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<a href="mol_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">mol.h - Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue.</span>
<a name="l00003"></a>00003 <span class="comment"> (the main header for Open Babel)</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.</span>
<a name="l00006"></a>00006 <span class="comment">Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison</span>
<a name="l00007"></a>00007 <span class="comment">Some portions Copyright (C) 2003 by Michael Banck</span>
<a name="l00008"></a>00008 <span class="comment"></span>
<a name="l00009"></a>00009 <span class="comment">This file is part of the Open Babel project.</span>
<a name="l00010"></a>00010 <span class="comment">For more information, see <http://openbabel.org/></span>
<a name="l00011"></a>00011 <span class="comment"></span>
<a name="l00012"></a>00012 <span class="comment">This program is free software; you can redistribute it and/or modify</span>
<a name="l00013"></a>00013 <span class="comment">it under the terms of the GNU General Public License as published by</span>
<a name="l00014"></a>00014 <span class="comment">the Free Software Foundation version 2 of the License.</span>
<a name="l00015"></a>00015 <span class="comment"></span>
<a name="l00016"></a>00016 <span class="comment">This program is distributed in the hope that it will be useful,</span>
<a name="l00017"></a>00017 <span class="comment">but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00018"></a>00018 <span class="comment">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00019"></a>00019 <span class="comment">GNU General Public License for more details.</span>
<a name="l00020"></a>00020 <span class="comment">***********************************************************************/</span>
<a name="l00021"></a>00021
<a name="l00022"></a>00022 <span class="preprocessor">#ifndef OB_MOL_H</span>
<a name="l00023"></a>00023 <span class="preprocessor"></span><span class="preprocessor">#define OB_MOL_H</span>
<a name="l00024"></a>00024 <span class="preprocessor"></span>
<a name="l00025"></a>00025 <span class="preprocessor">#include <openbabel/babelconfig.h></span>
<a name="l00026"></a>00026
<a name="l00027"></a>00027 <span class="preprocessor">#ifndef EXTERN</span>
<a name="l00028"></a>00028 <span class="preprocessor"></span><span class="preprocessor"># define EXTERN extern</span>
<a name="l00029"></a>00029 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
<a name="l00030"></a>00030 <span class="preprocessor"></span>
<a name="l00031"></a>00031 <span class="preprocessor">#include <math.h></span>
<a name="l00032"></a>00032 <span class="preprocessor">#include <float.h></span>
<a name="l00033"></a>00033
<a name="l00034"></a>00034 <span class="preprocessor">#include <vector></span>
<a name="l00035"></a>00035 <span class="preprocessor">#include <string></span>
<a name="l00036"></a>00036 <span class="preprocessor">#include <map></span>
<a name="l00037"></a>00037
<a name="l00038"></a>00038 <span class="comment">// Currently includes many headers for 2.x backwards compatibility</span>
<a name="l00039"></a>00039 <span class="comment">// \deprecated -- this will be cleaned up in 3.0 efforts</span>
<a name="l00040"></a>00040 <span class="comment">// to improve compile time significantly.</span>
<a name="l00041"></a>00041 <span class="comment">// Only include necessary headers and class declaration stubs.</span>
<a name="l00042"></a>00042 <span class="preprocessor">#include <<a class="code" href="atom_8h.shtml" title="Handle atoms.">openbabel/atom.h</a>></span>
<a name="l00043"></a>00043 <span class="preprocessor">#include <<a class="code" href="bond_8h.shtml" title="Handle bonds.">openbabel/bond.h</a>></span>
<a name="l00044"></a>00044 <span class="preprocessor">#include <<a class="code" href="base_8h.shtml" title="Base classes to build a graph.">openbabel/base.h</a>></span>
<a name="l00045"></a>00045 <span class="preprocessor">#include <<a class="code" href="data_8h.shtml" title="Global data and resource file parsers.">openbabel/data.h</a>></span>
<a name="l00046"></a>00046 <span class="preprocessor">#include <<a class="code" href="chains_8h.shtml" title="Parse for macromolecule chains and residues.">openbabel/chains.h</a>></span>
<a name="l00047"></a>00047 <span class="preprocessor">#include <<a class="code" href="vector3_8h.shtml" title="Handle 3D coordinates.">openbabel/math/vector3.h</a>></span>
<a name="l00048"></a>00048 <span class="preprocessor">#include <<a class="code" href="bitvec_8h.shtml" title="Fast and efficient bitstring class.">openbabel/bitvec.h</a>></span>
<a name="l00049"></a>00049 <span class="preprocessor">#include <<a class="code" href="residue_8h.shtml" title="Defines for residue properties, names, etc.">openbabel/residue.h</a>></span>
<a name="l00050"></a>00050 <span class="preprocessor">#include <<a class="code" href="ring_8h.shtml" title="Deal with rings, find smallest set of smallest rings (SSSR).">openbabel/ring.h</a>></span>
<a name="l00051"></a>00051 <span class="preprocessor">#include <<a class="code" href="generic_8h.shtml" title="Handle generic data classes. Custom data for atoms, bonds, etc.">openbabel/generic.h</a>></span>
<a name="l00052"></a>00052 <span class="preprocessor">#include <<a class="code" href="typer_8h.shtml" title="Open Babel atom and aromaticity typer.">openbabel/typer.h</a>></span>
<a name="l00053"></a>00053 <span class="preprocessor">#include <<a class="code" href="oberror_8h.shtml" title="Handle error messages, warnings, notices, etc.">openbabel/oberror.h</a>></span>
<a name="l00054"></a>00054 <span class="preprocessor">#include <<a class="code" href="obiter_8h.shtml" title="STL-style iterators for Open Babel.">openbabel/obiter.h</a>></span>
<a name="l00055"></a>00055 <span class="preprocessor">#include <<a class="code" href="internalcoord_8h.shtml" title="Declaration of OBInternalCoord class, conversion between Cartesian and Z-matrix form.">openbabel/internalcoord.h</a>></span>
<a name="l00056"></a>00056
<a name="l00057"></a>00057 <span class="keyword">namespace </span>OpenBabel
<a name="l00058"></a>00058 {
<a name="l00059"></a>00059
<a name="l00060"></a>00060 <span class="keyword">class </span>OBAtom;
<a name="l00061"></a>00061 <span class="keyword">class </span>OBBond;
<a name="l00062"></a>00062 <span class="keyword">class </span>OBInternalCoord;
<a name="l00063"></a>00063 <span class="keyword">class </span>OBConversion; <span class="comment">//used only as a pointer</span>
<a name="l00064"></a>00064
<a name="l00065"></a>00065 <span class="comment">// Class OBMol</span>
<a name="l00066"></a>00066 <span class="comment">//MOL Property Macros (flags) -- 32+ bits</span>
<a name="l00068"></a><a class="code" href="mol_8h.shtml#a1ab7f39b595f0f69b77c5907c804afc4">00068</a> <span class="comment"></span><span class="preprocessor">#define OB_SSSR_MOL (1<<1)</span>
<a name="l00069"></a>00069 <span class="preprocessor"></span>
<a name="l00070"></a><a class="code" href="mol_8h.shtml#ae9ad3600741ed030f463badacb48cbf9">00070</a> <span class="preprocessor">#define OB_RINGFLAGS_MOL (1<<2)</span>
<a name="l00071"></a>00071 <span class="preprocessor"></span>
<a name="l00072"></a><a class="code" href="mol_8h.shtml#a00796165b0d091f4b0987ee2a0ba5609">00072</a> <span class="preprocessor">#define OB_AROMATIC_MOL (1<<3)</span>
<a name="l00073"></a>00073 <span class="preprocessor"></span>
<a name="l00074"></a><a class="code" href="mol_8h.shtml#abf2d91f3d8e6d4db13029a0130a262a5">00074</a> <span class="preprocessor">#define OB_ATOMTYPES_MOL (1<<4)</span>
<a name="l00075"></a>00075 <span class="preprocessor"></span>
<a name="l00076"></a><a class="code" href="mol_8h.shtml#abdf1bef91d791e4ec64071377a06e491">00076</a> <span class="preprocessor">#define OB_CHIRALITY_MOL (1<<5)</span>
<a name="l00077"></a>00077 <span class="preprocessor"></span>
<a name="l00078"></a><a class="code" href="mol_8h.shtml#aade7aaf66074d41ccc89a88fde187ef0">00078</a> <span class="preprocessor">#define OB_PCHARGE_MOL (1<<6)</span>
<a name="l00079"></a>00079 <span class="preprocessor"></span>
<a name="l00080"></a><a class="code" href="mol_8h.shtml#a2609984a86f8eaca60bd0995ab1ff082">00080</a> <span class="preprocessor">#define OB_HYBRID_MOL (1<<8)</span>
<a name="l00081"></a>00081 <span class="preprocessor"></span>
<a name="l00082"></a><a class="code" href="mol_8h.shtml#a220b0e4aac833823ef37f6d10ac7a254">00082</a> <span class="preprocessor">#define OB_IMPVAL_MOL (1<<9)</span>
<a name="l00083"></a>00083 <span class="preprocessor"></span>
<a name="l00084"></a><a class="code" href="mol_8h.shtml#adb1c838e0460bae3347db0d94b4e63c7">00084</a> <span class="preprocessor">#define OB_KEKULE_MOL (1<<10)</span>
<a name="l00085"></a>00085 <span class="preprocessor"></span>
<a name="l00086"></a><a class="code" href="mol_8h.shtml#aa9b307d4356f47b80ba6516405bea32e">00086</a> <span class="preprocessor">#define OB_CLOSURE_MOL (1<<11)</span>
<a name="l00087"></a>00087 <span class="preprocessor"></span>
<a name="l00088"></a><a class="code" href="mol_8h.shtml#a488eaf115c8c8e3f8ac24384f80f6f88">00088</a> <span class="preprocessor">#define OB_H_ADDED_MOL (1<<12)</span>
<a name="l00089"></a>00089 <span class="preprocessor"></span>
<a name="l00090"></a><a class="code" href="mol_8h.shtml#af3ca96a4c05940f8ed8fdc159b93656a">00090</a> <span class="preprocessor">#define OB_PH_CORRECTED_MOL (1<<13)</span>
<a name="l00091"></a>00091 <span class="preprocessor"></span>
<a name="l00092"></a><a class="code" href="mol_8h.shtml#ad34e5e48a2b7f4c149070647189d9d71">00092</a> <span class="preprocessor">#define OB_AROM_CORRECTED_MOL (1<<14)</span>
<a name="l00093"></a>00093 <span class="preprocessor"></span>
<a name="l00094"></a><a class="code" href="mol_8h.shtml#a5aaff7bcb11a37508fe32d17ad57dea0">00094</a> <span class="preprocessor">#define OB_CHAINS_MOL (1<<15)</span>
<a name="l00095"></a>00095 <span class="preprocessor"></span>
<a name="l00096"></a><a class="code" href="mol_8h.shtml#a3168124e0bc8b31e2d4392f1da02fbd7">00096</a> <span class="preprocessor">#define OB_TCHARGE_MOL (1<<16)</span>
<a name="l00097"></a>00097 <span class="preprocessor"></span>
<a name="l00098"></a><a class="code" href="mol_8h.shtml#a8ae8b8d431ee5649e4dad8bbdfd5092d">00098</a> <span class="preprocessor">#define OB_TSPIN_MOL (1<<17)</span>
<a name="l00099"></a>00099 <span class="preprocessor"></span>
<a name="l00100"></a><a class="code" href="mol_8h.shtml#aaba06b0d4348eedb3f32f764d4c9b9f8">00100</a> <span class="preprocessor">#define OB_RINGTYPES_MOL (1<<18)</span>
