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<div id="projectname">The Gnome Chemistry Utils <span id="projectnumber">0.13.5</span></div>
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<li class="navelem"><a class="el" href="dir_e8e4833ad39bcb8c999c6b13aa077049.html">libs</a> </li>
<li class="navelem"><a class="el" href="dir_3ef3fbf7a050ca9d76c05bd6c83d6907.html">gcu</a> </li>
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<div class="title">formula.h</div> </div>
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<a href="formula_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">// -*- C++ -*-</span>
<a name="l00002"></a>00002
<a name="l00003"></a>00003 <span class="comment">/*</span>
<a name="l00004"></a>00004 <span class="comment"> * Gnome Chemistry Utils</span>
<a name="l00005"></a>00005 <span class="comment"> * formula.h</span>
<a name="l00006"></a>00006 <span class="comment"> *</span>
<a name="l00007"></a>00007 <span class="comment"> * Copyright (C) 2005-2010 Jean Bréfort <jean.brefort@normalesup.org></span>
<a name="l00008"></a>00008 <span class="comment"> *</span>
<a name="l00009"></a>00009 <span class="comment"> * This program is free software; you can redistribute it and/or</span>
<a name="l00010"></a>00010 <span class="comment"> * modify it under the terms of the GNU General Public License as</span>
<a name="l00011"></a>00011 <span class="comment"> * published by the Free Software Foundation; either version 2 of the</span>
<a name="l00012"></a>00012 <span class="comment"> * License, or (at your option) any later version.</span>
<a name="l00013"></a>00013 <span class="comment"> *</span>
<a name="l00014"></a>00014 <span class="comment"> * This program is distributed in the hope that it will be useful,</span>
<a name="l00015"></a>00015 <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00016"></a>00016 <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00017"></a>00017 <span class="comment"> * GNU General Public License for more details.</span>
<a name="l00018"></a>00018 <span class="comment"> *</span>
<a name="l00019"></a>00019 <span class="comment"> * You should have received a copy of the GNU General Public License</span>
<a name="l00020"></a>00020 <span class="comment"> * along with this program; if not, write to the Free Software</span>
<a name="l00021"></a>00021 <span class="comment"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301</span>
<a name="l00022"></a>00022 <span class="comment"> * USA</span>
<a name="l00023"></a>00023 <span class="comment"> */</span>
<a name="l00024"></a>00024
<a name="l00025"></a>00025 <span class="preprocessor">#ifndef GCU_FORMULA_H</span>
<a name="l00026"></a>00026 <span class="preprocessor"></span><span class="preprocessor">#define GCU_FORMULA_H</span>
<a name="l00027"></a>00027 <span class="preprocessor"></span>
<a name="l00028"></a>00028 <span class="preprocessor">#include <string></span>
<a name="l00029"></a>00029 <span class="preprocessor">#include <map></span>
<a name="l00030"></a>00030 <span class="preprocessor">#include <list></span>
<a name="l00031"></a>00031 <span class="preprocessor">#include <stdexcept></span>
<a name="l00032"></a>00032 <span class="preprocessor">#include "<a class="code" href="isotope_8h.html">isotope.h</a>"</span>
<a name="l00033"></a>00033 <span class="preprocessor">#include "<a class="code" href="macros_8h.html">macros.h</a>"</span>
<a name="l00034"></a>00034 <span class="preprocessor">#include "<a class="code" href="value_8h.html">value.h</a>"</span>
<a name="l00035"></a>00035
<a name="l00037"></a>00037 <span class="keyword">namespace </span>gcu
<a name="l00038"></a>00038 {
<a name="l00039"></a>00039
<a name="l00052"></a><a class="code" href="namespacegcu.html#a49392c345f0740efd3167eb30aca570e">00052</a> <span class="keyword">typedef</span> <span class="keyword">enum</span> {
