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<a href="mcdlutil_8h.shtml">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 <span class="comment"></span>
<a name="l00003"></a>00003 <span class="comment">**********************************************************************</span>
<a name="l00004"></a>00004 <span class="comment">Copyright (C) 2007,2008 by Sergei V. Trepalin sergey_trepalin@chemical-block.com</span>
<a name="l00005"></a>00005 <span class="comment">Copyright (C) 2007,2008 by Andrei Gakh andrei.gakh@nnsa.doe.gov</span>
<a name="l00006"></a>00006 <span class="comment"></span>
<a name="l00007"></a>00007 <span class="comment">This file is part of the Open Babel project.</span>
<a name="l00008"></a>00008 <span class="comment">For more information, see <http://openbabel.org/></span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">This program is free software; you can redistribute it and/or modify</span>
<a name="l00011"></a>00011 <span class="comment">it under the terms of the GNU General Public License as published by</span>
<a name="l00012"></a>00012 <span class="comment">the Free Software Foundation version 2 of the License.</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">*/</span>
<a name="l00020"></a>00020 <span class="comment">/*</span>
<a name="l00021"></a>00021 <span class="comment"> Diagram is generated using templates, which are stored in SD file templates.sdf</span>
<a name="l00022"></a>00022 <span class="comment"> The SD file is usual SD file, which contain chemical structures and might contain data.</span>
<a name="l00023"></a>00023 <span class="comment"> Only chemical structures are used. Subgraph isomorphisme search is executed and coordinates</span>
<a name="l00024"></a>00024 <span class="comment"> of atoms are determined from templates. See Molecules, 11, 129-141 (2006) for algorithm decription.</span>
<a name="l00025"></a>00025 <span class="comment"> Structures in SD file are converted in next manner:</span>
<a name="l00026"></a>00026 <span class="comment"> 1. All atoms, except explicit hydrogens, are replaced with generic ANY_ATOM (matched with any atom in subgraph isomorphisme search)</span>
<a name="l00027"></a>00027 <span class="comment"> 2. All bonds are replaces with generic ANY_BOND, which can be matched with any bond in molecule</span>
<a name="l00028"></a>00028 <span class="comment"> 3. All hydrogen are removed, but they are used for search-query and structure atom matching is believed fo be</span>
<a name="l00029"></a>00029 <span class="comment"> sucessfukk if chemical structure contains more or equal number of hydrogens, than query. Using explicitly-defined hydrogens</span>
<a name="l00030"></a>00030 <span class="comment"> on query enables ones to remove substitutors attachment for atom, which are sterically hidden on templates</span>
<a name="l00031"></a>00031 <span class="comment"> if the file will not be found, predefined templates will be used</span>
<a name="l00032"></a>00032 <span class="comment">*/</span>
<a name="l00033"></a>00033
<a name="l00034"></a>00034
<a name="l00035"></a>00035 <span class="keyword">namespace </span>OpenBabel {
<a name="l00036"></a>00036
<a name="l00037"></a>00037 <span class="comment">//common constants</span>
<a name="l00038"></a><a class="code" href="namespaceOpenBabel.shtml#a82ccfbdf4943a4e74a708edafcced9f6">00038</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#a82ccfbdf4943a4e74a708edafcced9f6">MAXBONDS</a>=300;
<a name="l00039"></a><a class="code" href="namespaceOpenBabel.shtml#a22febe826ea2f93f69725fbef532c921">00039</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#a22febe826ea2f93f69725fbef532c921">MAXFRAGS</a>=200;
<a name="l00040"></a><a class="code" href="namespaceOpenBabel.shtml#ab91841d785674a38b34fcf2fd9685142">00040</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#ab91841d785674a38b34fcf2fd9685142">MAXCHARS</a>=1000;
<a name="l00041"></a><a class="code" href="namespaceOpenBabel.shtml#ad087045047b2155479ef662be1be3abc">00041</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#ad087045047b2155479ef662be1be3abc">MAX_DEPTH</a>=10;
<a name="l00042"></a><a class="code" href="namespaceOpenBabel.shtml#ad1eec14ce20cfaf366e19721f1f27090">00042</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#ad1eec14ce20cfaf366e19721f1f27090">NELEMMAX</a>=120;
<a name="l00043"></a><a class="code" href="mcdlutil_8h.shtml#a02160f654223d43c521ab445b7eb7b2a">00043</a> <span class="preprocessor"> #define NELEMMCDL 121</span>
<a name="l00044"></a>00044 <span class="preprocessor"></span>
<a name="l00045"></a>00045 <span class="comment">// Return valency by hydrogen for given atomic position in the Periodic Table</span>