<a name="l00101"></a>00101 <span class="preprocessor"></span>
<a name="l00102"></a><a class="code" href="mol_8h.shtml#ad224f71d6aecaa29f7cb32ec475b8d58">00102</a> <span class="preprocessor">#define OB_PATTERN_STRUCTURE (1<<19)</span>
<a name="l00103"></a>00103 <span class="preprocessor"></span>
<a name="l00104"></a><a class="code" href="mol_8h.shtml#ae62d8140a1f27fe185152e8ca29f2255">00104</a> <span class="preprocessor">#define OB_LSSR_MOL (1<<20)</span>
<a name="l00105"></a>00105 <span class="preprocessor"></span> <span class="comment">// flags 21-32 unspecified</span>
<a name="l00106"></a><a class="code" href="mol_8h.shtml#ae7cd3ed4ac08cc188ed556c26ff26abe">00106</a> <span class="preprocessor">#define OB_CURRENT_CONFORMER -1</span>
<a name="l00107"></a>00107 <span class="preprocessor"></span>
<a name="l00108"></a>00108 <span class="comment">// class introduction in mol.cpp</span>
<a name="l00109"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml">00109</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>: <span class="keyword">public</span> <a class="code" href="classOpenBabel_1_1OBBase.shtml" title="Base Class.">OBBase</a>
<a name="l00110"></a>00110 {
<a name="l00111"></a>00111 <span class="keyword">protected</span>:
<a name="l00112"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aa4a61b1d913f2bee1e0ed5d9daf26549">00112</a> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aa4a61b1d913f2bee1e0ed5d9daf26549" title="bitfield of flags">_flags</a>;
<a name="l00113"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ac23878536c8da0ff97c0985627dd5646">00113</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ac23878536c8da0ff97c0985627dd5646" title="Assign partial charges automatically.">_autoPartialCharge</a>;
<a name="l00114"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ae1c74119422bd6a52bb7c384b42dca4c">00114</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ae1c74119422bd6a52bb7c384b42dca4c" title="Assign formal charges automatically.">_autoFormalCharge</a>;
<a name="l00115"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a1dda4ed41c70aef0a361682dd9b2b0f9">00115</a> std::string <a class="code" href="classOpenBabel_1_1OBMol.shtml#a1dda4ed41c70aef0a361682dd9b2b0f9" title="Molecule title.">_title</a>;
<a name="l00116"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ad3bcdbfad8eedc0452fe543badd080d5">00116</a> std::vector<OBAtom*> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ad3bcdbfad8eedc0452fe543badd080d5" title="vector of atoms">_vatom</a>;
<a name="l00117"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aba8a1b036f4544f328db00b0939cbaf0">00117</a> std::vector<OBAtom*> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aba8a1b036f4544f328db00b0939cbaf0" title="vector of atoms indexed by id">_atomIds</a>;
<a name="l00118"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a3c7208419c7703e947e9a1c365838b98">00118</a> std::vector<OBBond*> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a3c7208419c7703e947e9a1c365838b98" title="vector of bonds">_vbond</a>;
<a name="l00119"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ad07702b91130d560479a679ae1a536d2">00119</a> std::vector<OBBond*> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ad07702b91130d560479a679ae1a536d2" title="vector of bonds">_bondIds</a>;
<a name="l00120"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a601fbf5c8e5b7d92281dbe6a124d7f2c">00120</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a601fbf5c8e5b7d92281dbe6a124d7f2c" title="Dimensionality of coordinates.">_dimension</a>;
<a name="l00121"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aaaeee07c1d80b2638b8b9ace0095c9cd">00121</a> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aaaeee07c1d80b2638b8b9ace0095c9cd" title="Total charge on the molecule.">_totalCharge</a>;
<a name="l00122"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a7a92cb97f8aa52f145b2e928cf480a07">00122</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a7a92cb97f8aa52f145b2e928cf480a07" title="Total spin on the molecule (if not specified, assumes lowest possible spin)">_totalSpin</a>;
<a name="l00123"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a706bc4f751bf06cf864893451a7d21e4">00123</a> <span class="keywordtype">double</span> *<a class="code" href="classOpenBabel_1_1OBMol.shtml#a706bc4f751bf06cf864893451a7d21e4" title="coordinate array">_c</a>;
<a name="l00124"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a6fb1d704dcaeb179720ac771745850b1">00124</a> std::vector<double*> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a6fb1d704dcaeb179720ac771745850b1" title="vector of conformers">_vconf</a>;
<a name="l00125"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ad93165c379393f8eb17506f1f9820a1a">00125</a> <span class="keywordtype">double</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ad93165c379393f8eb17506f1f9820a1a" title="heat of formation">_energy</a>;
<a name="l00126"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a370c739afb1e8ed20a96680ec9f1b219">00126</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a370c739afb1e8ed20a96680ec9f1b219" title="Number of atoms.">_natoms</a>;
<a name="l00127"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a35a920486c1a28ca09de0eeb9dbb174c">00127</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a35a920486c1a28ca09de0eeb9dbb174c" title="Number of bonds.">_nbonds</a>;
<a name="l00128"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ae1c29d0efe6187e8726962008c81e956">00128</a> std::vector<OBResidue*> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ae1c29d0efe6187e8726962008c81e956" title="Residue information (if applicable)">_residue</a>;
<a name="l00129"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a6c2a9726c57abf03a40339776f5d9a0b">00129</a> std::vector<OBInternalCoord*> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a6c2a9726c57abf03a40339776f5d9a0b" title="Internal Coordinates (if applicable)">_internals</a>;
<a name="l00130"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a5db8eb0124fad1bf66ddaf930b4840f0">00130</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a5db8eb0124fad1bf66ddaf930b4840f0" title="Number of nested calls to BeginModify()">_mod</a>;
<a name="l00131"></a>00131
<a name="l00132"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a3a1dc0419a66d2e7288214342de43b7a">00132</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a3a1dc0419a66d2e7288214342de43b7a">HasFlag</a>(<span class="keywordtype">int</span> flag) { <span class="keywordflow">return</span>((_flags & flag) ? <span class="keyword">true</span> : <span class="keyword">false</span>); }
<a name="l00133"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#adcdab8f96dc4fdc2940749e527087245">00133</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#adcdab8f96dc4fdc2940749e527087245">SetFlag</a>(<span class="keywordtype">int</span> flag) { _flags |= flag; }
<a name="l00134"></a>00134
<a name="l00136"></a>00136
<a name="l00137"></a>00137 <span class="keywordtype">void</span> start_kekulize(std::vector <OBAtom*> &cycle, std::vector<int> &electron);
<a name="l00138"></a>00138 <span class="keywordtype">bool</span> expand_kekulize(<span class="keywordtype">int</span> bond_idx, std::vector<int> &atomState, std::vector<int> &bondState);
<a name="l00139"></a>00139 <span class="keywordtype">bool</span> has_no_leftover_electrons(std::vector<int> &atomState);
<a name="l00140"></a>00140 <span class="keywordtype">int</span> getorden(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *atom);
<a name="l00141"></a>00141 <span class="keywordtype">bool</span> expandcycle(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *atom, <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &avisit, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &potAromBonds);
<a name="l00143"></a>00143
<a name="l00144"></a>00144 <span class="keyword">public</span>:
<a name="l00145"></a>00145
<a name="l00147"></a>00147
<a name="l00148"></a>00148
<a name="l00149"></a>00149 <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>();
<a name="l00151"></a>00151 <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &);
<a name="l00153"></a>00153 <span class="keyword">virtual</span> ~<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>();
<a name="l00155"></a>00155 <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &operator=(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol);
<a name="l00157"></a>00157 <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &operator+=(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol);
<a name="l00158"></a>00158
<a name="l00161"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a723933398f0402a92916d1cfcb8dadd6">00161</a> <span class="keywordtype">void</span> ReserveAtoms(<span class="keywordtype">int</span> natoms)
<a name="l00162"></a>00162 {
<a name="l00163"></a>00163 <span class="keywordflow">if</span> (natoms > 0 && _mod) {
<a name="l00164"></a>00164 _vatom.reserve(natoms);
<a name="l00165"></a>00165 _atomIds.reserve(natoms);
<a name="l00166"></a>00166 }
<a name="l00167"></a>00167 }
<a name="l00168"></a>00168
<a name="l00171"></a>00171 <span class="keyword">virtual</span> <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *<a class="code" href="namespaceOpenBabel.shtml#a5ef07c8230811964a209e423abea11d2">CreateAtom</a>(<span class="keywordtype">void</span>);
<a name="l00174"></a>00174 <span class="keyword">virtual</span> <a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *<a class="code" href="namespaceOpenBabel.shtml#a0dc584d0582e8f76b7c9873dc1ccf569">CreateBond</a>(<span class="keywordtype">void</span>);
<a name="l00177"></a>00177 <span class="keyword">virtual</span> <a class="code" href="classOpenBabel_1_1OBResidue.shtml" title="Residue information.">OBResidue</a> *CreateResidue(<span class="keywordtype">void</span>);
<a name="l00180"></a>00180 <span class="keyword">virtual</span> <span class="keywordtype">void</span> DestroyAtom(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*);
<a name="l00183"></a>00183 <span class="keyword">virtual</span> <span class="keywordtype">void</span> DestroyBond(<a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a>*);
<a name="l00186"></a>00186 <span class="keyword">virtual</span> <span class="keywordtype">void</span> DestroyResidue(<a class="code" href="classOpenBabel_1_1OBResidue.shtml" title="Residue information.">OBResidue</a>*);
