
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