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- <li><a href="annotated.html"><span>Data Structures</span></a></li>
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- <li><a href="globals_defs.html"><span>Macros</span></a></li>
+ <li><a href="globals_defs.html"><span>Defines</span></a></li>
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<li><a href="#index_a"><span>a</span></a></li>
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-<div id="doc-content">
<div class="contents">
- 
+
-<h3><a class="anchor" id="index_a"></a>- a -</h3><ul>
+<h3><a class="anchor" id="index_a">- a -</a></h3><ul>
<li>add_root()
: <a class="el" href="RNAstruct_8h.html#a880d33066dd95441e5fbb73c57ed1c3e">RNAstruct.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_b"></a>- b -</h3><ul>
+<h3><a class="anchor" id="index_b">- b -</a></h3><ul>
<li>b2C()
: <a class="el" href="RNAstruct_8h.html#a9c80d92391f2833549a8b6dac92233f0">RNAstruct.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_c"></a>- c -</h3><ul>
+<h3><a class="anchor" id="index_c">- c -</a></h3><ul>
<li>centroid()
: <a class="el" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">part_func.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_d"></a>- d -</h3><ul>
+<h3><a class="anchor" id="index_d">- d -</a></h3><ul>
<li>destroy_TwoDfold_variables()
: <a class="el" href="group__kl__neighborhood__mfe.html#ga05bf4f31d216b1b160fd2d3d68e9b487">2Dfold.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_e"></a>- e -</h3><ul>
+<h3><a class="anchor" id="index_e">- e -</a></h3><ul>
<li>E_Hairpin()
: <a class="el" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">loop_energies.h</a>
</li>
: <a class="el" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">part_func.h</a>
</li>
<li>export_ali_bppm()
-: <a class="el" href="group__consensus__pf__fold.html#gadaaf83394216413505e48d913dbc1b4e">alifold.h</a>
+: <a class="el" href="group__consensus__pf__fold.html#ga11b6ab8bd9be1821fea352b190a01cab">alifold.h</a>
</li>
<li>export_bppm()
: <a class="el" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115">part_func.h</a>
</ul>
-<h3><a class="anchor" id="index_f"></a>- f -</h3><ul>
+<h3><a class="anchor" id="index_f">- f -</a></h3><ul>
<li>find_saddle()
: <a class="el" href="findpath_8h.html#ad0e14268e309af773ecd1fce6244ee50">findpath.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_g"></a>- g -</h3><ul>
+<h3><a class="anchor" id="index_g">- g -</a></h3><ul>
<li>get_alipf_arrays()
-: <a class="el" href="group__consensus__fold.html#ga0cc49457fd79eeb04d4a7f97c868b09b">alifold.h</a>
+: <a class="el" href="group__consensus__fold.html#ga5349960075b1847720a2e9df021e2675">alifold.h</a>
</li>
<li>get_boltzmann_factor_copy()
: <a class="el" href="group__energy__parameters.html#gacba212326a051734797e65987260fdd0">params.h</a>
: <a class="el" href="group__energy__parameters.html#ga6fc2f3eef5a3024d44963ac59a42e39d">params.h</a>
</li>
<li>get_boltzmann_factors_ali()
-: <a class="el" href="group__energy__parameters.html#gaaa049a8c9f1c2ed4398cb1b5a3d65a66">params.h</a>
+: <a class="el" href="group__energy__parameters.html#gaf0c74574b40f2778556535bf9d382828">params.h</a>
</li>
<li>get_centroid_struct_pl()
: <a class="el" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6">part_func.h</a>
</ul>
-<h3><a class="anchor" id="index_h"></a>- h -</h3><ul>
+<h3><a class="anchor" id="index_h">- h -</a></h3><ul>
<li>HairpinE()
: <a class="el" href="fold_8h.html#ab327ce11972f5ac069d52c8dedfdb700">fold.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_i"></a>- i -</h3><ul>
+<h3><a class="anchor" id="index_i">- i -</a></h3><ul>
<li>init_co_pf_fold()
: <a class="el" href="part__func__co_8h.html#aa12dda9dd6179cdd22bcce87c0682c07">part_func_co.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_l"></a>- l -</h3><ul>
+<h3><a class="anchor" id="index_l">- l -</a></h3><ul>
<li>Lfold()
: <a class="el" href="group__local__mfe__fold.html#ga16e5a70e60835bb969eaecbe6482f1be">Lfold.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
+<h3><a class="anchor" id="index_m">- m -</a></h3><ul>
<li>Make_bp_profile()
: <a class="el" href="profiledist_8h.html#a904c7eaf4a2413567c00ac4891749d18">profiledist.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_n"></a>- n -</h3><ul>
+<h3><a class="anchor" id="index_n">- n -</a></h3><ul>
<li>nrerror()
: <a class="el" href="utils_8h.html#a127ce946e56b5a5773781cabe68e38c5">utils.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_p"></a>- p -</h3><ul>
+<h3><a class="anchor" id="index_p">- p -</a></h3><ul>
<li>pack_structure()
: <a class="el" href="utils_8h.html#ac6dfa5e22928c087c6e09ff0054a7ced">utils.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_r"></a>- r -</h3><ul>
+<h3><a class="anchor" id="index_r">- r -</a></h3><ul>
<li>random_string()
: <a class="el" href="utils_8h.html#a1b95eac365a021572e1c37e5993a89be">utils.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
+<h3><a class="anchor" id="index_s">- s -</a></h3><ul>
<li>scale_parameters()
: <a class="el" href="group__energy__parameters.html#ga527ef619cd8210b84d5d53be1e0e29b6">params.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_t"></a>- t -</h3><ul>
+<h3><a class="anchor" id="index_t">- t -</a></h3><ul>
<li>time_stamp()
: <a class="el" href="utils_8h.html#a7afeb906cb36e9d77379eabc6907ac46">utils.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_u"></a>- u -</h3><ul>
+<h3><a class="anchor" id="index_u">- u -</a></h3><ul>
<li>unexpand_aligned_F()
: <a class="el" href="RNAstruct_8h.html#a1054c4477d53b31d79d4cb132100e87a">RNAstruct.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_w"></a>- w -</h3><ul>
+<h3><a class="anchor" id="index_w">- w -</a></h3><ul>
<li>warn_user()
: <a class="el" href="utils_8h.html#af2355fa8746f2f30fbe71db65dea3d51">utils.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_x"></a>- x -</h3><ul>
+<h3><a class="anchor" id="index_x">- x -</a></h3><ul>
<li>xrealloc()
: <a class="el" href="utils_8h.html#a9037ada838835b1b9db41581a021b0c8">utils.h</a>
</li>
</ul>
-<h3><a class="anchor" id="index_z"></a>- z -</h3><ul>
+<h3><a class="anchor" id="index_z">- z -</a></h3><ul>
<li>zukersubopt()
: <a class="el" href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90">cofold.h</a>
</li>
: <a class="el" href="group__subopt__zuker.html#ga6d98a9450d1affadf144ac79f543da8c">cofold.h</a>
</li>
</ul>
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- <a href="http://www.doxygen.org/index.html">
- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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+<a href="http://www.doxygen.org/index.html">
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