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<p><code>#include <<a class="el" href="fingerprint_8h_source.shtml">openbabel/fingerprint.h</a>></code></p>
<p><a href="classOpenBabel_1_1FastSearch-members.shtml">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1FastSearch.shtml#a4f4f7dec3fe4bb72fc8c8da2594c5787">ReadIndexFile</a> (std::string IndexFilename)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1FastSearch.shtml#a5a306c0d134e330a1d33ae0a6cbc10a1">ReadIndex</a> (std::istream *pIndexstream)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1FastSearch.shtml#a2d2d75247574ce3d0f7bbc0d4283b3c2">~FastSearch</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1FastSearch.shtml#a575cc7caa2b2a42bec8b47e7c0206a80">Find</a> (<a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> *pOb, std::vector< unsigned int > &SeekPositions, unsigned int MaxCandidates)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1FastSearch.shtml#a96dcab8b2694f95817af39be06f20d53">FindMatch</a> (<a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> *pOb, std::vector< unsigned int > &SeekPositions, unsigned int MaxCandidates)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1FastSearch.shtml#aff36c0fb2899c7d30277788ddc536340">FindSimilar</a> (<a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> *pOb, std::multimap< double, unsigned int > &SeekposMap, double MinTani, double MaxTani=1.1)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1FastSearch.shtml#af660415f38248e3b885bb22dc7805558">FindSimilar</a> (<a class="el" href="classOpenBabel_1_1OBBase.shtml">OBBase</a> *pOb, std::multimap< double, unsigned int > &SeekposMap, int nCandidates=0)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenBabel_1_1OBFingerprint.shtml">OBFingerprint</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1FastSearch.shtml#a753d677380f29e219da02952b7ef7430">GetFingerprint</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const <a class="el" href="structOpenBabel_1_1FptIndexHeader.shtml">FptIndexHeader</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1FastSearch.shtml#a6c00d74d4b0859279a48173737b1f8b1">GetIndexHeader</a> () const </td></tr>
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<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Class to search fingerprint index files. </p>
<p>The <a class="el" href="classOpenBabel_1_1FastSearch.shtml" title="Class to search fingerprint index files.">FastSearch</a> class searches an index to a datafile containing a list of molecules (or other objects) prepared by <a class="el" href="classOpenBabel_1_1FastSearchIndexer.shtml" title="Class to prepare fingerprint index files See FastSearch class for details.">FastSearchIndexer</a>.</p>
<p><a class="el" href="namespaceOpenBabel.shtml" title="Global namespace for all Open Babel code.">OpenBabel</a> can also search files for molecules containing a substructure specified by a SMARTS string, using <a class="el" href="classOpenBabel_1_1OBSmartsPattern.shtml" title="SMARTS (SMiles ARbitrary Target Specification) substructure searching.">OBSmartsPattern</a> or from the command line: </p>
<div class="fragment"><pre class="fragment"> babel datafile.xxx -outfile.yyy -sSMARTS
</pre></div><p> But when the data file contains more than about 10,000 molecules this becomes rather too slow to be used interactively. To do it more quickly, an index of the molecules containing their fingerprints (see <a class="el" href="classOpenBabel_1_1OBFingerprint.shtml" title="The base class for fingerprints.">OBFingerprint</a>) is prepared using <a class="el" href="classOpenBabel_1_1FastSearchIndexer.shtml" title="Class to prepare fingerprint index files See FastSearch class for details.">FastSearchIndexer</a>. The indexing process may take a long time but only has to be done once. The index can be searched very quickly with <a class="el" href="classOpenBabel_1_1FastSearch.shtml" title="Class to search fingerprint index files.">FastSearch</a>. Because of the nature of fingerprints a match to a bit does not guarantee the presence of a particular substructure or other molecular property, so that a definitive answer may require a subsequent search of the (much reduced) list of candidates by another method (like <a class="el" href="classOpenBabel_1_1OBSmartsPattern.shtml" title="SMARTS (SMiles ARbitrary Target Specification) substructure searching.">OBSmartsPattern</a>).</p>
<p>Note that the index files are not portable. They need to be prepared on the computer that will access them.</p>