<a name="l00187"></a>00187
<a name="l00190"></a>00190 <span class="keywordtype">bool</span> AddAtom(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>&);
<a name="l00193"></a>00193 <span class="keywordtype">bool</span> InsertAtom(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> &);
<a name="l00201"></a>00201 <span class="keywordtype">bool</span> AddBond(<span class="keywordtype">int</span> beginIdx, <span class="keywordtype">int</span> endIdx, <span class="keywordtype">int</span> order,
<a name="l00202"></a>00202 <span class="keywordtype">int</span> flags=0,<span class="keywordtype">int</span> insertpos=-1);
<a name="l00205"></a>00205 <span class="keywordtype">bool</span> AddBond(<a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a>&);
<a name="l00208"></a>00208 <span class="keywordtype">bool</span> AddResidue(<a class="code" href="classOpenBabel_1_1OBResidue.shtml" title="Residue information.">OBResidue</a>&);
<a name="l00209"></a>00209
<a name="l00213"></a>00213 <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *NewAtom();
<a name="l00217"></a>00217 <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *NewAtom(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>);
<a name="l00221"></a>00221 <a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *NewBond();
<a name="l00225"></a>00225 <a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *NewBond(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>);
<a name="l00227"></a>00227 <a class="code" href="classOpenBabel_1_1OBResidue.shtml" title="Residue information.">OBResidue</a> *NewResidue();
<a name="l00232"></a>00232 <span class="keywordtype">bool</span> DeleteAtom(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*, <span class="keywordtype">bool</span> destroyAtom = <span class="keyword">true</span>);
<a name="l00235"></a>00235 <span class="keywordtype">bool</span> DeleteBond(<a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a>*, <span class="keywordtype">bool</span> destroyBond = <span class="keyword">true</span>);
<a name="l00238"></a>00238 <span class="keywordtype">bool</span> DeleteResidue(<a class="code" href="classOpenBabel_1_1OBResidue.shtml" title="Residue information.">OBResidue</a>*, <span class="keywordtype">bool</span> destroyResidue = <span class="keyword">true</span>);
<a name="l00240"></a>00240
<a name="l00242"></a>00242
<a name="l00243"></a>00243
<a name="l00244"></a>00244
<a name="l00245"></a>00245
<a name="l00246"></a>00246 <span class="keyword">virtual</span> <span class="keywordtype">void</span> BeginModify(<span class="keywordtype">void</span>);
<a name="l00250"></a>00250 <span class="keyword">virtual</span> <span class="keywordtype">void</span> EndModify(<span class="keywordtype">bool</span> nukePerceivedData=<span class="keyword">true</span>);
<a name="l00252"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ac5103c8b3cbe4f961bd353209bf2860e">00252</a> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ac5103c8b3cbe4f961bd353209bf2860e">GetMod</a>() { <span class="keywordflow">return</span>(_mod); }
<a name="l00255"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#adc36b31f851665247f3c576cdd7aa0af">00255</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#adc36b31f851665247f3c576cdd7aa0af">IncrementMod</a>() { _mod++; }
<a name="l00258"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a8efda275b959c94452e1ded1f568c934">00258</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a8efda275b959c94452e1ded1f568c934">DecrementMod</a>() { _mod--; }
<a name="l00260"></a>00260
<a name="l00262"></a>00262
<a name="l00263"></a>00263
<a name="l00264"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aba761a006b56d62912a91e259ce11bb1">00264</a> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aba761a006b56d62912a91e259ce11bb1">GetFlags</a>() { <span class="keywordflow">return</span>(_flags); }
<a name="l00267"></a>00267 <span class="keyword">const</span> <span class="keywordtype">char</span> *GetTitle(<span class="keywordtype">bool</span> replaceNewlines = <span class="keyword">true</span>) <span class="keyword">const</span>;
<a name="l00269"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a0c317a10161689c407f29a6fcacdb852">00269</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a0c317a10161689c407f29a6fcacdb852">NumAtoms</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span>(_natoms); }
<a name="l00271"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a115132ab8bd21607d00d61bc1ba5cc16">00271</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a115132ab8bd21607d00d61bc1ba5cc16">NumBonds</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span>(_nbonds); }
<a name="l00273"></a>00273 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> NumHvyAtoms();
<a name="l00275"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ad1369fbd476ea326b847c08ff64f9331">00275</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ad1369fbd476ea326b847c08ff64f9331">NumResidues</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span>(static_cast<unsigned int> (_residue.size())); }
<a name="l00277"></a>00277 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> NumRotors();
<a name="l00278"></a>00278
<a name="l00281"></a>00281 <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *GetAtom(<span class="keywordtype">int</span> idx) <span class="keyword">const</span>;
<a name="l00283"></a>00283 <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *GetAtomById(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>) <span class="keyword">const</span>;
<a name="l00286"></a>00286 <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *GetFirstAtom() <span class="keyword">const</span>;
<a name="l00289"></a>00289 <a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *GetBond(<span class="keywordtype">int</span> idx) <span class="keyword">const</span>;
<a name="l00291"></a>00291 <a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *GetBondById(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>) <span class="keyword">const</span>;
<a name="l00294"></a>00294 <a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *GetBond(<span class="keywordtype">int</span> a, <span class="keywordtype">int</span> b) <span class="keyword">const</span>;
<a name="l00295"></a>00295 <span class="comment">// The safer version of the above method</span>
<a name="l00297"></a>00297 <span class="comment"></span> <a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *GetBond(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* bgn, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* end) <span class="keyword">const</span>;
<a name="l00300"></a>00300 <a class="code" href="classOpenBabel_1_1OBResidue.shtml" title="Residue information.">OBResidue</a> *GetResidue(<span class="keywordtype">int</span> idx) <span class="keyword">const</span>;
<a name="l00301"></a>00301 std::vector<OBInternalCoord*> GetInternalCoord();
<a name="l00306"></a>00306 <span class="keywordtype">double</span> GetTorsion(<span class="keywordtype">int</span>,<span class="keywordtype">int</span>,<span class="keywordtype">int</span>,<span class="keywordtype">int</span>);
<a name="l00311"></a>00311 <span class="keywordtype">double</span> GetTorsion(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* a,<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* b,<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* c,<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* d);
<a name="l00314"></a>00314 <span class="keywordtype">double</span> GetAngle(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* a, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* b, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* c);
<a name="l00316"></a>00316 std::string GetFormula();
<a name="l00318"></a>00318 std::string GetSpacedFormula(<span class="keywordtype">int</span> ones=0, <span class="keyword">const</span> <span class="keywordtype">char</span>* sp=<span class="stringliteral">" "</span>, <span class="keywordtype">bool</span> implicitH = <span class="keyword">true</span>);
<a name="l00320"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a898054d3301668a37b4d7c3612487157">00320</a> <span class="keywordtype">double</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a898054d3301668a37b4d7c3612487157">GetEnergy</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> _energy; }
<a name="l00322"></a>00322 <span class="keywordtype">double</span> GetMolWt(<span class="keywordtype">bool</span> implicitH = <span class="keyword">true</span>);
<a name="l00324"></a>00324 <span class="keywordtype">double</span> GetExactMass(<span class="keywordtype">bool</span> implicitH = <span class="keyword">true</span>);
<a name="l00326"></a>00326 <span class="keywordtype">int</span> GetTotalCharge();
<a name="l00328"></a>00328 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> GetTotalSpinMultiplicity();
<a name="l00330"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ae66fbb23621ae4f9e7937540d5072869">00330</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ae66fbb23621ae4f9e7937540d5072869">GetDimension</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> _dimension; }
<a name="l00332"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ad11003513310725bd54265ef5bf004c0">00332</a> <span class="keywordtype">double</span> *<a class="code" href="classOpenBabel_1_1OBMol.shtml#ad11003513310725bd54265ef5bf004c0">GetCoordinates</a>() { <span class="keywordflow">return</span>(_c); }
<a name="l00334"></a>00334 std::vector<OBRing*> &GetSSSR();
<a name="l00336"></a>00336 std::vector<OBRing*> &GetLSSR();
<a name="l00338"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a9f801729475d1d17415af6376458c81e">00338</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a9f801729475d1d17415af6376458c81e" title="Get the current flag for whether formal charges are set with pH correction.">AutomaticFormalCharge</a>() { <span class="keywordflow">return</span>(_autoFormalCharge); }
<a name="l00340"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#af2ee11d3efe6526c2eb352bb67684e6c">00340</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#af2ee11d3efe6526c2eb352bb67684e6c" title="Get the current flag for whether partial charges are auto-determined.">AutomaticPartialCharge</a>() { <span class="keywordflow">return</span>(_autoPartialCharge); }
<a name="l00342"></a>00342
<a name="l00343"></a>00343
<a name="l00345"></a>00345
<a name="l00346"></a>00346
