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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html">EnzymaticDigestion</a></li> </ul>
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<div class="title">EnzymaticDigestion Class Reference<div class="ingroups"><a class="el" href="group__Chemistry.html">Chemistry</a></div></div> </div>
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<p>Class for the enzymatic digestion of proteins.
<a href="classOpenMS_1_1EnzymaticDigestion.html#details">More...</a></p>
<p><code>#include <<a class="el" href="EnzymaticDigestion_8h_source.html">OpenMS/CHEMISTRY/EnzymaticDigestion.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1EnzymaticDigestion_1_1BindingSite.html">BindingSite</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1EnzymaticDigestion_1_1CleavageModel.html">CleavageModel</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:a91175883c1a1e1fb43ba67cbe7656832"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">Enzyme</a> { <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832a51fd9dba1ee652c686ffe2121104edaa">ENZYME_TRYPSIN</a>,
<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832a86f8c46f6a8efb101b6e20d0999d02dd">SIZE_OF_ENZYMES</a>
}</td></tr>
<tr class="memdesc:a91175883c1a1e1fb43ba67cbe7656832"><td class="mdescLeft"> </td><td class="mdescRight">Possible enzymes for the digestion (adapt NamesOfEnzymes & <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a845b477ffbafb15166974c1c2c40bc21" title="moves the iterator p behind (i.e., C-term) the next cleavage site of the sequence ...">nextCleavageSite_()</a> if you add more enzymes here) <a href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">More...</a><br/></td></tr>
<tr class="separator:a91175883c1a1e1fb43ba67cbe7656832"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2b6018f958ecd9fd2574082f0b6dfd07"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">Specificity</a> { <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07ab8adf0ebad3fded3c2fb5f43879fefaa">SPEC_FULL</a>,
<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07a18c1a21bdae6960556aa09273b67e51f">SPEC_SEMI</a>,
<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07a1407125146dcdb717cccfd32dc951def">SPEC_NONE</a>,
<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07a93f83a51d2c212082059f29550899d2d">SIZE_OF_SPECIFICITY</a>
}</td></tr>
<tr class="memdesc:a2b6018f958ecd9fd2574082f0b6dfd07"><td class="mdescLeft"> </td><td class="mdescRight">when querying for valid digestion products, this determines if the specificity of the two peptide ends is considered important <a href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">More...</a><br/></td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a8851474ff325858c19207fee9ca7b94e"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a8851474ff325858c19207fee9ca7b94e">EnzymaticDigestion</a> ()</td></tr>
<tr class="memdesc:a8851474ff325858c19207fee9ca7b94e"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a8851474ff325858c19207fee9ca7b94e">More...</a><br/></td></tr>
<tr class="separator:a8851474ff325858c19207fee9ca7b94e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad899d3c8bf319bad45b402f1da31db99"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#ad899d3c8bf319bad45b402f1da31db99">EnzymaticDigestion</a> (const <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html">EnzymaticDigestion</a> &rhs)</td></tr>
<tr class="memdesc:ad899d3c8bf319bad45b402f1da31db99"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#ad899d3c8bf319bad45b402f1da31db99">More...</a><br/></td></tr>
<tr class="separator:ad899d3c8bf319bad45b402f1da31db99"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a25f2adda7885facdec1f1e60b46c99b7"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html">EnzymaticDigestion</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a25f2adda7885facdec1f1e60b46c99b7">operator=</a> (const <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html">EnzymaticDigestion</a> &rhs)</td></tr>
<tr class="memdesc:a25f2adda7885facdec1f1e60b46c99b7"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#a25f2adda7885facdec1f1e60b46c99b7">More...</a><br/></td></tr>
<tr class="separator:a25f2adda7885facdec1f1e60b46c99b7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8551141c22a22b2e63b24a16f19ec91d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a8551141c22a22b2e63b24a16f19ec91d">getMissedCleavages</a> () const </td></tr>
<tr class="memdesc:a8551141c22a22b2e63b24a16f19ec91d"><td class="mdescLeft"> </td><td class="mdescRight">Returns the number of missed cleavages for the digestion. <a href="#a8551141c22a22b2e63b24a16f19ec91d">More...</a><br/></td></tr>
<tr class="separator:a8551141c22a22b2e63b24a16f19ec91d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a05d552a7a0f493692cb48aea619365d9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a05d552a7a0f493692cb48aea619365d9">setMissedCleavages</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> missed_cleavages)</td></tr>
<tr class="memdesc:a05d552a7a0f493692cb48aea619365d9"><td class="mdescLeft"> </td><td class="mdescRight">Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when log model is used. <a href="#a05d552a7a0f493692cb48aea619365d9">More...</a><br/></td></tr>