<h4>Using <a class="el" href="classOpenBabel_1_1FastSearch.shtml" title="Class to search fingerprint index files.">FastSearch</a> and <a class="el" href="classOpenBabel_1_1FastSearchIndexer.shtml" title="Class to prepare fingerprint index files See FastSearch class for details.">FastSearchIndexer</a> in a program</h4>
<p>The index has two tables:</p>
<ul>
<li>an array of fingerprints of the molecules</li>
<li>an array of the seek positions in the datasource file of all the molecules</li>
</ul>
<h4>To prepare an fastsearch index <a href="file:">file:</a></h4>
<ul>
<li>Open an ostream to the index file.</li>
<li>Make a <a class="el" href="classOpenBabel_1_1FastSearchIndexer.shtml" title="Class to prepare fingerprint index files See FastSearch class for details.">FastSearchIndexer</a> object on the heap or the stack, passing in as parameters:</li>
<li>the datafile name, the indexfile stream,</li>
<li>the id of the fingerprint type to be used,</li>
<li>the number of bits the fingerprint is to be folded down to, If it is to be left unfolded, set fpid to 0 or do not specify it.</li>
</ul>
<ul>
<li>For each molecule, call Add() with its pointer and its position in the datafile.<br/>
Currently the std::streampos value is implicitly cast to unsigned int so that for 32bit machines the datafile has to be no longer than about 2Gbyte.</li>
<li>The index file is written when the <a class="el" href="classOpenBabel_1_1FastSearchIndexer.shtml" title="Class to prepare fingerprint index files See FastSearch class for details.">FastSearchIndexer</a> object is deleted or goes out of scope.</li>
</ul>
<h4>To search in a fastsearch index file</h4>
<ul>
<li>Open a std::istream to the indexfile (in binary mode on some systems)</li>
<li>Make a <a class="el" href="classOpenBabel_1_1FastSearch.shtml" title="Class to search fingerprint index files.">FastSearch</a> object, read the index and open the datafile whose name it provides <div class="fragment"><pre class="fragment"> ifstream ifs(indexname,ios::binary);
FastSearch fs;
<span class="keywordtype">string</span> datafilename = fs.ReadIndex(&ifs);
<span class="keywordflow">if</span>(datafilename.empty()
<span class="keywordflow">return</span> <span class="keyword">false</span>;
ifstream datastream(datafilename);
<span class="keywordflow">if</span>(!datastream)
<span class="keywordflow">return</span> <span class="keyword">false</span>;
</pre></div></li>
</ul>
<p><b>To do a search for molecules which have all the substructure bits the <a class="el" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> object, patternMol</b> </p>
<div class="fragment"><pre class="fragment"> vector<unsigned int>& SeekPositions;
<span class="keywordflow">if</span>(!fs.Find(patternMol, SeekPositions, MaxCandidates))
<span class="keywordflow">for</span>(itr=SeekPositions.begin();itr!=SeekPositions.end();++itr)
{
datastream.seekg(*itr);
... read the candidate molecule
and subject to more rigorous test <span class="keywordflow">if</span> necessary
}
</pre></div><p><b>To do a similarity search based on the Tanimoto coefficient</b> This is defined as: <br/>
<em>Number of bits set in (patternFP & targetFP)/Number of bits in (patternFP | targetFP)</em><br/>
where the boolean operations between the fingerprints are bitwise<br/>
The Tanimoto coefficient has no absolute meaning and depends on the design of the fingerprint. </p>
<div class="fragment"><pre class="fragment"> multimap<double, unsigned int> SeekposMap;
<span class="comment">// to find n best molecules</span>
fs.FindSimilar(&patternMol, SeekposMap, n);
...or
<span class="comment">// to find molecules with Tanimoto coefficient > MinTani</span>
fs.FindSimilar(&patternMol, SeekposMap, MinTani);
multimap<double, unsigned int>::reverse_iterator itr;
<span class="keywordflow">for</span>(itr=SeekposMap.rbegin();itr!=SeekposMap.rend();++itr)
{
datastream.seekg(itr->second);
<span class="comment">// ... read the candidate molecule</span>
<span class="keywordtype">double</span> tani = itr->first;
}
</pre></div><p>The FastSearchFormat class facilitates the use of these routine from the command line or other front end program. For instance:</p>
<p><b>Prepare an index:</b> </p>
<div class="fragment"><pre class="fragment"> babel datafile.xxx index.fs
</pre></div><p> or </p>
<div class="fragment"><pre class="fragment"> babel datafile.xxx -ofs namedindex
</pre></div><p> With options you can specify:</p>
<ul>
<li>which type of fingerprint to be used, e.g. -xfFP2,</li>
<li>whether it is folded to a specified number of bits, e.g. -xn128 (which should be a power of2)</li>
<li>whether to pre-select the molecules which are indexed:</li>