<a name="l00347"></a>00347 <span class="keywordtype">void</span> SetTitle(<span class="keyword">const</span> <span class="keywordtype">char</span> *title);
<a name="l00349"></a>00349 <span class="keywordtype">void</span> SetTitle(std::string &title);
<a name="l00351"></a>00351 <span class="keywordtype">void</span> SetFormula(std::string molFormula);
<a name="l00353"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ab78fa0a100d47ad2beb88c7cabb80e62">00353</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ab78fa0a100d47ad2beb88c7cabb80e62" title="Set the heat of formation for this molecule (in kcal/mol)">SetEnergy</a>(<span class="keywordtype">double</span> energy) { _energy = energy; }
<a name="l00355"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#adc2702cffcab0a0d6907958e3327284b">00355</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#adc2702cffcab0a0d6907958e3327284b" title="Set the dimension of this molecule (i.e., 0, 1 , 2, 3)">SetDimension</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> <span class="keywordtype">int</span> d) { _dimension = d; }
<a name="l00357"></a>00357 <span class="keywordtype">void</span> SetTotalCharge(<span class="keywordtype">int</span> charge);
<a name="l00360"></a>00360 <span class="keywordtype">void</span> SetTotalSpinMultiplicity(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> spinMultiplicity);
<a name="l00366"></a>00366 <span class="keywordtype">void</span> SetInternalCoord(std::vector<OBInternalCoord*> int_coord);
<a name="l00368"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a31e0990c833c415708b3fc515dbb35d5">00368</a> <span class="keywordtype">void</span> SetAutomaticFormalCharge(<span class="keywordtype">bool</span> val)
<a name="l00369"></a>00369 { _autoFormalCharge=val; }
<a name="l00371"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aa8df95db3695e5e7ce263c484ce5533d">00371</a> <span class="keywordtype">void</span> SetAutomaticPartialCharge(<span class="keywordtype">bool</span> val)
<a name="l00372"></a>00372 { _autoPartialCharge=val; }
<a name="l00373"></a>00373
<a name="l00375"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aecd431b2cfaefa64d54c2dc4088551fb">00375</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aecd431b2cfaefa64d54c2dc4088551fb" title="Mark that aromaticity has been perceived for this molecule (see OBAromaticTyper)">SetAromaticPerceived</a>() { SetFlag(<a class="code" href="mol_8h.shtml#a00796165b0d091f4b0987ee2a0ba5609" title="Aromatic flags have been set for atoms and bonds.">OB_AROMATIC_MOL</a>); }
<a name="l00377"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aba303a094727738eb901cafbecd7c196">00377</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aba303a094727738eb901cafbecd7c196" title="Mark that Smallest Set of Smallest Rings has been run (see OBRing class)">SetSSSRPerceived</a>() { SetFlag(<a class="code" href="mol_8h.shtml#a1ab7f39b595f0f69b77c5907c804afc4" title="Smallest Set of Smallest Rings (SSSR) done. See OBRing and OBMol::FindSSSR.">OB_SSSR_MOL</a>); }
<a name="l00379"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a4641fea7bd6513949147bb7a53b6a7e1">00379</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a4641fea7bd6513949147bb7a53b6a7e1" title="Mark that Largest Set of Smallest Rings has been run (see OBRing class)">SetLSSRPerceived</a>() { SetFlag(<a class="code" href="mol_8h.shtml#ae62d8140a1f27fe185152e8ca29f2255" title="Largest Set of Smallest Rings (LSSR) done. See OBRing and OBMol::FindLSSR.">OB_LSSR_MOL</a>); }
<a name="l00381"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a0656401ba8b19bc9b9f2d3e8e833d3aa">00381</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a0656401ba8b19bc9b9f2d3e8e833d3aa" title="Mark that rings have been perceived (see OBRing class for details)">SetRingAtomsAndBondsPerceived</a>(){SetFlag(<a class="code" href="mol_8h.shtml#ae9ad3600741ed030f463badacb48cbf9" title="Ring flags have been set: See OBRing::FindRingAtomsAndBonds.">OB_RINGFLAGS_MOL</a>);}
<a name="l00383"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aa809ea95ee07e61c6dc00ae710d8a749">00383</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aa809ea95ee07e61c6dc00ae710d8a749" title="Mark that atom types have been perceived (see OBAtomTyper for details)">SetAtomTypesPerceived</a>() { SetFlag(<a class="code" href="mol_8h.shtml#abf2d91f3d8e6d4db13029a0130a262a5" title="Atom typing has been performed. See OBAtomTyper.">OB_ATOMTYPES_MOL</a>); }
<a name="l00385"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a08b5caf5aa6fc21e7b6fcd44e3d32f58">00385</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a08b5caf5aa6fc21e7b6fcd44e3d32f58" title="Mark that ring types have been perceived (see OBRingTyper for details)">SetRingTypesPerceived</a>() { SetFlag(<a class="code" href="mol_8h.shtml#aaba06b0d4348eedb3f32f764d4c9b9f8" title="Ring typing has been performed. See OBRingTyper.">OB_RINGTYPES_MOL</a>); }
<a name="l00387"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a537294f8e96a7ec5263a79de7454326e">00387</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a537294f8e96a7ec5263a79de7454326e" title="Mark that chains and residues have been perceived (see OBChainsParser)">SetChainsPerceived</a>() { SetFlag(<a class="code" href="mol_8h.shtml#a5aaff7bcb11a37508fe32d17ad57dea0" title="Biomolecular chains and residues have been set. See OBChainsParser.">OB_CHAINS_MOL</a>); }
<a name="l00389"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a608e6f965afea1f4f64cb0f499a0cb27">00389</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a608e6f965afea1f4f64cb0f499a0cb27" title="Mark that chirality has been perceived.">SetChiralityPerceived</a>() { SetFlag(<a class="code" href="mol_8h.shtml#abdf1bef91d791e4ec64071377a06e491" title="Chirality detection has been performed. See OBMol::IsChiral.">OB_CHIRALITY_MOL</a>); }
<a name="l00391"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a00fd4c76a7513a9c8087d975f5d8a51b">00391</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a00fd4c76a7513a9c8087d975f5d8a51b" title="Mark that partial charges have been assigned.">SetPartialChargesPerceived</a>(){ SetFlag(<a class="code" href="mol_8h.shtml#aade7aaf66074d41ccc89a88fde187ef0" title="Partial charges have been set or percieved.">OB_PCHARGE_MOL</a>); }
<a name="l00393"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a4b93b72694e8a9a970eee7f0b65ecf9a">00393</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a4b93b72694e8a9a970eee7f0b65ecf9a" title="Mark that hybridization of all atoms has been assigned.">SetHybridizationPerceived</a>() { SetFlag(<a class="code" href="mol_8h.shtml#a2609984a86f8eaca60bd0995ab1ff082" title="Atom hybridizations have been set. See OBAtomTyper.">OB_HYBRID_MOL</a>); }
<a name="l00395"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a9ecfb96410199c294c003f975d870832">00395</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a9ecfb96410199c294c003f975d870832" title="Mark that the implicit hydrogen valence of all atoms has been assigned.">SetImplicitValencePerceived</a>(){ SetFlag(<a class="code" href="mol_8h.shtml#a220b0e4aac833823ef37f6d10ac7a254" title="Implicit valence has been set. See OBAtomTyper.">OB_IMPVAL_MOL</a>); }
<a name="l00397"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a1e298bbe286ab2c5a6f3b086a07b1a2b">00397</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a1e298bbe286ab2c5a6f3b086a07b1a2b" title="Mark that Kekule forms have been assigned by Kekulize()">SetKekulePerceived</a>() { SetFlag(<a class="code" href="mol_8h.shtml#adb1c838e0460bae3347db0d94b4e63c7" title="Kekule form has been set. See OBMol::Kekulize.">OB_KEKULE_MOL</a>); }
<a name="l00399"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a7900736a9f73a041ab8bade19be84cc9">00399</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a7900736a9f73a041ab8bade19be84cc9" title="Mark that ring closure bonds have been assigned by graph traversal.">SetClosureBondsPerceived</a>(){ SetFlag(<a class="code" href="mol_8h.shtml#aa9b307d4356f47b80ba6516405bea32e" title="Ring "closure" bonds have been set. See OBBond::IsClosure.">OB_CLOSURE_MOL</a>); }
<a name="l00401"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a47b63124c405f9c2ecdb766c6de9c56e">00401</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a47b63124c405f9c2ecdb766c6de9c56e" title="Mark that explicit hydrogen atoms have been added.">SetHydrogensAdded</a>() { SetFlag(<a class="code" href="mol_8h.shtml#a488eaf115c8c8e3f8ac24384f80f6f88" title="Hyrdogen atoms have been added where needed. See OBMol::AddHydrogens.">OB_H_ADDED_MOL</a>); }
<a name="l00402"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#af56db37c6a9f7049ed16469ab0a270c2">00402</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#af56db37c6a9f7049ed16469ab0a270c2">SetCorrectedForPH</a>() { SetFlag(<a class="code" href="mol_8h.shtml#af3ca96a4c05940f8ed8fdc159b93656a" title="pH correction for hydrogen addition has been performed.">OB_PH_CORRECTED_MOL</a>);}
<a name="l00403"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a6438e097839dbc98916fb00a3dc67305">00403</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a6438e097839dbc98916fb00a3dc67305">SetAromaticCorrected</a>() { SetFlag(<a class="code" href="mol_8h.shtml#ad34e5e48a2b7f4c149070647189d9d71" title="Aromaticity has been corrected. See OBAtomTyper::CorrectAromaticNitrogens.">OB_AROM_CORRECTED_MOL</a>);}
<a name="l00404"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a2c81eeba803bc59d6c40f97b0e0e17fd">00404</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a2c81eeba803bc59d6c40f97b0e0e17fd">SetSpinMultiplicityAssigned</a>(){ SetFlag(<a class="code" href="mol_8h.shtml#a8ae8b8d431ee5649e4dad8bbdfd5092d" title="Total spin on this molecule has been set. See OBMol::SetTotalSpinMultiplicity.">OB_TSPIN_MOL</a>); }
<a name="l00405"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ab0922e1fa0939499c024e1006433adf3">00405</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ab0922e1fa0939499c024e1006433adf3">SetFlags</a>(<span class="keywordtype">int</span> flags) { _flags = flags; }
<a name="l00406"></a>00406
<a name="l00407"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a88f39becfe74f62c9d0ffedfb4098b77">00407</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a88f39becfe74f62c9d0ffedfb4098b77">UnsetAromaticPerceived</a>() { _flags &= (~(<a class="code" href="mol_8h.shtml#a00796165b0d091f4b0987ee2a0ba5609" title="Aromatic flags have been set for atoms and bonds.">OB_AROMATIC_MOL</a>)); }
