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