<li>by structure e.g only ethers and esters, -sCOC</li>
<li>by excluding molecules with bezene rings, -vc1ccccc1</li>
<li>by position in the datafile e.g. only mols 10 to 90, -f10 -l90</li>
</ul>
<p><b>Substructure search</b> in a previously prepared index file </p>
<div class="fragment"><pre class="fragment"> babel index.fs outfile.yyy -sSMILES
</pre></div><p> The datafile can also be used as the input file, provided the input format is specified as fs </p>
<div class="fragment"><pre class="fragment"> babel datafile.xxx outfile.yyy -sSMILES -ifs
</pre></div><p> A "slow" search not using fingerprints would be done on the same data by omitting -ifs. A "slow" search can use SMARTS strings, but the fast search is restricted to the subset which is valid SMILES.</p>
<p>With the -S option, the target can be specified as a molecule in a file of any format </p>
<div class="fragment"><pre class="fragment"> babel datafile.xxx outfile.yyy -Spattern_mol.zzz -ifs
</pre></div><p> These searches have two stages: a fingerprint search which produces a number of candidate molecules and a definitive search which selects from these using SMARTS pattern matching. The maximum number of candidates is 4000 by default but you can change this with an option e.g. -al 8000 (Note that you need the space between l and the number.) If the fingerprint search reaches the maximum number it will not look further and will tell you at what stage it stopped.</p>
<p><b>Similarity search</b> in a previously prepared index file<br/>
This rather done (rather than a substructure search) if the -at option is used, </p>
<div class="fragment"><pre class="fragment"> babel datafile.xxx outfile.yyy -sSMILES -ifs -at0.7
</pre></div><p> for instance</p>
<ul>
<li>-at0.7 will recover all molecules with Tanimoto greater than 0.7</li>
<li>-at15 (no decimal point) will recover the 15 molecules with largest coefficients.</li>
<li>-aa will add the Tanimoto coefficient to the titles of the output molecules.</li>
</ul>
<p>All stages, the indexing, the interpretation of the SMILES string in the -s option, the file in the -S option and the final SMARTS filter convert to <a class="el" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> and apply ConvertDativeBonds(). This ensures thatforms such as[N+]([O-])=O and N(=O)=O are recognized as chemically identical. </p>
</div><hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="a2d2d75247574ce3d0f7bbc0d4283b3c2"></a><!-- doxytag: member="OpenBabel::FastSearch::~FastSearch" ref="a2d2d75247574ce3d0f7bbc0d4283b3c2" args="()" -->
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<td class="memname">virtual ~<a class="el" href="classOpenBabel_1_1FastSearch.shtml">FastSearch</a> </td>
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<td><code> [inline, virtual]</code></td>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a4f4f7dec3fe4bb72fc8c8da2594c5787"></a><!-- doxytag: member="OpenBabel::FastSearch::ReadIndexFile" ref="a4f4f7dec3fe4bb72fc8c8da2594c5787" args="(std::string IndexFilename)" -->
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<td class="memname">string ReadIndexFile </td>
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<td class="paramname"><em>IndexFilename</em></td><td>)</td>
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<p>Loads an index from a file and returns the name of the datafile. </p>
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<a class="anchor" id="a5a306c0d134e330a1d33ae0a6cbc10a1"></a><!-- doxytag: member="OpenBabel::FastSearch::ReadIndex" ref="a5a306c0d134e330a1d33ae0a6cbc10a1" args="(std::istream *pIndexstream)" -->
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<td class="paramname"><em>pIndexstream</em></td><td>)</td>
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<a class="anchor" id="a575cc7caa2b2a42bec8b47e7c0206a80"></a><!-- doxytag: member="OpenBabel::FastSearch::Find" ref="a575cc7caa2b2a42bec8b47e7c0206a80" args="(OBBase *pOb, std::vector< unsigned int > &SeekPositions, unsigned int MaxCandidates)" -->
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<td class="memname">bool Find </td>
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<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="paramname"><em>SeekPositions</em>, </td>
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<p>Does substructure search and returns vector of the file positions of matches. </p>