<a name="l00408"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a116f93a9700551794731bf71cd17345a">00408</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a116f93a9700551794731bf71cd17345a">UnsetSSSRPerceived</a>() { _flags &= (~(<a class="code" href="mol_8h.shtml#a1ab7f39b595f0f69b77c5907c804afc4" title="Smallest Set of Smallest Rings (SSSR) done. See OBRing and OBMol::FindSSSR.">OB_SSSR_MOL</a>)); }
<a name="l00409"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a7d0001f1af294a0d5676a70e12115b43">00409</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a7d0001f1af294a0d5676a70e12115b43">UnsetRingTypesPerceived</a>() { _flags &= (~(<a class="code" href="mol_8h.shtml#aaba06b0d4348eedb3f32f764d4c9b9f8" title="Ring typing has been performed. See OBRingTyper.">OB_RINGTYPES_MOL</a>)); }
<a name="l00410"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a0b8a9f6292b91ec5c4022a487e9d6092">00410</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a0b8a9f6292b91ec5c4022a487e9d6092">UnsetPartialChargesPerceived</a>(){ _flags &= (~(<a class="code" href="mol_8h.shtml#aade7aaf66074d41ccc89a88fde187ef0" title="Partial charges have been set or percieved.">OB_PCHARGE_MOL</a>));}
<a name="l00411"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#af673e91c4869ca8c1057f006d4f06dae">00411</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#af673e91c4869ca8c1057f006d4f06dae">UnsetImplicitValencePerceived</a>(){_flags &= (~(<a class="code" href="mol_8h.shtml#a220b0e4aac833823ef37f6d10ac7a254" title="Implicit valence has been set. See OBAtomTyper.">OB_IMPVAL_MOL</a>)); }
<a name="l00412"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ac6df023071b8d662aa513a00579f076d">00412</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ac6df023071b8d662aa513a00579f076d">UnsetHydrogensAdded</a>() { UnsetFlag(<a class="code" href="mol_8h.shtml#a488eaf115c8c8e3f8ac24384f80f6f88" title="Hyrdogen atoms have been added where needed. See OBMol::AddHydrogens.">OB_H_ADDED_MOL</a>); }
<a name="l00413"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a401b99defa8a57195dc40a2604cee115">00413</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a401b99defa8a57195dc40a2604cee115">UnsetFlag</a>(<span class="keywordtype">int</span> flag) { _flags &= (~(flag)); }
<a name="l00415"></a>00415
<a name="l00417"></a>00417
<a name="l00418"></a>00418 <span class="comment">// Description in transform.cpp (command-line transformations to this molecule)</span>
<a name="l00419"></a>00419 <span class="keyword">virtual</span> <a class="code" href="classOpenBabel_1_1OBBase.shtml" title="Base Class.">OBBase</a>* DoTransformations(<span class="keyword">const</span> std::map<std::string,std::string>* pOptions,<a class="code" href="classOpenBabel_1_1OBConversion.shtml" title="Class to convert from one format to another.">OBConversion</a>* pConv);
<a name="l00420"></a>00420 <span class="comment">// Ditto (documentation on transformation options)</span>
<a name="l00421"></a>00421 <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* ClassDescription();
<a name="l00423"></a>00423 <span class="keywordtype">bool</span> Clear();
<a name="l00425"></a>00425 <span class="keywordtype">void</span> RenumberAtoms(std::vector<OBAtom*>&);
<a name="l00427"></a>00427 <span class="keywordtype">void</span> RenumberAtoms(std::vector<int>);
<a name="l00430"></a>00430 <span class="keywordtype">void</span> SetCoordinates(<span class="keywordtype">double</span> *c);
<a name="l00432"></a>00432 <span class="keywordtype">void</span> ToInertialFrame(<span class="keywordtype">int</span> conf, <span class="keywordtype">double</span> *rmat);
<a name="l00434"></a>00434 <span class="keywordtype">void</span> ToInertialFrame();
<a name="l00436"></a>00436 <span class="keywordtype">void</span> Translate(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> &v);
<a name="l00438"></a>00438 <span class="keywordtype">void</span> Translate(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> &v, <span class="keywordtype">int</span> conf);
<a name="l00440"></a>00440 <span class="keywordtype">void</span> Rotate(<span class="keyword">const</span> <span class="keywordtype">double</span> u[3][3]);
<a name="l00442"></a>00442 <span class="keywordtype">void</span> Rotate(<span class="keyword">const</span> <span class="keywordtype">double</span> m[9]);
<a name="l00444"></a>00444 <span class="keywordtype">void</span> Rotate(<span class="keyword">const</span> <span class="keywordtype">double</span> m[9],<span class="keywordtype">int</span> nconf);
<a name="l00446"></a>00446 <span class="keywordtype">void</span> Center();
<a name="l00448"></a>00448
<a name="l00449"></a>00449 <span class="keywordtype">bool</span> Kekulize();
<a name="l00450"></a>00450 <span class="keywordtype">bool</span> PerceiveKekuleBonds();
<a name="l00451"></a>00451
<a name="l00452"></a>00452 <span class="keywordtype">void</span> NewPerceiveKekuleBonds();
<a name="l00453"></a>00453
<a name="l00456"></a>00456 <span class="keywordtype">bool</span> DeleteHydrogens();
<a name="l00459"></a>00459 <span class="keywordtype">bool</span> DeleteHydrogens(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*);
<a name="l00462"></a>00462 <span class="keywordtype">bool</span> DeleteNonPolarHydrogens();
<a name="l00465"></a>00465 <span class="keywordtype">bool</span> DeleteHydrogen(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*);
<a name="l00472"></a>00472 <span class="keywordtype">bool</span> AddHydrogens(<span class="keywordtype">bool</span> polaronly=<span class="keyword">false</span>,<span class="keywordtype">bool</span> correctForPH=<span class="keyword">false</span>, <span class="keywordtype">double</span> pH=7.4);
<a name="l00474"></a>00474 <span class="keywordtype">bool</span> AddHydrogens(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*);
<a name="l00476"></a>00476 <span class="keywordtype">bool</span> AddPolarHydrogens();
<a name="l00477"></a>00477
<a name="l00481"></a>00481 <span class="keywordtype">bool</span> StripSalts(<span class="keywordtype">int</span> threshold=0);
<a name="l00483"></a>00483 std::vector<OBMol> Separate(<span class="keywordtype">int</span> StartIndex=1);
<a name="l00485"></a>00485 <span class="keywordtype">bool</span> GetNextFragment( <a class="code" href="classOpenBabel_1_1OBMolAtomDFSIter.shtml" title="Iterate over all atoms in an OBMol in a depth-first search (DFS)">OpenBabel::OBMolAtomDFSIter</a>& iter, <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>& newMol );
<a name="l00487"></a>00487 <span class="keywordtype">bool</span> ConvertDativeBonds();
<a name="l00488"></a>00488
<a name="l00490"></a>00490 <span class="keywordtype">bool</span> CorrectForPH(<span class="keywordtype">double</span> pH=7.4);
<a name="l00491"></a>00491 <span class="comment">// docs in mol.cpp</span>
<a name="l00492"></a>00492 <span class="keywordtype">bool</span> AssignSpinMultiplicity(<span class="keywordtype">bool</span> NoImplicitH=<span class="keyword">false</span>);
<a name="l00494"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a0f0310aa379033994230e29e206106c7">00494</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a0f0310aa379033994230e29e206106c7" title="The OBMol is a pattern, not a complete molecule. Left unchanged by Clear().">SetIsPatternStructure</a>() { SetFlag(<a class="code" href="mol_8h.shtml#ad224f71d6aecaa29f7cb32ec475b8d58" title="A pattern, not a complete molecule.">OB_PATTERN_STRUCTURE</a>);}
<a name="l00495"></a>00495
<a name="l00498"></a>00498 <a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> Center(<span class="keywordtype">int</span> nconf);
<a name="l00504"></a>00504 <span class="keywordtype">void</span> SetTorsion(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*,<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*,<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*,<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*,<span class="keywordtype">double</span> ang);
<a name="l00506"></a>00506
<a name="l00508"></a>00508
<a name="l00509"></a>00509
<a name="l00510"></a>00510 <span class="keywordtype">void</span> FindSSSR();
<a name="l00512"></a>00512 <span class="keywordtype">void</span> FindLSSR();
<a name="l00514"></a>00514 <span class="keywordtype">void</span> FindRingAtomsAndBonds();
<a name="l00517"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a3368586a5a86bd9684f4b25ac53d2e44">00517</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a3368586a5a86bd9684f4b25ac53d2e44">FindChiralCenters</a>() { IsChiral(); }
<a name="l00518"></a>00518 <span class="comment">// documented in mol.cpp -- locates all atom indexes which can reach 'end'</span>
<a name="l00519"></a>00519 <span class="keywordtype">void</span> FindChildren(std::vector<int> & children,<span class="keywordtype">int</span> bgnIdx,<span class="keywordtype">int</span> endIdx);
<a name="l00520"></a>00520 <span class="comment">// documented in mol.cpp -- locates all atoms which can reach 'end'</span>
<a name="l00521"></a>00521 <span class="keywordtype">void</span> FindChildren(std::vector<OBAtom*>& children,<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* bgn,<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>* end);
<a name="l00526"></a>00526 <span class="keywordtype">void</span> FindLargestFragment(<a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &frag);
<a name="l00529"></a>00529 <span class="keywordtype">void</span> ContigFragList(std::vector<std::vector<int> >&);
<a name="l00531"></a>00531 <span class="keywordtype">void</span> Align(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*,<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*,<a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a>&,<a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a>&);
<a name="l00533"></a>00533 <span class="keywordtype">void</span> ConnectTheDots();
<a name="l00535"></a>00535 <span class="keywordtype">void</span> PerceiveBondOrders();
<a name="l00537"></a>00537 <span class="keywordtype">void</span> FindAngles();
<a name="l00539"></a>00539 <span class="keywordtype">void</span> FindTorsions();
<a name="l00540"></a>00540 <span class="comment">// documented in mol.cpp: graph-theoretical distance for each atom</span>
<a name="l00541"></a>00541 <span class="keywordtype">bool</span> GetGTDVector(std::vector<int> &);
<a name="l00542"></a>00542 <span class="comment">// documented in mol.cpp: graph-invariant index for each atom</span>
<a name="l00543"></a>00543 <span class="keywordtype">void</span> GetGIVector(std::vector<unsigned int> &);