<tr class="separator:a05d552a7a0f493692cb48aea619365d9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad27cb192ce4529a5bedbcf7b96ced0aa"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">Enzyme</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#ad27cb192ce4529a5bedbcf7b96ced0aa">getEnzyme</a> () const </td></tr>
<tr class="memdesc:ad27cb192ce4529a5bedbcf7b96ced0aa"><td class="mdescLeft"> </td><td class="mdescRight">Returns the enzyme for the digestion. <a href="#ad27cb192ce4529a5bedbcf7b96ced0aa">More...</a><br/></td></tr>
<tr class="separator:ad27cb192ce4529a5bedbcf7b96ced0aa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a52950aaa75317825a1a5e00f4250edee"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a52950aaa75317825a1a5e00f4250edee">setEnzyme</a> (<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">Enzyme</a> enzyme)</td></tr>
<tr class="memdesc:a52950aaa75317825a1a5e00f4250edee"><td class="mdescLeft"> </td><td class="mdescRight">Sets the enzyme for the digestion (default is ENZYME_TRYPSIN). <a href="#a52950aaa75317825a1a5e00f4250edee">More...</a><br/></td></tr>
<tr class="separator:a52950aaa75317825a1a5e00f4250edee"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad509f7f1f3595f04d5784c8c51a8cb13"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">Specificity</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#ad509f7f1f3595f04d5784c8c51a8cb13">getSpecificity</a> () const </td></tr>
<tr class="memdesc:ad509f7f1f3595f04d5784c8c51a8cb13"><td class="mdescLeft"> </td><td class="mdescRight">Returns the specificity for the digestion. <a href="#ad509f7f1f3595f04d5784c8c51a8cb13">More...</a><br/></td></tr>
<tr class="separator:ad509f7f1f3595f04d5784c8c51a8cb13"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acf2e52de630367c50bb14cfbb6e7f5f5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#acf2e52de630367c50bb14cfbb6e7f5f5">setSpecificity</a> (<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">Specificity</a> spec)</td></tr>
<tr class="memdesc:acf2e52de630367c50bb14cfbb6e7f5f5"><td class="mdescLeft"> </td><td class="mdescRight">Sets the specificity for the digestion (default is SPEC_FULL). <a href="#acf2e52de630367c50bb14cfbb6e7f5f5">More...</a><br/></td></tr>
<tr class="separator:acf2e52de630367c50bb14cfbb6e7f5f5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a95585ce3a919169a2091f3a6a7325470"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a95585ce3a919169a2091f3a6a7325470">digest</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &protein, std::vector< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> > &output) const </td></tr>
<tr class="memdesc:a95585ce3a919169a2091f3a6a7325470"><td class="mdescLeft"> </td><td class="mdescRight">Performs the enzymatic digestion of a protein. <a href="#a95585ce3a919169a2091f3a6a7325470">More...</a><br/></td></tr>
<tr class="separator:a95585ce3a919169a2091f3a6a7325470"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad0d24e15a1dd611eceb19eb9c421c579"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#ad0d24e15a1dd611eceb19eb9c421c579">peptideCount</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &protein)</td></tr>
<tr class="memdesc:ad0d24e15a1dd611eceb19eb9c421c579"><td class="mdescLeft"> </td><td class="mdescRight">Returns the number of peptides a digestion of <code>protein</code> would yield under the current enzyme and missed cleavage settings. <a href="#ad0d24e15a1dd611eceb19eb9c421c579">More...</a><br/></td></tr>
<tr class="separator:ad0d24e15a1dd611eceb19eb9c421c579"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af33849e754f800c2b5f1079c62f97c50"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#af33849e754f800c2b5f1079c62f97c50">isLogModelEnabled</a> () const </td></tr>
<tr class="memdesc:af33849e754f800c2b5f1079c62f97c50"><td class="mdescLeft"> </td><td class="mdescRight">use trained model when digesting? <a href="#af33849e754f800c2b5f1079c62f97c50">More...</a><br/></td></tr>
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<tr class="memitem:ad405dd431aa99698dde78f5a0c6af361"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#ad405dd431aa99698dde78f5a0c6af361">setLogModelEnabled</a> (bool enabled)</td></tr>
<tr class="memdesc:ad405dd431aa99698dde78f5a0c6af361"><td class="mdescLeft"> </td><td class="mdescRight">enables/disabled the trained model <a href="#ad405dd431aa99698dde78f5a0c6af361">More...</a><br/></td></tr>
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<tr class="memitem:a1f9fdff2100ff69e54268e85785b4b5c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a1f9fdff2100ff69e54268e85785b4b5c">getLogThreshold</a> () const </td></tr>
<tr class="memdesc:a1f9fdff2100ff69e54268e85785b4b5c"><td class="mdescLeft"> </td><td class="mdescRight">Returns the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data) <a href="#a1f9fdff2100ff69e54268e85785b4b5c">More...</a><br/></td></tr>
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<tr class="memitem:a2cd035e01ac44d9b69646df81fbda686"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2cd035e01ac44d9b69646df81fbda686">setLogThreshold</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> threshold)</td></tr>
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<tr class="memitem:add1d3e1f2d5c7c41de9991d25c17da1e"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#add1d3e1f2d5c7c41de9991d25c17da1e">isValidProduct</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &protein, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> pep_pos, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> pep_length)</td></tr>
