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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<title>OBOp Class Reference</title>
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<li class="navelem"><a class="el" href="namespaceOpenBabel.shtml">OpenBabel</a> </li>
<li class="navelem"><a class="el" href="classOpenBabel_1_1OBOp.shtml">OBOp</a> </li>
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<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pub-static-methods">Static Public Member Functions</a> |
<a href="#pro-static-methods">Static Protected Member Functions</a> |
<a href="#pro-attribs">Protected Attributes</a> </div>
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<div class="title">OBOp Class Reference</div> </div>
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<!-- doxytag: class="OpenBabel::OBOp" --><!-- doxytag: inherits="OpenBabel::OBPlugin" -->
<p><code>#include <<a class="el" href="op_8h_source.shtml">openbabel/op.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for OBOp:</div>
<div class="dyncontent">
<div class="center"><img src="classOpenBabel_1_1OBOp__inherit__graph.png" border="0" usemap="#OBOp_inherit__map" alt="Inheritance graph"/></div>
<map name="OBOp_inherit__map" id="OBOp_inherit__map">
<area shape="rect" id="node5" href="classOpenBabel_1_1OpTransform.shtml" title="Applies molecular reactions/transforms (OBChemTsfm class) read from a datafile." alt="" coords="5,160,112,189"/><area shape="rect" id="node2" href="classOpenBabel_1_1OBPlugin.shtml" title="Base class for all types of dynamic classes discovered at runtime." alt="" coords="17,5,100,35"/></map>
<center><span class="legend">[<a href="graph_legend.shtml">legend</a>]</span></center></div>
<p><a href="classOpenBabel_1_1OBOp-members.shtml">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef const std::map<br class="typebreak"/>
< std::string, std::string > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBOp.shtml#a4e98002937e35472f2b829eaf98913d3">OpMap</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef std::map< const char <br class="typebreak"/>
*, <a class="el" href="classOpenBabel_1_1OBPlugin.shtml">OBPlugin</a> *, <a class="el" href="structOpenBabel_1_1CharPtrLess.shtml">CharPtrLess</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
PluginMapType::const_iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga8fac85f5497f873a2dd8734b47f0bdc0">PluginIterator</a></td></tr>
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBOp.shtml#a45dfda1fb13d3c26ab7f8f7631e3351c">TypeID</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBOp.shtml#ad1f068b2923689e4c4c48a76a3e885e4">Do</a> (<a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> *pOb, const char *OptionText=NULL, <a class="el" href="classOpenBabel_1_1OBOp.shtml#a4e98002937e35472f2b829eaf98913d3">OpMap</a> *pOptions=NULL, <a class="el" href="classOpenBabel_1_1OBConversion.shtml">OBConversion</a> *pConv=NULL)=0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBOp.shtml#a841238ff5ff03c1c9341dea0105469c6">WorksWith</a> (<a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> *pOb) const =0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBOp.shtml#ad3d67611882dee42047de32adf603602">ProcessVec</a> (std::vector< <a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> * > &)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga4a6b8d1611d5d963fc29982cc1ebcbf7">Description</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gae0859fdbf134af95a8231eb32c73b7db">Display</a> (std::string &txt, const char *param, const char *ID=NULL)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenBabel_1_1OBPlugin.shtml">OBPlugin</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga9399e9568ab809d714385f1b237a9335">MakeInstance</a> (const std::vector< std::string > &)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga3e0b39e1326de703012f81ac2be7feba">Init</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga753a34173c6750388d33e5294556790f">GetID</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gaabc1385cbe63145ffec6edf1f2c3be98">GetMap</a> () const =0</td></tr>
<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBOp.shtml#a64e598f68f30107a74319b9fc6d26cd0">OpOptions</a> (<a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> *pOb)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBOp.shtml#a139b43c8cee15687f02550c031e558d7">DoOps</a> (<a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> *pOb, <a class="el" href="classOpenBabel_1_1OBOp.shtml#a4e98002937e35472f2b829eaf98913d3">OpMap</a> *pOptions, <a class="el" href="classOpenBabel_1_1OBConversion.shtml">OBConversion</a> *pConv)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenBabel_1_1OBPlugin.shtml">OBPlugin</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga295dc7f1b94da710821c562bff3e7c97">GetPlugin</a> (const char *Type, const char *ID)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static bool </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gaf95953a5793333ba51e978c4a0a00103">ListAsVector</a> (const char *PluginID, const char *param, std::vector< std::string > &vlist)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga9fabfd2513038ae6ac475ac0ff2c73cd">List</a> (const char *PluginID, const char *param=NULL, std::ostream *os=&std::cout)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gaba22c5352d36c7f058299af7ddffb03e">ListAsString</a> (const char *PluginID, const char *param=NULL)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga84fc973fdf4bba5a6b0e2d402077991c">FirstLine</a> (const char *txt)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__plugins.shtml#ga8fac85f5497f873a2dd8734b47f0bdc0">PluginIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga1d4d73999ab0518ee471c635bd0a7e87">Begin</a> (const char *PluginID)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__plugins.shtml#ga8fac85f5497f873a2dd8734b47f0bdc0">PluginIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga9a330280c1cd2e7119dac87a6fd0b762">End</a> (const char *PluginID)</td></tr>