<a name="l00053"></a>00053 GCU_FORMULA_PARSE_GUESS,
<a name="l00054"></a>00054 GCU_FORMULA_PARSE_ATOM,
<a name="l00055"></a>00055 GCU_FORMULA_PARSE_RESIDUE,
<a name="l00056"></a>00056 GCU_FORMULA_PARSE_ASK,
<a name="l00057"></a>00057 GCU_FORMULA_PARSE_NO_CASE=8
<a name="l00058"></a>00058 } <a class="code" href="namespacegcu.html#a49392c345f0740efd3167eb30aca570e">FormulaParseMode</a>;
<a name="l00059"></a>00059
<a name="l00065"></a><a class="code" href="classgcu_1_1parse__error.html">00065</a> <span class="keyword">class </span><a class="code" href="classgcu_1_1parse__error.html">parse_error</a>: <span class="keyword">public</span> std::exception
<a name="l00066"></a>00066 {
<a name="l00067"></a>00067 <span class="keyword">public</span>:
<a name="l00071"></a>00071 <span class="keyword">explicit</span>
<a name="l00072"></a>00072 <a class="code" href="classgcu_1_1parse__error.html#a67d6ea5315e55a0ba5aaf0e71e8e7f89">parse_error</a> (<span class="keyword">const</span> std::string& __arg, <span class="keywordtype">int</span> start, <span class="keywordtype">int</span> length);
<a name="l00073"></a>00073
<a name="l00074"></a>00074 <span class="keyword">virtual</span>
<a name="l00075"></a>00075 ~<a class="code" href="classgcu_1_1parse__error.html">parse_error</a> () <span class="keywordflow">throw</span> ();
<a name="l00076"></a>00076
<a name="l00080"></a>00080 <span class="keyword">virtual</span> <span class="keyword">const</span> <span class="keywordtype">char</span>*
<a name="l00081"></a>00081 <a class="code" href="classgcu_1_1parse__error.html#aee39bffc5241d2976eae9c21591f2e53">what</a> () <span class="keyword">const</span> <span class="keywordflow">throw</span> ();
<a name="l00085"></a>00085 <span class="keyword">const</span> <span class="keywordtype">char</span>*
<a name="l00086"></a>00086 <a class="code" href="classgcu_1_1parse__error.html#aee39bffc5241d2976eae9c21591f2e53">what</a> (<span class="keywordtype">int</span>& start, <span class="keywordtype">int</span>& length) <span class="keyword">const</span> <span class="keywordflow">throw</span> ();
<a name="l00087"></a>00087
<a name="l00091"></a><a class="code" href="classgcu_1_1parse__error.html#a4639987ffe080e3b0e8d44be2b7647bd">00091</a> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1parse__error.html#a4639987ffe080e3b0e8d44be2b7647bd">add_offset</a> (<span class="keywordtype">int</span> offset) {m_start += offset;}
<a name="l00092"></a>00092
<a name="l00093"></a>00093 <span class="keyword">private</span>:
<a name="l00094"></a>00094 std::string m_msg;
<a name="l00095"></a>00095 <span class="keywordtype">int</span> m_start, m_length;
<a name="l00096"></a>00096
<a name="l00097"></a>00097 };
<a name="l00098"></a>00098
<a name="l00103"></a><a class="code" href="classgcu_1_1FormulaElt.html">00103</a> <span class="keyword">class </span><a class="code" href="classgcu_1_1FormulaElt.html">FormulaElt</a>
<a name="l00104"></a>00104 {
<a name="l00105"></a>00105 <span class="keyword">public</span>:
<a name="l00109"></a>00109 <a class="code" href="classgcu_1_1FormulaElt.html#af1eab0c0e8e950ce5c3a3211fb171fc2">FormulaElt</a> ();
<a name="l00113"></a>00113 <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1FormulaElt.html#acadada2049798143f988afe7cabbe2a7">~FormulaElt</a> ();
<a name="l00117"></a>00117 <span class="keyword">virtual</span> std::string <a class="code" href="classgcu_1_1FormulaElt.html#a76cc52d2a13c7c6d793f84fe4128f07a">Markup</a> ();
<a name="l00121"></a>00121 <span class="keyword">virtual</span> std::string <a class="code" href="classgcu_1_1FormulaElt.html#a8e42ff57439e027ce915d154ce25426f">Text</a> ();
<a name="l00128"></a>00128 <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1FormulaElt.html#a08a50700b8e01a8e8dc7e7de0d57b455">BuildRawFormula</a> (std::map<int, int> &raw) = 0;