<tr class="memdesc:add1d3e1f2d5c7c41de9991d25c17da1e"><td class="mdescLeft"> </td><td class="mdescRight">Returns true if peptide at position <code>pep_pos</code> with length <code>pep_length</code> within protein <code>protein</code> was generated by the current model. <a href="#add1d3e1f2d5c7c41de9991d25c17da1e">More...</a><br/></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:aabaf8ac45613530e9f5d761c6eff1236"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">Enzyme</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#aabaf8ac45613530e9f5d761c6eff1236">getEnzymeByName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
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<tr class="memitem:a48c2bffa3ca3db5c25185d0d4548d5f7"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">Specificity</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a48c2bffa3ca3db5c25185d0d4548d5f7">getSpecificityByName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-attribs"></a>
Static Public Attributes</h2></td></tr>
<tr class="memitem:a32907f3699f2abadfe83840927074ff7"><td class="memItemLeft" align="right" valign="top">static const std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a32907f3699f2abadfe83840927074ff7">NamesOfEnzymes</a> [<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832a86f8c46f6a8efb101b6e20d0999d02dd">SIZE_OF_ENZYMES</a>]</td></tr>
<tr class="memdesc:a32907f3699f2abadfe83840927074ff7"><td class="mdescLeft"> </td><td class="mdescRight">Names of the Enzymes. <a href="#a32907f3699f2abadfe83840927074ff7">More...</a><br/></td></tr>
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<tr class="memitem:aaf3a33358d6edb8dc36d4961ba8bca73"><td class="memItemLeft" align="right" valign="top">static const std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#aaf3a33358d6edb8dc36d4961ba8bca73">NamesOfSpecificity</a> [<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07a93f83a51d2c212082059f29550899d2d">SIZE_OF_SPECIFICITY</a>]</td></tr>
<tr class="memdesc:aaf3a33358d6edb8dc36d4961ba8bca73"><td class="mdescLeft"> </td><td class="mdescRight">Names of the Specificity. <a href="#aaf3a33358d6edb8dc36d4961ba8bca73">More...</a><br/></td></tr>
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Protected Member Functions</h2></td></tr>
<tr class="memitem:a845b477ffbafb15166974c1c2c40bc21"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a845b477ffbafb15166974c1c2c40bc21">nextCleavageSite_</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &sequence, <a class="el" href="classOpenMS_1_1AASequence_1_1ConstIterator.html">AASequence::ConstIterator</a> &p) const </td></tr>
<tr class="memdesc:a845b477ffbafb15166974c1c2c40bc21"><td class="mdescLeft"> </td><td class="mdescRight">moves the iterator <code>p</code> behind (i.e., C-term) the next cleavage site of the <code>sequence</code> <a href="#a845b477ffbafb15166974c1c2c40bc21">More...</a><br/></td></tr>
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<tr class="memitem:ad7a9bdc16bf6d6f3bf20a206966bc736"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#ad7a9bdc16bf6d6f3bf20a206966bc736">isCleavageSite_</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &sequence, const <a class="el" href="classOpenMS_1_1AASequence_1_1ConstIterator.html">AASequence::ConstIterator</a> &p) const </td></tr>
<tr class="memdesc:ad7a9bdc16bf6d6f3bf20a206966bc736"><td class="mdescLeft"> </td><td class="mdescRight">tests if position pointed to by <code>p</code> (N-term side) is a valid cleavage site <a href="#ad7a9bdc16bf6d6f3bf20a206966bc736">More...</a><br/></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a0e59f7d18d922485572d0c3aa68d1bd5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a0e59f7d18d922485572d0c3aa68d1bd5">missed_cleavages_</a></td></tr>
<tr class="memdesc:a0e59f7d18d922485572d0c3aa68d1bd5"><td class="mdescLeft"> </td><td class="mdescRight">Number of missed cleavages. <a href="#a0e59f7d18d922485572d0c3aa68d1bd5">More...</a><br/></td></tr>
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<tr class="memitem:a9313c2f0d74b529f53d40e556eacf84e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">Enzyme</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a9313c2f0d74b529f53d40e556eacf84e">enzyme_</a></td></tr>
<tr class="memdesc:a9313c2f0d74b529f53d40e556eacf84e"><td class="mdescLeft"> </td><td class="mdescRight">Used enzyme. <a href="#a9313c2f0d74b529f53d40e556eacf84e">More...</a><br/></td></tr>
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<tr class="memitem:a04cd0213e02625af1faa390e4d4c52da"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">Specificity</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a04cd0213e02625af1faa390e4d4c52da">specificity_</a></td></tr>
<tr class="memdesc:a04cd0213e02625af1faa390e4d4c52da"><td class="mdescLeft"> </td><td class="mdescRight">specificity of enzyme <a href="#a04cd0213e02625af1faa390e4d4c52da">More...</a><br/></td></tr>
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<tr class="memitem:a6abc9d3839325bd6c46fb822d598175c"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a6abc9d3839325bd6c46fb822d598175c">use_log_model_</a></td></tr>
<tr class="memdesc:a6abc9d3839325bd6c46fb822d598175c"><td class="mdescLeft"> </td><td class="mdescRight">use the log model or naive digestion (with missed cleavages) <a href="#a6abc9d3839325bd6c46fb822d598175c">More...</a><br/></td></tr>