<tr><td colspan="2"><h2><a name="pro-static-methods"></a>
Static Protected Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gac40457336d7b12bb632b4ac4e8955a3a">PluginMap</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gadfcf9fda27cfbc4301fc94517a4250ef">GetTypeMap</a> (const char *PluginID)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenBabel_1_1OBPlugin.shtml">OBPlugin</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga1e58b1811ec8c1b88254ee46ccef0b78">BaseFindType</a> (<a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a> &Map, const char *ID)</td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga1f8d25dafb0bc13814ca451035f67955">_id</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Operations to modify molecules before output. </p>
<dl class="since"><dt><b>Since:</b></dt><dd>version 2.2</dd></dl>
<p>Classes derived from <a class="el" href="classOpenBabel_1_1OBOp.shtml" title="Operations to modify molecules before output.">OBOp</a> implement options for the babel program (for both its commandline and GUI interfaces). It is intended for options that carry out some modification on the molecule(or reaction) after it has been input, but before it is output. An example is the --center option implemented in the OpCenter class in ops.cpp, which is a duplicate of the built in -c option for centering coordinates.</p>
<p>The advantage of plugin classes is that no existing code has to be modified when a new class is added. You can list those that are present by babel -L ops or from a menu item in the GUI.</p>
<p>Any <a class="el" href="classOpenBabel_1_1OBOp.shtml" title="Operations to modify molecules before output.">OBOp</a> derived class has to have a constructor, a function returning a short description, and a <a class="el" href="classOpenBabel_1_1OBOp.shtml#ad1f068b2923689e4c4c48a76a3e885e4" title="Required function that does the work. Normally return true, unless object is not to be output...">Do()</a> function which does the work. It also needs a <a class="el" href="classOpenBabel_1_1OBOp.shtml#a841238ff5ff03c1c9341dea0105469c6">WorksWith()</a> function which is always the same when operating on <a class="el" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> objects. (It is not made a default to reducecode dependencies.) A single global instance of the class needs to be instantiated to define the ID, by which the class is subsequently accessed.</p>
<p><a class="el" href="classOpenBabel_1_1OBOp.shtml" title="Operations to modify molecules before output.">OBOp</a> works by two of its static functions being called from code in <a class="el" href="transform_8cpp.shtml" title="Perform command-line requested transformations for OBMol and SMARTS filtering.">transform.cpp</a>:</p>
<ul>
<li>OpOptions(OBBase* pOb, OpMap* pOptions) returns a string describing each of the derivated classes relevant to objects of the class of the <a class="el" href="classOpenBabel_1_1OBBase.shtml" title="Base Class.">OBBase</a> parameter, for use in the help text and to set checkboxes in the GUI;</li>
<li>DoOps(OBBase* pOb) applies each option whose ID is listed in the Opmap parameter to the object (ususally an <a class="el" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>) in the <a class="el" href="classOpenBabel_1_1OBBase.shtml" title="Base Class.">OBBase</a> parameter.</li>
</ul>
<p>Options which need parameters are passed these (space delimited) in the text parameter of the <a class="el" href="classOpenBabel_1_1OBOp.shtml#ad1f068b2923689e4c4c48a76a3e885e4" title="Required function that does the work. Normally return true, unless object is not to be output...">Do()</a> function. They can also access other general options specified on the command line by examining the the OpMap parameter.</p>
<p>To use an <a class="el" href="classOpenBabel_1_1OBOp.shtml" title="Operations to modify molecules before output.">OBOp</a> class from the API it is necessary to use an extra step in case it isn't present. So to apply the <a class="el" href="classOpenBabel_1_1OBOp.shtml" title="Operations to modify molecules before output.">OBOp</a> clas with ID gen3D to your mol</p>
<p>OBOp* pOp = OBOp::FindType("gen3D"); if(!pOp) ...report error pOp->Do(mol); </p>
</div><hr/><h2>Member Typedef Documentation</h2>
<a class="anchor" id="a4e98002937e35472f2b829eaf98913d3"></a><!-- doxytag: member="OpenBabel::OBOp::OpMap" ref="a4e98002937e35472f2b829eaf98913d3" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">typedef const std::map<std::string, std::string> <a class="el" href="classOpenBabel_1_1OBOp.shtml#a4e98002937e35472f2b829eaf98913d3">OpMap</a></td>
</tr>
</table>
</div>
<div class="memdoc">
</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a45dfda1fb13d3c26ab7f8f7631e3351c"></a><!-- doxytag: member="OpenBabel::OBOp::TypeID" ref="a45dfda1fb13d3c26ab7f8f7631e3351c" args="()" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
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<td class="memname">virtual const char* TypeID </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td><code> [inline, virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Provides the name of this kind of plugin. Use -L "ops" to list from commandline. </p>