<a name="l00132"></a>00132 <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code" href="classgcu_1_1FormulaElt.html#a912a90e4b8ffb4771247361a00abf537">GetValence</a> () = 0;
<a name="l00136"></a><a class="code" href="classgcu_1_1FormulaElt.html#a7f55ccd3dee7068ab604ecba0d9c4a4b">00136</a> <span class="keywordtype">int</span> <a class="code" href="classgcu_1_1FormulaElt.html#a7f55ccd3dee7068ab604ecba0d9c4a4b">stoich</a>;
<a name="l00140"></a><a class="code" href="classgcu_1_1FormulaElt.html#a2bba7b1588a7a029af6cdc31b2b25c65">00140</a> <span class="keywordtype">unsigned</span> <a class="code" href="classgcu_1_1FormulaElt.html#a2bba7b1588a7a029af6cdc31b2b25c65">start</a>;
<a name="l00144"></a><a class="code" href="classgcu_1_1FormulaElt.html#a32d28fde9104f82a6495e87403691b8a">00144</a> <span class="keywordtype">unsigned</span> <a class="code" href="classgcu_1_1FormulaElt.html#a32d28fde9104f82a6495e87403691b8a">end</a>;
<a name="l00145"></a>00145 };
<a name="l00146"></a>00146
<a name="l00151"></a><a class="code" href="classgcu_1_1FormulaAtom.html">00151</a> <span class="keyword">class </span><a class="code" href="classgcu_1_1FormulaAtom.html">FormulaAtom</a>: <span class="keyword">public</span> <a class="code" href="classgcu_1_1FormulaElt.html">FormulaElt</a>
<a name="l00152"></a>00152 {
<a name="l00153"></a>00153 <span class="keyword">public</span>:
<a name="l00157"></a>00157 <a class="code" href="classgcu_1_1FormulaAtom.html#a22967d0473697eecb1c56b7210f4eba7">FormulaAtom</a> (<span class="keywordtype">int</span> Z);
<a name="l00161"></a>00161 <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1FormulaAtom.html#af73d0e436957c60490f0a8c7dacdd2c3">~FormulaAtom</a> ();
<a name="l00165"></a>00165 std::string <a class="code" href="classgcu_1_1FormulaAtom.html#a0bbe8e6741b6584a4264b3497bc777f9">Markup</a> ();
<a name="l00169"></a>00169 std::string <a class="code" href="classgcu_1_1FormulaAtom.html#aaed2da3254eed84843258f75fa239e9f">Text</a> ();
<a name="l00175"></a>00175 <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1FormulaAtom.html#a087c6dc30e4faf8ad12c07d1380b8211">BuildRawFormula</a> (std::map<int, int> &raw);
<a name="l00179"></a>00179 <span class="keywordtype">int</span> <a class="code" href="classgcu_1_1FormulaAtom.html#afc657924ed05abc49b383d9820d5bfce">GetValence</a> ();
<a name="l00182"></a>00182 <span class="keywordtype">int</span> elt;
<a name="l00183"></a>00183 };
<a name="l00184"></a>00184
<a name="l00189"></a><a class="code" href="classgcu_1_1FormulaBlock.html">00189</a> <span class="keyword">class </span><a class="code" href="classgcu_1_1FormulaBlock.html">FormulaBlock</a>: <span class="keyword">public</span> <a class="code" href="classgcu_1_1FormulaElt.html">FormulaElt</a>
<a name="l00190"></a>00190 {
<a name="l00191"></a>00191 <span class="keyword">public</span>:
<a name="l00194"></a>00194 <a class="code" href="classgcu_1_1FormulaBlock.html">FormulaBlock</a> ();
<a name="l00198"></a>00198 <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1FormulaBlock.html#a6cfd916a2670c08ed029ae1af3a495d1">~FormulaBlock</a> ();
<a name="l00202"></a>00202 std::string <a class="code" href="classgcu_1_1FormulaBlock.html#acf651c6e064d87682dc5686e94240473">Markup</a> ();
<a name="l00206"></a>00206 std::string <a class="code" href="classgcu_1_1FormulaBlock.html#a29d128ae409d114119b4e70b8952448a">Text</a> ();
<a name="l00213"></a>00213 <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1FormulaBlock.html#a8d381366d13f20e982aea9320aa15b6f">BuildRawFormula</a> (std::map<int, int> &raw);
<a name="l00217"></a>00217 <span class="keywordtype">int</span> <a class="code" href="classgcu_1_1FormulaBlock.html#a30012ed31f4d7c2bd95ccf7528b0be17">GetValence</a> ();
<a name="l00221"></a><a class="code" href="classgcu_1_1FormulaBlock.html#aba4805e38d8d08e2a1d3ca505be41efc">00221</a> std::list<FormulaElt *> <a class="code" href="classgcu_1_1FormulaBlock.html#aba4805e38d8d08e2a1d3ca505be41efc">children</a>;