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<tr class="memitem:a1425224248d0b55f9c73debd388995b6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a1425224248d0b55f9c73debd388995b6">log_model_threshold_</a></td></tr>
<tr class="memdesc:a1425224248d0b55f9c73debd388995b6"><td class="mdescLeft"> </td><td class="mdescRight">Threshold to decide if position is cleaved or missed (only for the model) <a href="#a1425224248d0b55f9c73debd388995b6">More...</a><br/></td></tr>
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<tr class="memitem:a1b081b49461b28bef181e8b69bd1a3e9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="structOpenMS_1_1EnzymaticDigestion_1_1BindingSite.html">BindingSite</a>, <a class="el" href="structOpenMS_1_1EnzymaticDigestion_1_1CleavageModel.html">CleavageModel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a1b081b49461b28bef181e8b69bd1a3e9">model_data_</a></td></tr>
<tr class="memdesc:a1b081b49461b28bef181e8b69bd1a3e9"><td class="mdescLeft"> </td><td class="mdescRight">Holds the cleavage model. <a href="#a1b081b49461b28bef181e8b69bd1a3e9">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Class for the enzymatic digestion of proteins. </p>
<p><a class="el" href="classOpenMS_1_1Digestion.html" title="Meta information about digestion of a sample. ">Digestion</a> can be performed using simple regular expressions, e.g. [KR] | [^P] for trypsin. Also missed cleavages can be modelled, i.e. adjacent peptides are not cleaved due to enzyme malfunction/access restrictions. If <em>n</em> missed cleavages are given, all possible resulting peptides (cleaved and uncleaved) with up to <em>n</em> missed cleavages are returned. Thus <b>no</b> random selection of just <em>n</em> specific missed cleavage sites is performed.</p>
<p>An alternative model is also available, where the protein is cleaved only at positions where a cleavage model trained on real data, exceeds a certain threshold. The model is published in Siepen et al. (2007), "Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.", doi: 10.1021/pr060507u The model is only available for trypsin and ignores the missed cleavage setting. You should however use <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2cd035e01ac44d9b69646df81fbda686">setLogThreshold()</a> to adjust FP vs FN rates. A higher threshold increases the number of cleavages predicted. </p>
</div><h2 class="groupheader">Member Enumeration Documentation</h2>
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<td class="memname">enum <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">Enzyme</a></td>
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<p>Possible enzymes for the digestion (adapt NamesOfEnzymes & <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a845b477ffbafb15166974c1c2c40bc21" title="moves the iterator p behind (i.e., C-term) the next cleavage site of the sequence ...">nextCleavageSite_()</a> if you add more enzymes here) </p>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="a91175883c1a1e1fb43ba67cbe7656832a51fd9dba1ee652c686ffe2121104edaa"></a>ENZYME_TRYPSIN</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="a91175883c1a1e1fb43ba67cbe7656832a86f8c46f6a8efb101b6e20d0999d02dd"></a>SIZE_OF_ENZYMES</em> </td><td class="fielddoc">
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<td class="memname">enum <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">Specificity</a></td>
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<p>when querying for valid digestion products, this determines if the specificity of the two peptide ends is considered important </p>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="a2b6018f958ecd9fd2574082f0b6dfd07ab8adf0ebad3fded3c2fb5f43879fefaa"></a>SPEC_FULL</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="a2b6018f958ecd9fd2574082f0b6dfd07a18c1a21bdae6960556aa09273b67e51f"></a>SPEC_SEMI</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="a2b6018f958ecd9fd2574082f0b6dfd07a1407125146dcdb717cccfd32dc951def"></a>SPEC_NONE</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="a2b6018f958ecd9fd2574082f0b6dfd07a93f83a51d2c212082059f29550899d2d"></a>SIZE_OF_SPECIFICITY</em> </td><td class="fielddoc">
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html">EnzymaticDigestion</a> </td>
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<p>Default constructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html">EnzymaticDigestion</a> </td>
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<p>Copy constructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void digest </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> & </td>
<td class="paramname"><em>protein</em>, </td>
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<p>Performs the enzymatic digestion of a protein. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">Enzyme</a> getEnzyme </td>
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<p>Returns the enzyme for the digestion. </p>
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<td class="memname">static <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">Enzyme</a> getEnzymeByName </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<p>convert enzyme string name to enum returns SIZE_OF_ENZYMES if <code>name</code> is not valid </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getLogThreshold </td>
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<p>Returns the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data) </p>