<a name="l00046"></a>00046 OBMCDL <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#a47053116206f7c8cf7b278aec7e35cb1">hydrogenValency</a>(<span class="keywordtype">int</span> na);
<a name="l00047"></a>00047 OBMCDL <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#aa51b217d32346d4f341a227be63de160">maxValency</a>(<span class="keywordtype">int</span> na);
<a name="l00048"></a>00048
<a name="l00049"></a>00049 <span class="comment">//Alternate overloaded methods</span>
<a name="l00050"></a>00050 OBMCDL <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#a54363eb76ba264ec754bece9848198c8">alternate</a>(OBMol * pmol, <span class="keyword">const</span> <span class="keywordtype">int</span> nH[], <span class="keywordtype">int</span> bondOrders []); <span class="comment">//This method does not work!</span>
<a name="l00051"></a>00051 <span class="comment">//Zero-based atomic numeration should be in connection matrix arrays iA1 and iA2-so first atom has indez zero</span>
<a name="l00052"></a>00052 OBMCDL <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#a54363eb76ba264ec754bece9848198c8">alternate</a>(<span class="keyword">const</span> std::vector<int> aPosition,<span class="keyword">const</span> std::vector<int> aCharge,
<a name="l00053"></a>00053 <span class="keyword">const</span> std::vector<int> aRad,<span class="keyword">const</span> std::vector<int> nHydr, <span class="keyword">const</span> std::vector<int> iA1,
<a name="l00054"></a>00054 <span class="keyword">const</span> std::vector<int> iA2, std::vector<int> & bondOrders, <span class="keywordtype">int</span> nAtoms, <span class="keywordtype">int</span> nBonds);
<a name="l00058"></a>00058 <span class="comment">//Diagram generation overloaded methods</span>
<a name="l00059"></a>00059 OBMCDL <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#aec2830d51995ac9802efa4aad43121ca">generateDiagram</a>(OBMol * pmol);
<a name="l00060"></a>00060 <span class="comment">//Zero-based atomic numeration should be in connection matrix arrays iA1 and iA2-so first atom has indez zero</span>
<a name="l00061"></a>00061 OBMCDL <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#aec2830d51995ac9802efa4aad43121ca">generateDiagram</a>(<span class="keyword">const</span> std::vector<int> iA1, <span class="keyword">const</span> std::vector<int> iA2,
<a name="l00062"></a>00062 std::vector<double>& rx, std::vector<double>& ry, <span class="keywordtype">int</span> nAtoms, <span class="keywordtype">int</span> nBonds);
<a name="l00063"></a>00063 OBMCDL <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#aec2830d51995ac9802efa4aad43121ca">generateDiagram</a>(OBMol * pmol, std::ostream & ofs); <span class="comment">//for testing purposes only</span>
<a name="l00064"></a>00064
<a name="l00065"></a>00065 <span class="comment">//Fragment search - pure subgraph isomorphisme</span>
<a name="l00066"></a>00066 <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenBabel.shtml#a60aab5dcc934001076e5079960cb9be4">fragmentSearch</a>(OBMol * query, OBMol * structure);
<a name="l00067"></a>00067 <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenBabel.shtml#a60aab5dcc934001076e5079960cb9be4">fragmentSearch</a>(<span class="keyword">const</span> std::vector<int> aPositionQuery, <span class="keyword">const</span> std::vector<int> iA1Query,
<a name="l00068"></a>00068 <span class="keyword">const</span> std::vector<int> iA2Query, <span class="keyword">const</span> std::vector<int> bondTypesQuery,
<a name="l00069"></a>00069 <span class="keyword">const</span> std::vector<int> aPositionStructure, <span class="keyword">const</span> std::vector<int> iA1Structure,
<a name="l00070"></a>00070 <span class="keyword">const</span> std::vector<int> iA2Structure, <span class="keyword">const</span> std::vector<int> bondTypesStructure,
<a name="l00071"></a>00071 <span class="keywordtype">int</span> nAtomsQuery, <span class="keywordtype">int</span> nBondsQuery, <span class="keywordtype">int</span> nAtomsStructure, <span class="keywordtype">int</span> nBondsStructure);
<a name="l00073"></a>00073 OBMCDL <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a16e9982dc3b96f14397fe55ede7b8f1f" title="Equivalence list generation.">equivalenceList</a>(OBMol * pmol, std::vector<int>& eqList);
<a name="l00074"></a>00074 <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a16e9982dc3b96f14397fe55ede7b8f1f" title="Equivalence list generation.">equivalenceList</a>(<span class="keyword">const</span> std::vector<int> aPosition,<span class="keyword">const</span> std::vector<int> aCharge,
<a name="l00075"></a>00075 <span class="keyword">const</span> std::vector<int> aRad, <span class="keyword">const</span> std::vector<int> iA1, <span class="keyword">const</span> std::vector<int> iA2,