<a name="l00225"></a><a class="code" href="classgcu_1_1FormulaBlock.html#a3ad275a4ea5dffac2032cc75c5f41b63">00225</a> <span class="keywordtype">int</span> <a class="code" href="classgcu_1_1FormulaBlock.html#a3ad275a4ea5dffac2032cc75c5f41b63">parenthesis</a>;
<a name="l00226"></a>00226 };
<a name="l00227"></a>00227
<a name="l00228"></a>00228 <span class="keyword">class </span><a class="code" href="classgcu_1_1Residue.html">Residue</a>;
<a name="l00229"></a>00229
<a name="l00236"></a><a class="code" href="classgcu_1_1FormulaResidue.html">00236</a> <span class="keyword">class </span><a class="code" href="classgcu_1_1FormulaResidue.html" title="Residue.">FormulaResidue</a>: <span class="keyword">public</span> <a class="code" href="classgcu_1_1FormulaElt.html">FormulaElt</a>
<a name="l00237"></a>00237 {
<a name="l00238"></a>00238 <span class="keyword">public</span>:
<a name="l00244"></a>00244 <a class="code" href="classgcu_1_1FormulaResidue.html#ac97865ff1970377a9eff9ad5a9fb1872">FormulaResidue</a> (<a class="code" href="classgcu_1_1Residue.html">Residue</a> <span class="keyword">const</span> *res, <span class="keywordtype">char</span> <span class="keyword">const</span> *symbol, <span class="keywordtype">int</span> Z);
<a name="l00248"></a>00248 <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1FormulaResidue.html#ac8c7a2880a27a74bab5abbffc011284a">~FormulaResidue</a> ();
<a name="l00252"></a>00252 std::string <a class="code" href="classgcu_1_1FormulaResidue.html#aea9d0af58133907701496bdf8a39f216">Markup</a> ();
<a name="l00256"></a>00256 std::string <a class="code" href="classgcu_1_1FormulaResidue.html#aad3fca53d48084689db755595dcf2244">Text</a> ();
<a name="l00263"></a>00263 <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1FormulaResidue.html#a6f58c8a43bde3d4c9f9fa47caa462795">BuildRawFormula</a> (std::map<int, int> &raw);
<a name="l00267"></a>00267 <span class="keywordtype">int</span> <a class="code" href="classgcu_1_1FormulaResidue.html#ac0f8028a11ddabeabf57c990edda4fd8">GetValence</a> ();
<a name="l00271"></a><a class="code" href="classgcu_1_1FormulaResidue.html#a369b1201247ea8fd82c6d6aa58ac8990">00271</a> <a class="code" href="classgcu_1_1Residue.html">Residue</a> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1FormulaResidue.html#a369b1201247ea8fd82c6d6aa58ac8990">residue</a>;
<a name="l00275"></a><a class="code" href="classgcu_1_1FormulaResidue.html#aadc733b09d3163992efbebb3a3b21b25">00275</a> std::string <a class="code" href="classgcu_1_1FormulaResidue.html#aadc733b09d3163992efbebb3a3b21b25">Symbol</a>;
<a name="l00279"></a><a class="code" href="classgcu_1_1FormulaResidue.html#a868a29cbb195af080a57e8bacd321c6a">00279</a> <a class="code" href="macros_8h.html#ae59df402113b58e8e28a7898e09a19a2">GCU_RO_PROP</a> (<span class="keywordtype">int</span>, Z);
<a name="l00280"></a>00280 };
<a name="l00281"></a>00281
<a name="l00282"></a>00282
<a name="l00288"></a><a class="code" href="classgcu_1_1Formula.html">00288</a> <span class="keyword">class </span><a class="code" href="classgcu_1_1Formula.html">Formula</a>
<a name="l00289"></a>00289 {
<a name="l00290"></a>00290 <span class="keyword">public</span>:
<a name="l00297"></a>00297 <a class="code" href="classgcu_1_1Formula.html#ae1c51535d0054f7c5cbdd057534d11e7">Formula</a> (std::string entry, <a class="code" href="namespacegcu.html#a49392c345f0740efd3167eb30aca570e">FormulaParseMode</a> mode = GCU_FORMULA_PARSE_GUESS) <span class="keywordflow">throw</span> (<a class="code" href="classgcu_1_1parse__error.html">parse_error</a>);
<a name="l00298"></a>00298
<a name="l00302"></a>00302 <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1Formula.html#ac5ebbcba608d87e5fcb30eb80f3f0a7a">~Formula</a> ();
