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<div class="title">chains.h</div> </div>
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<a href="chains_8h.shtml">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/**********************************************************************</span>
<a name="l00002"></a>00002 <span class="comment">chains.h - Parse for macromolecule chains and residues</span>
<a name="l00003"></a>00003 <span class="comment"></span>
<a name="l00004"></a>00004 <span class="comment">Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.</span>
<a name="l00005"></a>00005 <span class="comment">Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison</span>
<a name="l00006"></a>00006 <span class="comment">Some portions Copyright (C) 2008 by Tim Vandermeersch</span>
<a name="l00007"></a>00007 <span class="comment"></span>
<a name="l00008"></a>00008 <span class="comment">This file is part of the Open Babel project.</span>
<a name="l00009"></a>00009 <span class="comment">For more information, see <http://openbabel.org/></span>
<a name="l00010"></a>00010 <span class="comment"></span>
<a name="l00011"></a>00011 <span class="comment">This program is free software; you can redistribute it and/or modify</span>
<a name="l00012"></a>00012 <span class="comment">it under the terms of the GNU General Public License as published by</span>
<a name="l00013"></a>00013 <span class="comment">the Free Software Foundation version 2 of the License.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">This program is distributed in the hope that it will be useful,</span>
<a name="l00016"></a>00016 <span class="comment">but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00017"></a>00017 <span class="comment">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00018"></a>00018 <span class="comment">GNU General Public License for more details.</span>
<a name="l00019"></a>00019 <span class="comment">***********************************************************************/</span>
<a name="l00020"></a>00020
<a name="l00021"></a>00021 <span class="preprocessor">#ifndef OB_CHAINS_H</span>
<a name="l00022"></a>00022 <span class="preprocessor"></span><span class="preprocessor">#define OB_CHAINS_H</span>
<a name="l00023"></a>00023 <span class="preprocessor"></span>
<a name="l00024"></a><a class="code" href="chains_8h.shtml#a0a30b6310d4dca99e49673f6e530bdc4">00024</a> <span class="preprocessor">#define MaxMonoAtom 20</span>
<a name="l00025"></a><a class="code" href="chains_8h.shtml#ad6c9530ebbe94406872e1a4eb18b3b7c">00025</a> <span class="preprocessor"></span><span class="preprocessor">#define MaxMonoBond 20</span>
<a name="l00026"></a>00026 <span class="preprocessor"></span>
<a name="l00027"></a>00027 <span class="preprocessor">#include <openbabel/babelconfig.h></span>
<a name="l00028"></a>00028 <span class="preprocessor">#include <vector></span>
<a name="l00029"></a>00029
<a name="l00030"></a>00030 <span class="keyword">namespace </span>OpenBabel
<a name="l00031"></a>00031 {
<a name="l00032"></a>00032
<a name="l00033"></a>00033 <span class="keyword">class </span>OBAtom;
<a name="l00034"></a>00034 <span class="keyword">class </span>OBMol;
<a name="l00035"></a>00035
<a name="l00037"></a>00037 <span class="comment">// implementation in chains.cpp</span>
<a name="l00038"></a>00038 <span class="keyword">struct </span><a class="code" href="namespaceOpenBabel.shtml#a8eff09d0456c2308e2afb34e824d9c33" title="Structure template for atomic patterns in residues for OBChainsParser.">Template</a>;
<a name="l00039"></a><a class="code" href="namespaceOpenBabel.shtml#a8eff09d0456c2308e2afb34e824d9c33">00039</a> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="namespaceOpenBabel.shtml#a8eff09d0456c2308e2afb34e824d9c33" title="Structure template for atomic patterns in residues for OBChainsParser.">Template</a> <a class="code" href="namespaceOpenBabel.shtml#a8eff09d0456c2308e2afb34e824d9c33" title="Structure template for atomic patterns in residues for OBChainsParser.">Template</a>;
<a name="l00040"></a>00040