<a name="l00544"></a>00544 <span class="comment">// documented in mol.cpp: calculate symmetry-unique identifiers</span>
<a name="l00545"></a>00545 <span class="keywordtype">void</span> GetGIDVector(std::vector<unsigned int> &);
<a name="l00547"></a>00547
<a name="l00549"></a>00549
<a name="l00550"></a>00550
<a name="l00551"></a>00551 <span class="keywordtype">bool</span> Has2D(<span class="keywordtype">bool</span> Not3D=<span class="keyword">false</span>);
<a name="l00553"></a>00553 <span class="keywordtype">bool</span> Has3D();
<a name="l00555"></a>00555 <span class="keywordtype">bool</span> HasNonZeroCoords();
<a name="l00557"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a783c51919c69da3287d51f34b2fa53a0">00557</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a783c51919c69da3287d51f34b2fa53a0" title="Has aromatic perception been performed?">HasAromaticPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#a00796165b0d091f4b0987ee2a0ba5609" title="Aromatic flags have been set for atoms and bonds.">OB_AROMATIC_MOL</a>)); }
<a name="l00559"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aac2c45d000ac10ad770ec5e5eff97f30">00559</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aac2c45d000ac10ad770ec5e5eff97f30" title="Has the smallest set of smallest rings (FindSSSR) been performed?">HasSSSRPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#a1ab7f39b595f0f69b77c5907c804afc4" title="Smallest Set of Smallest Rings (SSSR) done. See OBRing and OBMol::FindSSSR.">OB_SSSR_MOL</a>)); }
<a name="l00561"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a3771eaf33a336f55348f80ca857a159f">00561</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a3771eaf33a336f55348f80ca857a159f" title="Has the largest set of smallest rings (FindLSSR) been performed?">HasLSSRPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#ae62d8140a1f27fe185152e8ca29f2255" title="Largest Set of Smallest Rings (LSSR) done. See OBRing and OBMol::FindLSSR.">OB_LSSR_MOL</a>)); }
<a name="l00563"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a0329d4256b426a4967afa867f415d06b">00563</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a0329d4256b426a4967afa867f415d06b" title="Have ring atoms and bonds been assigned?">HasRingAtomsAndBondsPerceived</a>(){<span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#ae9ad3600741ed030f463badacb48cbf9" title="Ring flags have been set: See OBRing::FindRingAtomsAndBonds.">OB_RINGFLAGS_MOL</a>));}
<a name="l00565"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a0ba2ebe76f1b15c48a8f1538efc8f9b4">00565</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a0ba2ebe76f1b15c48a8f1538efc8f9b4" title="Have atom types been assigned by OBAtomTyper?">HasAtomTypesPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#abf2d91f3d8e6d4db13029a0130a262a5" title="Atom typing has been performed. See OBAtomTyper.">OB_ATOMTYPES_MOL</a>));}
<a name="l00567"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#adfe42a839d62e3d8f31ce3c28dc2e4e0">00567</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#adfe42a839d62e3d8f31ce3c28dc2e4e0" title="Have ring types been assigned by OBRingTyper?">HasRingTypesPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#aaba06b0d4348eedb3f32f764d4c9b9f8" title="Ring typing has been performed. See OBRingTyper.">OB_RINGTYPES_MOL</a>));}
<a name="l00569"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a39df67d7e225b9dd721b9b8c7df809ce">00569</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a39df67d7e225b9dd721b9b8c7df809ce" title="Has atom chirality been assigned?">HasChiralityPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#abdf1bef91d791e4ec64071377a06e491" title="Chirality detection has been performed. See OBMol::IsChiral.">OB_CHIRALITY_MOL</a>));}
<a name="l00571"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a87c2cd2043f749d5433a98df4ad8277d">00571</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a87c2cd2043f749d5433a98df4ad8277d" title="Have atomic Gasteiger partial charges been assigned by OBGastChrg?">HasPartialChargesPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#aade7aaf66074d41ccc89a88fde187ef0" title="Partial charges have been set or percieved.">OB_PCHARGE_MOL</a>));}
<a name="l00573"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a908e2d394d3a47cf821014899344ca37">00573</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a908e2d394d3a47cf821014899344ca37" title="Has atomic hybridization been assigned by OBAtomTyper?">HasHybridizationPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#a2609984a86f8eaca60bd0995ab1ff082" title="Atom hybridizations have been set. See OBAtomTyper.">OB_HYBRID_MOL</a>)); }
<a name="l00575"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a7fe699ef7fee62ca46743d6aa78bdea5">00575</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a7fe699ef7fee62ca46743d6aa78bdea5" title="Has implicit hydrogen valence been assigned by OBAtomTyper?">HasImplicitValencePerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#a220b0e4aac833823ef37f6d10ac7a254" title="Implicit valence has been set. See OBAtomTyper.">OB_IMPVAL_MOL</a>));}
<a name="l00577"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aafddb1ded7f589afbdd56062368602db">00577</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aafddb1ded7f589afbdd56062368602db" title="Has aromaticity and Kekule forms been assigned by Kekulize?">HasKekulePerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#adb1c838e0460bae3347db0d94b4e63c7" title="Kekule form has been set. See OBMol::Kekulize.">OB_KEKULE_MOL</a>)); }
<a name="l00579"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#afb25b05d950ca109bf9c6333b906a9ee">00579</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#afb25b05d950ca109bf9c6333b906a9ee" title="Have ring "closure" bonds been assigned? (e.g., OBBond::IsClosure())">HasClosureBondsPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#aa9b307d4356f47b80ba6516405bea32e" title="Ring "closure" bonds have been set. See OBBond::IsClosure.">OB_CLOSURE_MOL</a>)); }
<a name="l00581"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ac31a6af8f2b96fa35170523b6318c459">00581</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ac31a6af8f2b96fa35170523b6318c459" title="Have biomolecule chains and residues been assigned by OBChainsParser?">HasChainsPerceived</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#a5aaff7bcb11a37508fe32d17ad57dea0" title="Biomolecular chains and residues have been set. See OBChainsParser.">OB_CHAINS_MOL</a>)); }
<a name="l00583"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aefc6e71556f0cd4afdd34e4a99d06025">00583</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#aefc6e71556f0cd4afdd34e4a99d06025" title="Have hydrogens been added to the molecule?">HasHydrogensAdded</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#a488eaf115c8c8e3f8ac24384f80f6f88" title="Hyrdogen atoms have been added where needed. See OBMol::AddHydrogens.">OB_H_ADDED_MOL</a>)); }
<a name="l00585"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ab57a4b5dd9752e593e2fdb80f48909d8">00585</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ab57a4b5dd9752e593e2fdb80f48909d8" title="Have aromatic nitrogens been "corrected?" (deprecated)">HasAromaticCorrected</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#ad34e5e48a2b7f4c149070647189d9d71" title="Aromaticity has been corrected. See OBAtomTyper::CorrectAromaticNitrogens.">OB_AROM_CORRECTED_MOL</a>));}
<a name="l00587"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#afc44b8ad27a62b9cfc670d4fd29bb52f">00587</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#afc44b8ad27a62b9cfc670d4fd29bb52f" title="Has the molecule been corrected for pH by CorrectForPH?">IsCorrectedForPH</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#af3ca96a4c05940f8ed8fdc159b93656a" title="pH correction for hydrogen addition has been performed.">OB_PH_CORRECTED_MOL</a>)); }
<a name="l00589"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a4a45f2c821b749250e070c3594289103">00589</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a4a45f2c821b749250e070c3594289103" title="Has total spin multiplicity been assigned?">HasSpinMultiplicityAssigned</a>() { <span class="keywordflow">return</span>(HasFlag(<a class="code" href="mol_8h.shtml#a8ae8b8d431ee5649e4dad8bbdfd5092d" title="Total spin on this molecule has been set. See OBMol::SetTotalSpinMultiplicity.">OB_TSPIN_MOL</a>)); }
<a name="l00591"></a>00591 <span class="keywordtype">bool</span> IsChiral();
<a name="l00593"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a31d1053aee208079bcc3c5e1884774df">00593</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a31d1053aee208079bcc3c5e1884774df" title="Are there any atoms in this molecule?">Empty</a>() { <span class="keywordflow">return</span>(_natoms == 0); }
<a name="l00595"></a>00595
<a name="l00597"></a>00597
<a name="l00598"></a>00598
<a name="l00599"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a37e5c0caf3b51ae81d8d3abc6ffb1a9c">00599</a> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a37e5c0caf3b51ae81d8d3abc6ffb1a9c">NumConformers</a>() { <span class="keywordflow">return</span>((_vconf.empty())?0:static_cast<int> (_vconf.size())); }
<a name="l00601"></a>00601 <span class="keywordtype">void</span> SetConformers(std::vector<double*> &v);
<a name="l00603"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a7b80e7015d000221e0cc92fd3cf6f9e4">00603</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a7b80e7015d000221e0cc92fd3cf6f9e4" title="Add a new set of coordinates f as a new conformer.">AddConformer</a>(<span class="keywordtype">double</span> *f) { _vconf.push_back(f); }
<a name="l00606"></a>00606 <span class="keywordtype">void</span> SetConformer(<span class="keywordtype">int</span> i);
<a name="l00609"></a>00609 <span class="keywordtype">void</span> CopyConformer(<span class="keywordtype">double</span>* c,<span class="keywordtype">int</span> nconf);
<a name="l00611"></a>00611 <span class="keywordtype">void</span> DeleteConformer(<span class="keywordtype">int</span> nconf);
<a name="l00613"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#aeae833c9dcc30e182f18554bd40242d6">00613</a> <span class="keywordtype">double</span> *<a class="code" href="classOpenBabel_1_1OBMol.shtml#aeae833c9dcc30e182f18554bd40242d6">GetConformer</a>(<span class="keywordtype">int</span> i) { <span class="keywordflow">return</span>(_vconf[i]); }