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<td class="memname"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> getMissedCleavages </td>
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<p>Returns the number of missed cleavages for the digestion. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">Specificity</a> getSpecificity </td>
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<p>Returns the specificity for the digestion. </p>
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<td class="memname">static <a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">Specificity</a> getSpecificityByName </td>
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<p>convert spec string name to enum returns SIZE_OF_SPECIFICITY if <code>name</code> is not valid </p>
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<td class="memname">bool isCleavageSite_ </td>
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<td class="paramname"><em>sequence</em>, </td>
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<p>tests if position pointed to by <code>p</code> (N-term side) is a valid cleavage site </p>
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<p>use trained model when digesting? </p>
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<p>Returns true if peptide at position <code>pep_pos</code> with length <code>pep_length</code> within protein <code>protein</code> was generated by the current model. </p>
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<td class="memname">void nextCleavageSite_ </td>
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<p>moves the iterator <code>p</code> behind (i.e., C-term) the next cleavage site of the <code>sequence</code> </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html">EnzymaticDigestion</a>& operator= </td>
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<p>Assignment operator. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peptideCount </td>
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<p>Returns the number of peptides a digestion of <code>protein</code> would yield under the current enzyme and missed cleavage settings. </p>
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<td class="memname">void setEnzyme </td>
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<p>Sets the enzyme for the digestion (default is ENZYME_TRYPSIN). </p>
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<p>enables/disabled the trained model </p>
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<td class="memname">void setLogThreshold </td>
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<p>Sets the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data) Default is 0.25 </p>
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<td class="memname">void setMissedCleavages </td>
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<p>Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when log model is used. </p>
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<td class="memname">void setSpecificity </td>
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<td class="paramname"><em>spec</em></td><td>)</td>
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<p>Sets the specificity for the digestion (default is SPEC_FULL). </p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832">Enzyme</a> enzyme_</td>
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<p>Used enzyme. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> log_model_threshold_</td>
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<p>Threshold to decide if position is cleaved or missed (only for the model) </p>
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<td class="memname"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> missed_cleavages_</td>
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<p>Number of missed cleavages. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1Map.html">Map</a><<a class="el" href="structOpenMS_1_1EnzymaticDigestion_1_1BindingSite.html">BindingSite</a>, <a class="el" href="structOpenMS_1_1EnzymaticDigestion_1_1CleavageModel.html">CleavageModel</a>> model_data_</td>
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<p>Holds the cleavage model. </p>
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<td class="memname">const std::string NamesOfEnzymes[<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a91175883c1a1e1fb43ba67cbe7656832a86f8c46f6a8efb101b6e20d0999d02dd">SIZE_OF_ENZYMES</a>]</td>
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<p>Names of the Enzymes. </p>
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<td class="memname">const std::string NamesOfSpecificity[<a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07a93f83a51d2c212082059f29550899d2d">SIZE_OF_SPECIFICITY</a>]</td>
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<p>Names of the Specificity. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1EnzymaticDigestion.html#a2b6018f958ecd9fd2574082f0b6dfd07">Specificity</a> specificity_</td>
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<p>specificity of enzyme </p>
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<td class="memname">bool use_log_model_</td>
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<p>use the log model or naive digestion (with missed cleavages) </p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5</font></TD>
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