<a name="l00049"></a><a class="code" href="classOpenBabel_1_1OBChainsParser.shtml">00049</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBChainsParser.shtml" title="Perceives peptide or nucleotide chains and residues in an OBMol.">OBChainsParser</a>
<a name="l00050"></a>00050 {
<a name="l00051"></a>00051 <span class="keyword">public</span>:
<a name="l00052"></a>00052
<a name="l00053"></a>00053 <a class="code" href="classOpenBabel_1_1OBChainsParser.shtml" title="Perceives peptide or nucleotide chains and residues in an OBMol.">OBChainsParser</a>(<span class="keywordtype">void</span>);
<a name="l00054"></a>00054 ~<a class="code" href="classOpenBabel_1_1OBChainsParser.shtml" title="Perceives peptide or nucleotide chains and residues in an OBMol.">OBChainsParser</a>(<span class="keywordtype">void</span>);
<a name="l00055"></a>00055
<a name="l00062"></a>00062 <span class="keywordtype">bool</span> PerceiveChains(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">bool</span> nukeSingleResidue = <span class="keyword">false</span>);
<a name="l00063"></a>00063
<a name="l00064"></a>00064 <span class="keyword">private</span>: <span class="comment">// internal methods</span>
<a name="l00065"></a>00065
<a name="l00067"></a>00067
<a name="l00068"></a>00068
<a name="l00075"></a>00075 <span class="keywordtype">bool</span> DetermineHetAtoms(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &);
<a name="l00077"></a>00077
<a name="l00079"></a>00079
<a name="l00080"></a>00080
<a name="l00089"></a>00089 <span class="keywordtype">bool</span> DetermineConnectedChains(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &);
<a name="l00098"></a>00098 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> RecurseChain(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">int</span> c);
<a name="l00100"></a>00100
<a name="l00102"></a>00102
<a name="l00103"></a>00103
<a name="l00110"></a>00110 <span class="keywordtype">bool</span> DeterminePeptideBackbone(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &);
<a name="l00121"></a>00121 <span class="keywordtype">void</span> ConstrainBackbone(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <a class="code" href="namespaceOpenBabel.shtml#a8eff09d0456c2308e2afb34e824d9c33" title="Structure template for atomic patterns in residues for OBChainsParser.">Template</a> *templ, <span class="keywordtype">int</span> tmax);
<a name="l00125"></a>00125 <span class="keywordtype">bool</span> MatchConstraint(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *atom, <span class="keywordtype">int</span> mask);
<a name="l00130"></a>00130 <span class="keywordtype">bool</span> Match2Constraints(<a class="code" href="namespaceOpenBabel.shtml#a8eff09d0456c2308e2afb34e824d9c33" title="Structure template for atomic patterns in residues for OBChainsParser.">Template</a> *templ, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *na, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *nb);
<a name="l00135"></a>00135 <span class="keywordtype">bool</span> Match3Constraints(<a class="code" href="namespaceOpenBabel.shtml#a8eff09d0456c2308e2afb34e824d9c33" title="Structure template for atomic patterns in residues for OBChainsParser.">Template</a> *templ, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *na, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *nb, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *nc);
<a name="l00140"></a>00140 <span class="keywordtype">bool</span> Match4Constraints(<a class="code" href="namespaceOpenBabel.shtml#a8eff09d0456c2308e2afb34e824d9c33" title="Structure template for atomic patterns in residues for OBChainsParser.">Template</a> *templ, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *na, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *nb, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *nc, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *nd);
<a name="l00150"></a>00150 <span class="keywordtype">void</span> TracePeptideChain(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">int</span> r);
<a name="l00152"></a>00152
<a name="l00154"></a>00154
<a name="l00155"></a>00155
<a name="l00161"></a>00161 <span class="keywordtype">bool</span> DeterminePeptideSidechains(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &);