<a name="l00076"></a>00076 <span class="keyword">const</span> std::vector<int> bondTypes, std::vector<int>& eqList, <span class="keywordtype">int</span> nAtoms, <span class="keywordtype">int</span> nBonds);
<a name="l00077"></a>00077 <span class="comment">//Fragment addition</span>
<a name="l00078"></a>00078 OBMCDL <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#adaa889d3747ea9e2ba1a83207556dce3">addFragment</a>(OBMol * molecule, OBMol * fragment, <span class="keywordtype">int</span> molAN, <span class="keywordtype">int</span> fragAN, <span class="keywordtype">int</span> molBN,
<a name="l00079"></a>00079 <span class="keywordtype">int</span> fragBN, <span class="keywordtype">bool</span> isAddition);
<a name="l00080"></a>00080
<a name="l00081"></a>00081 <span class="comment">//routines below have no common meaning, but are necessary to process stereo information</span>
<a name="l00082"></a>00082 OBMCDL <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#abce282c45ee77ea965aaacd47b4e8d72">createStereoLists</a>(OBMol * pmol, std::vector<int>& bondStereoList,
<a name="l00083"></a>00083 std::vector<int>& atomStereoList, std::vector<int>& eqList);
<a name="l00084"></a>00084 OBMCDL std::string <a class="code" href="namespaceOpenBabel.shtml#a29e765f8943f7aa7b50aca9380196e96">getAtomMCDL</a>(OBMol * pmol, <span class="keywordtype">int</span> ntatoms, <span class="keyword">const</span> std::vector<int> ix,
<a name="l00085"></a>00085 <span class="keyword">const</span> std::vector<int> aNumber, <span class="keyword">const</span> std::vector<int> atomStereoList, <span class="keyword">const</span> std::vector<int> eqList);
<a name="l00086"></a>00086 OBMCDL std::string <a class="code" href="namespaceOpenBabel.shtml#acd680ed8783717254f074205cd6b24a4">getBondMCDL</a>(OBMol * pmol, <span class="keywordtype">int</span> nbStore, <span class="keywordtype">int</span> ntatoms, <span class="keyword">const</span> std::vector<int> ix,
<a name="l00087"></a>00087 <span class="keyword">const</span> std::vector<int> aNumber, <span class="keywordtype">int</span> bonds[<a class="code" href="namespaceOpenBabel.shtml#a82ccfbdf4943a4e74a708edafcced9f6">MAXBONDS</a>][4], <span class="keyword">const</span> std::vector<int> bondStereoList,
<a name="l00088"></a>00088 <span class="keyword">const</span> std::vector<int> eqList);
<a name="l00089"></a>00089 OBMCDL <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a3c50491b940d1a3d368bf7eba3bebfa1">implementAtomStereo</a>(std::vector<int>& iA1, std::vector<int>& iA2, std::vector<int>& stereoBonds,
<a name="l00090"></a>00090 <span class="keyword">const</span> std::vector<double>rx, <span class="keyword">const</span> std::vector<double> ry, <span class="keywordtype">int</span> acount, <span class="keywordtype">int</span> bcount, std::string astereo);
<a name="l00091"></a>00091 OBMCDL <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a417a2925a2ec60c86ff3edc04ce4142c">implementBondStereo</a>(<span class="keyword">const</span> std::vector<int> iA1, <span class="keyword">const</span> std::vector<int> iA2,
<a name="l00092"></a>00092 std::vector<double>& rx, std::vector<double>& ry, <span class="keywordtype">int</span> acount, <span class="keywordtype">int</span> bcount, std::string bstereo);
<a name="l00093"></a>00093
<a name="l00094"></a>00094
<a name="l00095"></a>00095 OBMCDL <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#a23997cd29f45df86f90e4f7de02baccd">groupRedraw</a>(OBMol * pmol, <span class="keywordtype">int</span> bondN, <span class="keywordtype">int</span> atomN, <span class="keywordtype">bool</span> atomNInGroup);
<a name="l00096"></a>00096 <span class="comment">//int groupRedrawFrameAtom(OBMol * pmol, int bondN, int atomInFrame);</span>
<a name="l00097"></a>00097
<a name="l00098"></a>00098 OBMCDL <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#a82011594cefb0a924a4cc938800de614">canonizeMCDL</a>(<span class="keyword">const</span> std::string atomBlock, std::vector<std::string> & structureList);
<a name="l00099"></a>00099 OBMCDL <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenBabel.shtml#a6a41a690c691e47bc63facef0e2e449d">parseFormula</a>(<span class="keyword">const</span> std::string formulaString, std::vector <int>& enumber, <span class="keywordtype">int</span> & valency);
<a name="l00100"></a>00100
<a name="l00101"></a>00101 OBMCDL <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#aaa14c59df78025ce6e8dfd3f27feb106">prepareTest</a>(OBMol * pmol, std::ostream & ofs);
<a name="l00102"></a>00102
<a name="l00103"></a>00103 } <span class="comment">// namespace OpenBabel</span>
<a name="l00104"></a>00104
</pre></div></div>
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