<a name="l00303"></a>00303
<a name="l00307"></a>00307 <span class="keywordtype">char</span> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Formula.html#a11e89053abc2f9633e0664a3579a5deb">GetMarkup</a> ();
<a name="l00311"></a>00311 std::map<int,int> &<a class="code" href="classgcu_1_1Formula.html#ab1c834fc7ba943809bf26976e938fca9">GetRawFormula</a> ();
<a name="l00315"></a>00315 <span class="keywordtype">char</span> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Formula.html#a08f21e12b0f6bf643a0ac12422f7d6f3">GetRawMarkup</a> ();
<a name="l00322"></a>00322 <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Formula.html#a890a3386514b2dffec1f7f1562d9cc72">SetFormula</a> (std::string entry) <span class="keywordflow">throw</span> (<a class="code" href="classgcu_1_1parse__error.html">parse_error</a>);
<a name="l00326"></a>00326 <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Formula.html#a71a32179a7a25aaa067b2340a3dd6cdc">Clear</a> ();
<a name="l00332"></a>00332 <a class="code" href="classgcu_1_1DimensionalValue.html">DimensionalValue</a> <a class="code" href="classgcu_1_1Formula.html#a4c72c8bedf531762c85a2350b049d571">GetMolecularWeight</a> (<span class="keywordtype">bool</span> &artificial);
<a name="l00338"></a>00338 <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Formula.html#a8672e0b7f13cfe9e925c7cf4a5098f63">CalculateIsotopicPattern</a> (<a class="code" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> &pattern);
<a name="l00339"></a>00339
<a name="l00343"></a><a class="code" href="classgcu_1_1Formula.html#ab36e337dd70844ef94ce2cb79be12c2b">00343</a> std::list<FormulaElt *> <span class="keyword">const</span> &<a class="code" href="classgcu_1_1Formula.html#ab36e337dd70844ef94ce2cb79be12c2b">GetElements</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> Details;}
<a name="l00344"></a>00344
<a name="l00345"></a>00345 <span class="keyword">private</span>:
<a name="l00346"></a>00346 <span class="keywordtype">bool</span> BuildConnectivity ();
<a name="l00347"></a>00347 <span class="keywordtype">void</span> Parse (std::string &formula, std::list<FormulaElt *>&result) <span class="keywordflow">throw</span> (<a class="code" href="classgcu_1_1parse__error.html">parse_error</a>);
<a name="l00348"></a>00348 <span class="keywordtype">bool</span> AnalString (<span class="keywordtype">char</span> *sz, std::list<FormulaElt *> &result, <span class="keywordtype">bool</span> &ambiguous, <span class="keywordtype">int</span> offset);
<a name="l00349"></a>00349 <span class="keywordtype">bool</span> TryReplace (std::list<FormulaElt *> &result, std::list<FormulaElt *>::iterator it);
<a name="l00350"></a>00350
<a name="l00351"></a>00351 <span class="keyword">private</span>:
<a name="l00352"></a>00352 std::string Entry, Markup, RawMarkup;
<a name="l00353"></a>00353 std::map<int,int> Raw;
<a name="l00354"></a>00354 std::list<FormulaElt *> Details;
<a name="l00355"></a>00355 <a class="code" href="classgcu_1_1DimensionalValue.html">DimensionalValue</a> m_Weight;
<a name="l00356"></a>00356 <span class="keywordtype">bool</span> m_WeightCached;
<a name="l00357"></a>00357 <span class="keywordtype">bool</span> m_Artificial;
<a name="l00358"></a>00358 <span class="keywordtype">bool</span> m_ConnectivityCached;
<a name="l00359"></a>00359
<a name="l00371"></a><a class="code" href="classgcu_1_1Formula.html#a690dd9ba76a7475a2b6e764d6c7f888a">00371</a> <a class="code" href="macros_8h.html#a2e6e8322502a538f4583d41206cea297">GCU_PROP</a> (<a class="code" href="namespacegcu.html#a49392c345f0740efd3167eb30aca570e">FormulaParseMode</a>, ParseMode);
<a name="l00372"></a>00372 };
<a name="l00373"></a>00373
<a name="l00374"></a>00374 }
<a name="l00375"></a>00375
<a name="l00376"></a>00376 <span class="preprocessor">#endif // GCU_FORMULA_H</span>
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