<a name="l00173"></a>00173 <span class="keywordtype">int</span> IdentifyResidue(<span class="keywordtype">void</span> *tree, <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> seed, <span class="keywordtype">int</span> resno); <span class="comment">// ByteCode *</span>
<a name="l00181"></a>00181 <span class="comment"></span> <span class="keywordtype">void</span> AssignResidue(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">int</span> r, <span class="keywordtype">int</span> c, <span class="keywordtype">int</span> i);
<a name="l00183"></a>00183
<a name="l00185"></a>00185
<a name="l00186"></a>00186
<a name="l00190"></a>00190 <span class="keywordtype">bool</span> DetermineHydrogens(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &);
<a name="l00192"></a>00192
<a name="l00194"></a>00194
<a name="l00195"></a>00195
<a name="l00201"></a>00201 <span class="keywordtype">void</span> SetResidueInformation(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &, <span class="keywordtype">bool</span> nukeSingleResidue);
<a name="l00203"></a>00203
<a name="l00205"></a>00205
<a name="l00206"></a>00206
<a name="l00213"></a>00213 <span class="keywordtype">bool</span> DetermineNucleicBackbone(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &);
<a name="l00221"></a>00221 <span class="keywordtype">void</span> TraceNucleicChain(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">int</span> r);
<a name="l00228"></a>00228 <span class="keywordtype">bool</span> DetermineNucleicSidechains(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &);
<a name="l00230"></a>00230
<a name="l00235"></a>00235 <span class="keywordtype">void</span> SetupMol(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &);
<a name="l00239"></a>00239 <span class="keywordtype">void</span> ClearResidueInformation(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol);
<a name="l00243"></a>00243 <span class="keywordtype">void</span> CleanupMol();
<a name="l00250"></a>00250 <span class="keywordtype">void</span> DefineMonomer(<span class="keywordtype">void</span> **tree, <span class="keywordtype">int</span> resid, <span class="keyword">const</span> <span class="keywordtype">char</span> *smiles); <span class="comment">// ByteCode **</span>
<a name="l00255"></a>00255 <span class="comment"></span> <span class="keywordtype">int</span> IdentifyElement(<span class="keywordtype">char</span> *ptr);
<a name="l00261"></a>00261 <span class="keyword">const</span> <span class="keywordtype">char</span> *ParseSmiles(<span class="keyword">const</span> <span class="keywordtype">char</span> *smiles, <span class="keywordtype">int</span> prev);
<a name="l00265"></a>00265 <span class="keywordtype">void</span> DumpState();
<a name="l00266"></a>00266
<a name="l00267"></a>00267 <span class="keywordtype">void</span> *PDecisionTree;
<a name="l00268"></a>00268 <span class="keywordtype">void</span> *NDecisionTree;
<a name="l00269"></a>00269
<a name="l00270"></a>00270 <span class="keywordtype">int</span> ResMonoAtom[<a class="code" href="chains_8h.shtml#a0a30b6310d4dca99e49673f6e530bdc4">MaxMonoAtom</a>];
<a name="l00271"></a>00271 <span class="keywordtype">int</span> ResMonoBond[<a class="code" href="chains_8h.shtml#ad6c9530ebbe94406872e1a4eb18b3b7c">MaxMonoBond</a>];
<a name="l00272"></a>00272
<a name="l00273"></a>00273 std::vector<unsigned short> bitmasks;
<a name="l00274"></a>00274 std::vector<bool> visits;
<a name="l00275"></a>00275 std::vector<unsigned char> resids;
<a name="l00276"></a>00276 std::vector<unsigned char> flags;
<a name="l00277"></a>00277 std::vector<bool> hetflags;
<a name="l00278"></a>00278 std::vector<int> atomids;
<a name="l00279"></a>00279 std::vector<short> resnos;
<a name="l00280"></a>00280 std::vector<short> sernos;
<a name="l00281"></a>00281 std::vector<char> hcounts;
<a name="l00282"></a>00282 std::vector<char> chains;
<a name="l00283"></a>00283 };
<a name="l00284"></a>00284
<a name="l00285"></a>00285 }
<a name="l00286"></a>00286 <span class="preprocessor">#endif // OB_CHAINS_H</span>
<a name="l00287"></a>00287 <span class="preprocessor"></span>
</pre></div></div>
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