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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_1ProtonDistributionModel.html">ProtonDistributionModel</a></li>  </ul>
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<div class="title">ProtonDistributionModel Member List</div>  </div>
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<p>This is the complete list of members for <a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a>, including all inherited members.</p>
<table class="directory">
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a7370324991f61a4df4ba20d0d23fe62b">bb_charge_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#aa6d590db0f8599dbf18188497e1e1650">bb_charge_full_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a78c071afeb8c51f33b687f2a286582f3">bb_charge_ion_c_term_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a6b424aa22cb8dde5f09dbaa216671880">bb_charge_ion_n_term_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a47c4115ba83a04355a44004cd3936183">calcChargeStateIntensities_</a>(const AASequence &amp;peptide, const AASequence &amp;n_term_ion, const AASequence &amp;c_term_ion, Int charge, Residue::ResidueType n_term_type, std::vector&lt; DoubleReal &gt; &amp;n_term_intensities, std::vector&lt; DoubleReal &gt; &amp;c_term_intensities, FragmentationType type)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#ad5d0c039e4ec9961378dd0d556e95d2c">calcChargeStateIntensities_</a>(const AASequence &amp;peptide, const AASequence &amp;n_term_ion, const AASequence &amp;c_term_ion, Int charge, Residue::ResidueType n_term_type, DoubleReal &amp;n_term1, DoubleReal &amp;c_term1, DoubleReal &amp;n_term2, DoubleReal &amp;c_term2, FragmentationType type)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a9cdd344a3df943090411aec15270c076">calculateProtonDistribution_</a>(const AASequence &amp;peptide, Int charge, Residue::ResidueType res_type=Residue::YIon, bool fixed_proton=false, Size cleavage_site=0, bool use_most_basic_site=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a3352d5f0f3b9cbeafed385e3cdc2b7b2">calculateProtonDistributionCharge1_</a>(const AASequence &amp;peptide, Residue::ResidueType res_type)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#aacc20fa10b2727afad06b263984075c4">calculateProtonDistributionCharge2_</a>(const AASequence &amp;peptide, Residue::ResidueType res_type, bool fixed_proton, Size cleavage_site, bool use_most_basic_site)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a7fb5032f5fd2d12e2ce2d0646fbaaf50">calculateProtonDistributionGreater2_</a>(const AASequence &amp;peptide, Int charge, Residue::ResidueType res_type)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#afca7fd50e8be58aa5e800a66e32e93a2">calculateProtonDistributionIonPair_</a>(const AASequence &amp;peptide, Residue::ResidueType type, Size cleavage_site)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a5055b9c9ca29c431fe310614df608816a39da8a096dc075314c1465f4169341f6">ChargeDirected</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a5055b9c9ca29c431fe310614df608816a20334f501aa89adc3903952b8250d682">ChargeRemote</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a>(const String &amp;name)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a>(const DefaultParamHandler &amp;rhs)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a1fd4e9c35f60a377cba89d21c4232167">E_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a06f97871f78a3ab989dca747e027d280">E_c_term_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#ae57c0268319b84b66134ce707f8d0146">E_n_term_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a5055b9c9ca29c431fe310614df608816">FragmentationType</a> enum name</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#ac7698415329fc951182e1342e0a303ae">getChargeStateIntensities</a>(const AASequence &amp;peptide, const AASequence &amp;n_term_ion, const AASequence &amp;c_term_ion, Int charge, Residue::ResidueType n_term_type, std::vector&lt; DoubleReal &gt; &amp;n_term_intensities, std::vector&lt; DoubleReal &gt; &amp;c_term_intensities, FragmentationType type)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#aae7f88039a1881d9e891f97064cb3a55">getLeftAndRightGBValues_</a>(const AASequence &amp;peptide, DoubleReal &amp;left_gb, DoubleReal &amp;right_gb, Size position)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#acf1715a5b840765924018dfd2685312c">getProtonDistribution</a>(std::vector&lt; DoubleReal &gt; &amp;bb_charges, std::vector&lt; DoubleReal &gt; &amp;sc_charges, const AASequence &amp;peptide, Int charge, Residue::ResidueType res_type=Residue::YIon)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a82111146761e32549d95d73165b78e2a">operator=</a>(const ProtonDistributionModel &amp;pdm)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">OpenMS::DefaultParamHandler::operator=</a>(const DefaultParamHandler &amp;rhs)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a>(const DefaultParamHandler &amp;rhs) const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#ac604e4908188b66571c88ff8c56c9fe0">ProtonDistributionModel</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a0877b0187ef0bb86ebe31eb81edab5f5">ProtonDistributionModel</a>(const ProtonDistributionModel &amp;model)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#aeba96c81aa036f9e9e658fa7c741f52c">sc_charge_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a0cd8e3bc1a2d8b32a3c5e5802bbb03e7">sc_charge_full_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#aace91416b20bc29b31b0123695af710a">sc_charge_ion_c_term_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#ab77bcb9c69455e96c5d355dfc602ee35">sc_charge_ion_n_term_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a>(const String &amp;name)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(const Param &amp;param)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a20580da4cc198885e3eb646e9e4c2b2e">setPeptideProtonDistribution</a>(const std::vector&lt; DoubleReal &gt; &amp;bb_charge, const std::vector&lt; DoubleReal &gt; &amp;sc_charge)</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#a5055b9c9ca29c431fe310614df608816a793256fc5819baefb4774d249d9238a1">SideChain</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html#ae8b633bf91a7532620de08282295d635">~ProtonDistributionModel</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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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 11:19:26 using doxygen 1.8.5</font></TD>
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