<p>Finds chemical objects in datafilename (which must previously have been indexed) that have all the same bits set in their fingerprints as in the fingerprint of a pattern object. (Usually a substructure search in molecules.) The type of fingerprint and its degree of folding does not have to be specified here because the values in the index file are used. The positions of the candidate matching molecules in the original datafile are returned. </p>
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<a class="anchor" id="a96dcab8b2694f95817af39be06f20d53"></a><!-- doxytag: member="OpenBabel::FastSearch::FindMatch" ref="a96dcab8b2694f95817af39be06f20d53" args="(OBBase *pOb, std::vector< unsigned int > &SeekPositions, unsigned int MaxCandidates)" -->
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<td class="memname">bool FindMatch </td>
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<p>Similar to <a class="el" href="classOpenBabel_1_1FastSearch.shtml#a575cc7caa2b2a42bec8b47e7c0206a80" title="Does substructure search and returns vector of the file positions of matches.">Find()</a> but all bits of matching fingerprints have to be the same. </p>
<dl class="since"><dt><b>Since:</b></dt><dd>version 2.1 </dd></dl>
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<a class="anchor" id="aff36c0fb2899c7d30277788ddc536340"></a><!-- doxytag: member="OpenBabel::FastSearch::FindSimilar" ref="aff36c0fb2899c7d30277788ddc536340" args="(OBBase *pOb, std::multimap< double, unsigned int > &SeekposMap, double MinTani, double MaxTani=1.1)" -->
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<td class="memname">bool FindSimilar </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">std::multimap< double, unsigned int > & </td>
<td class="paramname"><em>SeekposMap</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">double </td>
<td class="paramname"><em>MinTani</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">double </td>
<td class="paramname"><em>MaxTani</em> = <code>1.1</code> </td>
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<td>)</td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>A multimap containing objects whose Tanimoto coefficients with the target is greater than the value specified. </dd></dl>
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<a class="anchor" id="af660415f38248e3b885bb22dc7805558"></a><!-- doxytag: member="OpenBabel::FastSearch::FindSimilar" ref="af660415f38248e3b885bb22dc7805558" args="(OBBase *pOb, std::multimap< double, unsigned int > &SeekposMap, int nCandidates=0)" -->
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<td class="memname">bool FindSimilar </td>
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<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">std::multimap< double, unsigned int > & </td>
<td class="paramname"><em>SeekposMap</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>nCandidates</em> = <code>0</code> </td>
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<td>)</td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>A multimap containing the nCandidates objects with largest Tanimoto coefficients with the target. </dd></dl>
<p>If nCandidates is zero or omitted the original size of the multimap is used </p>
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<a class="anchor" id="a753d677380f29e219da02952b7ef7430"></a><!-- doxytag: member="OpenBabel::FastSearch::GetFingerprint" ref="a753d677380f29e219da02952b7ef7430" args="() const " -->
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<td class="memname"><a class="el" href="classOpenBabel_1_1OBFingerprint.shtml">OBFingerprint</a>* GetFingerprint </td>
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<td> const<code> [inline]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>a pointer to the fingerprint type used to constuct the index </dd></dl>
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<a class="anchor" id="a6c00d74d4b0859279a48173737b1f8b1"></a><!-- doxytag: member="OpenBabel::FastSearch::GetIndexHeader" ref="a6c00d74d4b0859279a48173737b1f8b1" args="() const " -->
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<td class="memname">const <a class="el" href="structOpenBabel_1_1FptIndexHeader.shtml">FptIndexHeader</a>& GetIndexHeader </td>
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<td> const<code> [inline]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>a pointer to the index header containing size info etc. </dd></dl>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="fingerprint_8h_source.shtml">fingerprint.h</a></li>
<li><a class="el" href="fingerprint_8cpp.shtml">fingerprint.cpp</a></li>
</ul>
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