<a name="l00615"></a>00615 <span class="keywordtype">void</span> SetEnergies(std::vector<double> &energies);
<a name="l00617"></a>00617 std::vector<double> GetEnergies();
<a name="l00620"></a>00620 <span class="keywordtype">double</span> GetEnergy(<span class="keywordtype">int</span> ci);
<a name="l00623"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a43bacf0671104e33b04835408b5c3785">00623</a> <span class="keywordtype">double</span> *BeginConformer(std::vector<double*>::iterator&i)
<a name="l00624"></a>00624 { i = _vconf.begin();
<a name="l00625"></a>00625 <span class="keywordflow">return</span>((i == _vconf.end()) ? NULL:*i); }
<a name="l00628"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#abd4311945a4de0a47d2f036e9632a4b9">00628</a> <span class="keywordtype">double</span> *NextConformer(std::vector<double*>::iterator&i)
<a name="l00629"></a>00629 { ++i;
<a name="l00630"></a>00630 <span class="keywordflow">return</span>((i == _vconf.end()) ? NULL:*i); }
<a name="l00632"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a5246a44bf82aa31c2f428665db94bfb8">00632</a> std::vector<double*> &<a class="code" href="classOpenBabel_1_1OBMol.shtml#a5246a44bf82aa31c2f428665db94bfb8">GetConformers</a>() { <span class="keywordflow">return</span>(_vconf); }
<a name="l00634"></a>00634
<a name="l00636"></a>00636
<a name="l00637"></a>00637
<a name="l00638"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ae3b07b388e733d5a0e9ee9654a4411a1">00638</a> <a class="code" href="namespaceOpenBabel.shtml#aed11ccd81d7abaccbdf10486a5ae0402" title="A standard iterator over a vector of atoms.">OBAtomIterator</a> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ae3b07b388e733d5a0e9ee9654a4411a1">BeginAtoms</a>() { <span class="keywordflow">return</span> _vatom.begin(); }
<a name="l00640"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a81afb84c73fe3e57e8edd5a472e175f6">00640</a> <a class="code" href="namespaceOpenBabel.shtml#aed11ccd81d7abaccbdf10486a5ae0402" title="A standard iterator over a vector of atoms.">OBAtomIterator</a> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a81afb84c73fe3e57e8edd5a472e175f6">EndAtoms</a>() { <span class="keywordflow">return</span> _vatom.begin() + NumAtoms() ; }
<a name="l00642"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#ac4ea48df79e239b506d3501dd42adde9">00642</a> <a class="code" href="namespaceOpenBabel.shtml#a54495d3eb8f9749d0237e6bda59e0abe" title="A standard iterator over a vector of bonds.">OBBondIterator</a> <a class="code" href="classOpenBabel_1_1OBMol.shtml#ac4ea48df79e239b506d3501dd42adde9">BeginBonds</a>() { <span class="keywordflow">return</span> _vbond.begin(); }
<a name="l00644"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a87859f951e8ea33345b76d93014486c9">00644</a> <a class="code" href="namespaceOpenBabel.shtml#a54495d3eb8f9749d0237e6bda59e0abe" title="A standard iterator over a vector of bonds.">OBBondIterator</a> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a87859f951e8ea33345b76d93014486c9">EndBonds</a>() { <span class="keywordflow">return</span> _vbond.begin() + NumBonds() ; }
<a name="l00646"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a35e5693cfdc3b993440d29540ab0509d">00646</a> <a class="code" href="namespaceOpenBabel.shtml#aa52bc907b6b29c913a85671c48ff8ad7" title="A standard iterator over a vector of residues.">OBResidueIterator</a> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a35e5693cfdc3b993440d29540ab0509d">BeginResidues</a>() { <span class="keywordflow">return</span> _residue.begin(); }
<a name="l00648"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a62b81baba8ee7151f0aae8fb01e90358">00648</a> <a class="code" href="namespaceOpenBabel.shtml#aa52bc907b6b29c913a85671c48ff8ad7" title="A standard iterator over a vector of residues.">OBResidueIterator</a> <a class="code" href="classOpenBabel_1_1OBMol.shtml#a62b81baba8ee7151f0aae8fb01e90358">EndResidues</a>() { <span class="keywordflow">return</span> _residue.end(); }
<a name="l00649"></a>00649
<a name="l00652"></a>00652 <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *BeginAtom(<a class="code" href="namespaceOpenBabel.shtml#aed11ccd81d7abaccbdf10486a5ae0402" title="A standard iterator over a vector of atoms.">OBAtomIterator</a> &i);
<a name="l00655"></a>00655 <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *NextAtom(<a class="code" href="namespaceOpenBabel.shtml#aed11ccd81d7abaccbdf10486a5ae0402" title="A standard iterator over a vector of atoms.">OBAtomIterator</a> &i);
<a name="l00658"></a>00658 <a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *BeginBond(<a class="code" href="namespaceOpenBabel.shtml#a54495d3eb8f9749d0237e6bda59e0abe" title="A standard iterator over a vector of bonds.">OBBondIterator</a> &i);
<a name="l00661"></a>00661 <a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *NextBond(<a class="code" href="namespaceOpenBabel.shtml#a54495d3eb8f9749d0237e6bda59e0abe" title="A standard iterator over a vector of bonds.">OBBondIterator</a> &i);
<a name="l00664"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a49f6fa37f54e72323ae1b9597fdca02e">00664</a> <a class="code" href="classOpenBabel_1_1OBResidue.shtml" title="Residue information.">OBResidue</a> *BeginResidue(<a class="code" href="namespaceOpenBabel.shtml#aa52bc907b6b29c913a85671c48ff8ad7" title="A standard iterator over a vector of residues.">OBResidueIterator</a> &i)
<a name="l00665"></a>00665 {
<a name="l00666"></a>00666 i = _residue.begin();
<a name="l00667"></a>00667 <span class="keywordflow">return</span>((i == _residue.end()) ? NULL:*i);
<a name="l00668"></a>00668 }
<a name="l00671"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#af3747253310ab328967a8bcaf32842d3">00671</a> <a class="code" href="classOpenBabel_1_1OBResidue.shtml" title="Residue information.">OBResidue</a> *NextResidue(<a class="code" href="namespaceOpenBabel.shtml#aa52bc907b6b29c913a85671c48ff8ad7" title="A standard iterator over a vector of residues.">OBResidueIterator</a> &i)
<a name="l00672"></a>00672 {
<a name="l00673"></a>00673 ++i;
<a name="l00674"></a>00674 <span class="keywordflow">return</span>((i == _residue.end()) ? NULL:*i);
<a name="l00675"></a>00675 }
<a name="l00679"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a67c061a9d850cf30b4bf5ea394760d43">00679</a> <a class="code" href="classOpenBabel_1_1OBInternalCoord.shtml" title="Used to transform from z-matrix to cartesian coordinates.">OBInternalCoord</a> *BeginInternalCoord(std::vector<OBInternalCoord*>::iterator &i)
<a name="l00680"></a>00680 {
<a name="l00681"></a>00681 i = _internals.begin();
<a name="l00682"></a>00682 <span class="keywordflow">return</span>((i == _internals.end()) ? NULL:*i);
<a name="l00683"></a>00683 }
<a name="l00687"></a><a class="code" href="classOpenBabel_1_1OBMol.shtml#a6680c695e3cdceb7e42a554a0ffc8a19">00687</a> <a class="code" href="classOpenBabel_1_1OBInternalCoord.shtml" title="Used to transform from z-matrix to cartesian coordinates.">OBInternalCoord</a> *NextInternalCoord(std::vector<OBInternalCoord*>::iterator &i)
<a name="l00688"></a>00688 {
<a name="l00689"></a>00689 ++i;
<a name="l00690"></a>00690 <span class="keywordflow">return</span>((i == _internals.end()) ? NULL:*i);
<a name="l00691"></a>00691 }
<a name="l00693"></a>00693
<a name="l00694"></a>00694 };
<a name="l00695"></a>00695
<a name="l00696"></a>00696 <span class="comment">// Utility function prototypes</span>
<a name="l00697"></a>00697 <span class="comment">//tokenize and Trim declarations moved to base.h</span>
<a name="l00698"></a>00698 <span class="comment">// Deprecated -- use OBMessageHandler class instead (docs in obutil.cpp)</span>
<a name="l00699"></a>00699 OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a32ba50e0b43cb1dfdf1978d1e72099c5">ThrowError</a>(<span class="keywordtype">char</span> *str);
<a name="l00700"></a>00700 <span class="comment">// Deprecated -- use OBMessageHandler class instead (docs in obutil.cpp)</span>
<a name="l00701"></a>00701 OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a32ba50e0b43cb1dfdf1978d1e72099c5">ThrowError</a>(std::string &str);
<a name="l00703"></a>00703 OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a7145217d4de73e243d2d3888dac404ba" title="Convert Cartesian XYZ to a set of OBInternalCoord coordinates.">CartesianToInternal</a>(std::vector<OBInternalCoord*>&,OBMol&);
<a name="l00705"></a>00705 OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#ae82e7b7b74e5212eada681c15afb77f4" title="Convert set of OBInternalCoord coordinates into Cartesian XYZ.">InternalToCartesian</a>(std::vector<OBInternalCoord*>&,OBMol&);
<a name="l00706"></a>00706 <span class="comment">// Replace the last extension in str with a new one (docs in obutil.cpp)</span>
<a name="l00707"></a>00707 OBAPI std::string <a class="code" href="namespaceOpenBabel.shtml#ac1c62bdae6cf7a9195c470e7d0e29883" title="Utility function: replace the last extension in string &src with new extension char *ext...">NewExtension</a>(std::string&,<span class="keywordtype">char</span>*);
<a name="l00708"></a>00708
<a name="l00709"></a>00709 <span class="comment">//global definitions</span>
<a name="l00711"></a><a class="code" href="namespaceOpenBabel.shtml#a1e53ca6bf87ac2f6447c9ef2332c9418">00711</a> <span class="comment"></span> EXTERN <a class="code" href="classOpenBabel_1_1OBElementTable.shtml" title="Periodic Table of the Elements.">OBElementTable</a> <a class="code" href="namespaceOpenBabel.shtml#a1e53ca6bf87ac2f6447c9ef2332c9418" title="Global OBElementTable for element properties.">etab</a>;
<a name="l00714"></a><a class="code" href="namespaceOpenBabel.shtml#ab8d4d5690031703bcccb95ddbe7ebf0a">00714</a> EXTERN <a class="code" href="classOpenBabel_1_1OBTypeTable.shtml" title="Atom Type Translation Table.">OBTypeTable</a> <a class="code" href="namespaceOpenBabel.shtml#ab8d4d5690031703bcccb95ddbe7ebf0a">ttab</a>;
<a name="l00716"></a><a class="code" href="namespaceOpenBabel.shtml#a35082995377e56142ee5a9fd351c7a70">00716</a> EXTERN <a class="code" href="classOpenBabel_1_1OBIsotopeTable.shtml" title="Table of atomic isotope masses.">OBIsotopeTable</a> <a class="code" href="namespaceOpenBabel.shtml#a35082995377e56142ee5a9fd351c7a70" title="Global OBIsotopeTable for isotope properties.">isotab</a>;
<a name="l00718"></a><a class="code" href="namespaceOpenBabel.shtml#a36c0ee580e088fa888f7d96c16e969bd">00718</a> EXTERN <a class="code" href="classOpenBabel_1_1OBAromaticTyper.shtml" title="Assigns aromatic typing to atoms and bonds.">OBAromaticTyper</a> <a class="code" href="namespaceOpenBabel.shtml#a36c0ee580e088fa888f7d96c16e969bd" title="Global OBAromaticTyper for detecting aromatic atoms and bonds.">aromtyper</a>;