<p>Reimplemented from <a class="el" href="group__plugins.shtml#ga45dfda1fb13d3c26ab7f8f7631e3351c">OBPlugin</a>.</p>
</div>
</div>
<a class="anchor" id="ad1f068b2923689e4c4c48a76a3e885e4"></a><!-- doxytag: member="OpenBabel::OBOp::Do" ref="ad1f068b2923689e4c4c48a76a3e885e4" args="(OBBase *pOb, const char *OptionText=NULL, OpMap *pOptions=NULL, OBConversion *pConv=NULL)=0" -->
<div class="memitem">
<div class="memproto">
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<td class="memname">virtual bool Do </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> * </td>
<td class="paramname"><em>pOb</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>OptionText</em> = <code>NULL</code>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBOp.shtml#a4e98002937e35472f2b829eaf98913d3">OpMap</a> * </td>
<td class="paramname"><em>pOptions</em> = <code>NULL</code>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBConversion.shtml">OBConversion</a> * </td>
<td class="paramname"><em>pConv</em> = <code>NULL</code> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td><code> [pure virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Required function that does the work. Normally return true, unless object is not to be output. </p>
<p>Implemented in <a class="el" href="classOpenBabel_1_1OpTransform.shtml#a6d16b63b2ed4cf1fe9c8038388d3b4db">OpTransform</a>.</p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBOp.shtml#a139b43c8cee15687f02550c031e558d7">OBOp::DoOps()</a>.</p>
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<a class="anchor" id="a841238ff5ff03c1c9341dea0105469c6"></a><!-- doxytag: member="OpenBabel::OBOp::WorksWith" ref="a841238ff5ff03c1c9341dea0105469c6" args="(OBBase *pOb) const =0" -->
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<td class="memname">virtual bool WorksWith </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> * </td>
<td class="paramname"><em>pOb</em></td><td>)</td>
<td> const<code> [pure virtual]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>true if this op is designed to work with the class of pOb, e.g. <a class="el" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> </dd></dl>
<p>Implemented in <a class="el" href="classOpenBabel_1_1OpTransform.shtml#a1ca500aeb02418c2928d551c55d4efc1">OpTransform</a>.</p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBOp.shtml#a64e598f68f30107a74319b9fc6d26cd0">OBOp::OpOptions()</a>.</p>
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<a class="anchor" id="ad3d67611882dee42047de32adf603602"></a><!-- doxytag: member="OpenBabel::OBOp::ProcessVec" ref="ad3d67611882dee42047de32adf603602" args="(std::vector< OBBase * > &)" -->
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<td class="memname">virtual bool ProcessVec </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> * > & </td>
<td class="paramname"></td><td>)</td>
<td><code> [inline, virtual]</code></td>
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<p>Do something with an array of objects. Used a a callback routine in OpSort, etc. </p>
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<a class="anchor" id="a64e598f68f30107a74319b9fc6d26cd0"></a><!-- doxytag: member="OpenBabel::OBOp::OpOptions" ref="a64e598f68f30107a74319b9fc6d26cd0" args="(OBBase *pOb)" -->
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<td class="memname">static std::string OpOptions </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> * </td>
<td class="paramname"><em>pOb</em></td><td>)</td>
<td><code> [inline, static]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>string describing options, for display with -H and to make checkboxes in GUI </dd></dl>
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<a class="anchor" id="a139b43c8cee15687f02550c031e558d7"></a><!-- doxytag: member="OpenBabel::OBOp::DoOps" ref="a139b43c8cee15687f02550c031e558d7" args="(OBBase *pOb, OpMap *pOptions, OBConversion *pConv)" -->
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<td class="memname">static bool DoOps </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> * </td>
<td class="paramname"><em>pOb</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBOp.shtml#a4e98002937e35472f2b829eaf98913d3">OpMap</a> * </td>
<td class="paramname"><em>pOptions</em>, </td>
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<td></td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBConversion.shtml">OBConversion</a> * </td>
<td class="paramname"><em>pConv</em> </td>
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<td>)</td>
<td></td><td><code> [inline, static]</code></td>
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<p>Call <a class="el" href="classOpenBabel_1_1OBOp.shtml#ad1f068b2923689e4c4c48a76a3e885e4" title="Required function that does the work. Normally return true, unless object is not to be output...">Do()</a> of all the OBOps whose ID is a key in the map. Called from DoTransformations(). The map has general options like -x or --multicharoption The key is the option name and the value, if any, is text which follows the option name. In some cases, there may be several parameters, space separated) </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>false indicating object should not be output, if any <a class="el" href="classOpenBabel_1_1OBOp.shtml#ad1f068b2923689e4c4c48a76a3e885e4" title="Required function that does the work. Normally return true, unless object is not to be output...">Do()</a> returns false </dd></dl>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="op_8h_source.shtml">op.h</a></li>
</ul>
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