<a name="l00721"></a><a class="code" href="namespaceOpenBabel.shtml#a717e026b570e71d0e648d851d34b6482">00721</a> EXTERN <a class="code" href="classOpenBabel_1_1OBAtomTyper.shtml" title="Assigns atom types, hybridization, implicit valence and formal charges.">OBAtomTyper</a> <a class="code" href="namespaceOpenBabel.shtml#a717e026b570e71d0e648d851d34b6482">atomtyper</a>;
<a name="l00723"></a><a class="code" href="namespaceOpenBabel.shtml#ab81925dbd111f3bf1733a4cbba547131">00723</a> EXTERN <a class="code" href="classOpenBabel_1_1OBChainsParser.shtml" title="Perceives peptide or nucleotide chains and residues in an OBMol.">OBChainsParser</a> <a class="code" href="namespaceOpenBabel.shtml#ab81925dbd111f3bf1733a4cbba547131" title="Global OBChainsParser for detecting macromolecular chains and residues.">chainsparser</a>;
<a name="l00725"></a>00725 OBERROR <span class="keyword">extern</span> <a class="code" href="classOpenBabel_1_1OBMessageHandler.shtml" title="Handle error messages, warnings, debugging information and the like.">OBMessageHandler</a> <a class="code" href="namespaceOpenBabel.shtml#a394eef44b3dd6a9174067715712c2d16" title="Global OBMessageHandler error handler.">obErrorLog</a>;
<a name="l00727"></a><a class="code" href="namespaceOpenBabel.shtml#a30154f62f3bd1a1b8613a080444e69d7">00727</a> EXTERN <a class="code" href="classOpenBabel_1_1OBResidueData.shtml" title="Table of common biomolecule residues (for PDB or other files).">OBResidueData</a> <a class="code" href="namespaceOpenBabel.shtml#a30154f62f3bd1a1b8613a080444e69d7" title="Global OBResidueData biomolecule residue database.">resdat</a>;
<a name="l00728"></a>00728
<a name="l00730"></a><a class="code" href="namespaceOpenBabel_1_1detail.shtml">00730</a> <span class="keyword">namespace </span>detail {
<a name="l00733"></a>00733 <span class="keyword">template</span><<span class="keyword">typename</span> T, <span class="keywordtype">int</span> size = sizeof(T)>
<a name="l00734"></a><a class="code" href="structOpenBabel_1_1detail_1_1max__value.shtml">00734</a> <span class="keyword">struct </span><a class="code" href="structOpenBabel_1_1detail_1_1max__value.shtml" title="a C++ template to return the maximum value of a type (e.g., int)">max_value</a>
<a name="l00735"></a>00735 {
<a name="l00736"></a><a class="code" href="structOpenBabel_1_1detail_1_1max__value.shtml#ac7d461ddec7ac180a645b11e023314a8">00736</a> <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="namespaceOpenBabel_1_1OBResidueIndex.shtml#abc5c98fcc1211af2b80116dd6e0a035da21f40778b7db9343a6ca75ec2c41ccce">T</a> <a class="code" href="structOpenBabel_1_1detail_1_1max__value.shtml#ac7d461ddec7ac180a645b11e023314a8">result</a> = (<span class="keyword">static_cast<</span><a class="code" href="namespaceOpenBabel_1_1OBResidueIndex.shtml#abc5c98fcc1211af2b80116dd6e0a035da21f40778b7db9343a6ca75ec2c41ccce">T</a><span class="keyword">></span>(0xFF) << (size-1)*8) + <a class="code" href="structOpenBabel_1_1detail_1_1max__value.shtml" title="a C++ template to return the maximum value of a type (e.g., int)">max_value<T, size-1>::result</a>;
<a name="l00737"></a>00737 };
<a name="l00738"></a>00738
<a name="l00740"></a>00740 <span class="keyword">template</span><<span class="keyword">typename</span> T>
<a name="l00741"></a><a class="code" href="structOpenBabel_1_1detail_1_1max__value_3_01T_00_010_01_4.shtml">00741</a> <span class="keyword">struct </span><a class="code" href="structOpenBabel_1_1detail_1_1max__value.shtml" title="a C++ template to return the maximum value of a type (e.g., int)">max_value</a><<a class="code" href="namespaceOpenBabel_1_1OBResidueIndex.shtml#abc5c98fcc1211af2b80116dd6e0a035da21f40778b7db9343a6ca75ec2c41ccce">T</a>, 0>
<a name="l00742"></a>00742 {
<a name="l00743"></a><a class="code" href="structOpenBabel_1_1detail_1_1max__value_3_01T_00_010_01_4.shtml#ac7d461ddec7ac180a645b11e023314a8">00743</a> <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="namespaceOpenBabel_1_1OBResidueIndex.shtml#abc5c98fcc1211af2b80116dd6e0a035da21f40778b7db9343a6ca75ec2c41ccce">T</a> <a class="code" href="structOpenBabel_1_1detail_1_1max__value.shtml#ac7d461ddec7ac180a645b11e023314a8">result</a> = 0;
<a name="l00744"></a>00744 };
<a name="l00745"></a>00745 }
<a name="l00746"></a>00746
<a name="l00747"></a>00747 <span class="comment">// No unique id</span>
<a name="l00748"></a><a class="code" href="namespaceOpenBabel.shtml#a99dab86ea7c23d635f350a07644c16a6">00748</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <a class="code" href="namespaceOpenBabel.shtml#a99dab86ea7c23d635f350a07644c16a6">NoId</a> = <a class="code" href="structOpenBabel_1_1detail_1_1max__value.shtml" title="a C++ template to return the maximum value of a type (e.g., int)">detail::max_value<unsigned long>::result</a>;
<a name="l00749"></a>00749
<a name="l00750"></a>00750 <span class="comment">//Utility Macros</span>
<a name="l00751"></a>00751
<a name="l00752"></a>00752 <span class="preprocessor">#ifndef BUFF_SIZE</span>
<a name="l00753"></a><a class="code" href="mol_8h.shtml#a6c7cd32e1bac137f05e4a752b4ad10af">00753</a> <span class="preprocessor"></span><span class="preprocessor">#define BUFF_SIZE 32768</span>
<a name="l00754"></a>00754 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
<a name="l00755"></a>00755 <span class="preprocessor"></span>
<a name="l00756"></a>00756 <span class="preprocessor">#ifndef EQ</span>
<a name="l00757"></a><a class="code" href="mol_8h.shtml#ac07acfbb082b04f5bea72998c8976b3c">00757</a> <span class="preprocessor"></span><span class="preprocessor">#define EQ(a,b) (!strcmp((a), (b)))</span>
<a name="l00758"></a>00758 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
<a name="l00759"></a>00759 <span class="preprocessor"></span>
<a name="l00760"></a>00760 <span class="preprocessor">#ifndef EQn</span>
<a name="l00761"></a><a class="code" href="mol_8h.shtml#aff7047a291906910f63dcfc17c88ed12">00761</a> <span class="preprocessor"></span><span class="preprocessor">#define EQn(a,b,n) (!strncmp((a), (b), (n)))</span>
<a name="l00762"></a>00762 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
<a name="l00763"></a>00763 <span class="preprocessor"></span>
<a name="l00764"></a>00764 <span class="preprocessor">#ifndef SQUARE</span>
<a name="l00765"></a><a class="code" href="mol_8h.shtml#aa1cf70a99e21bc2032e8867c6cafbb43">00765</a> <span class="preprocessor"></span><span class="preprocessor">#define SQUARE(x) ((x)*(x))</span>
<a name="l00766"></a>00766 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
<a name="l00767"></a>00767 <span class="preprocessor"></span>
<a name="l00768"></a>00768 <span class="preprocessor">#ifndef IsUnsatType</span>
<a name="l00769"></a><a class="code" href="mol_8h.shtml#ae7364e14af885f05220a63486ca6d516">00769</a> <span class="preprocessor"></span><span class="preprocessor">#define IsUnsatType(x) (EQ(x,"Car") || EQ(x,"C2") || EQ(x,"Sox") || EQ(x,"Sac") || EQ(x,"Pac") || EQ(x,"So2"))</span>
<a name="l00770"></a>00770 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
<a name="l00771"></a>00771 <span class="preprocessor"></span>
<a name="l00772"></a>00772 <span class="preprocessor">#ifndef __KCC</span>
<a name="l00773"></a>00773 <span class="preprocessor"></span> <span class="keyword">extern</span> <span class="stringliteral">"C"</span>
<a name="l00774"></a>00774 {
<a name="l00775"></a>00775 OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a8aa7959b427e1c630f14732c2ad642c8">get_rmat</a>(<span class="keywordtype">double</span>*,<span class="keywordtype">double</span>*,<span class="keywordtype">double</span>*,<span class="keywordtype">int</span>);
<a name="l00776"></a>00776 OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a7e02cd2874a2a4826c8587da507f62ef">ob_make_rmat</a>(<span class="keywordtype">double</span> mat[3][3],<span class="keywordtype">double</span> rmat[9]);
<a name="l00777"></a>00777 OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a594933a93529376dbae80405cf23afa8">qtrfit</a> (<span class="keywordtype">double</span> *r,<span class="keywordtype">double</span> *f,<span class="keywordtype">int</span> size,<span class="keywordtype">double</span> u[3][3]);
<a name="l00778"></a>00778 OBAPI <span class="keywordtype">double</span> <a class="code" href="namespaceOpenBabel.shtml#a2c5374c2c0b42dee2fd36cd475a3cb1c">superimpose</a>(<span class="keywordtype">double</span>*,<span class="keywordtype">double</span>*,<span class="keywordtype">int</span>);
<a name="l00779"></a>00779 }
<a name="l00780"></a>00780 <span class="preprocessor">#else</span>
<a name="l00781"></a>00781 <span class="preprocessor"></span> OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a8aa7959b427e1c630f14732c2ad642c8">get_rmat</a>(<span class="keywordtype">double</span>*,<span class="keywordtype">double</span>*,<span class="keywordtype">double</span>*,<span class="keywordtype">int</span>);
<a name="l00782"></a>00782 OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a7e02cd2874a2a4826c8587da507f62ef">ob_make_rmat</a>(<span class="keywordtype">double</span> mat[3][3],<span class="keywordtype">double</span> rmat[9]);
<a name="l00783"></a>00783 OBAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenBabel.shtml#a594933a93529376dbae80405cf23afa8">qtrfit</a> (<span class="keywordtype">double</span> *r,<span class="keywordtype">double</span> *f,<span class="keywordtype">int</span> size,<span class="keywordtype">double</span> u[3][3]);
<a name="l00784"></a>00784 OBAPI <span class="keywordtype">double</span> <a class="code" href="namespaceOpenBabel.shtml#a2c5374c2c0b42dee2fd36cd475a3cb1c">superimpose</a>(<span class="keywordtype">double</span>*,<span class="keywordtype">double</span>*,<span class="keywordtype">int</span>);
<a name="l00785"></a>00785 <span class="preprocessor">#endif // __KCC</span>
<a name="l00786"></a>00786 <span class="preprocessor"></span>
<a name="l00787"></a>00787 <span class="comment">// extern OBMol* (*CreateMolecule) (void);</span>
<a name="l00788"></a>00788
<a name="l00789"></a>00789 } <span class="comment">// end namespace OpenBabel</span>
<a name="l00790"></a>00790
<a name="l00791"></a>00791 <span class="preprocessor">#endif // OB_MOL_H</span>
<a name="l00792"></a>00792 <span class="preprocessor"></span>
</pre></div></div>
</div>
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