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+<a href="#define-members">Macros</a> |
+<a href="#func-members">Functions</a> </div>
+ <div class="headertitle">
+<div class="title">Converting energy parameter files</div> </div>
+<div class="ingroups"><a class="el" href="group__energy__parameters__rw.html">Reading/Writing energy parameter sets from/to File</a></div></div><!--header-->
+<div class="contents">
+
+<p>Convert energy parameter files into the latest format.
+<a href="#details">More...</a></p>
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Converting energy parameter files:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
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+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
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+<map name="group____energy____parameters____convert" id="group____energy____parameters____convert">
+<area shape="rect" id="node1" href="group__energy__parameters__rw.html" title="Read and Write energy parameter sets from and to text files." alt="" coords="5,5,205,46"/></map>
+</td></tr></table></center>
+</div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="files"></a>
+Files</h2></td></tr>
+<tr class="memitem:convert__epars_8h"><td class="memItemLeft" align="right" valign="top">file  </td><td class="memItemRight" valign="bottom"><a class="el" href="convert__epars_8h.html">convert_epars.h</a></td></tr>
+<tr class="memdesc:convert__epars_8h"><td class="mdescLeft"> </td><td class="mdescRight">Functions and definitions for energy parameter file format conversion. <br/></td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="define-members"></a>
+Macros</h2></td></tr>
+<tr class="memitem:ga8dc6aee5a806c49b71557152f9616bc4"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#ga8dc6aee5a806c49b71557152f9616bc4">VRNA_CONVERT_OUTPUT_ALL</a>   1U</td></tr>
+<tr class="memitem:gaf66fe2cb11dfcfd32d791049c254a8a4"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#gaf66fe2cb11dfcfd32d791049c254a8a4">VRNA_CONVERT_OUTPUT_HP</a>   2U</td></tr>
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+<tr class="memitem:ga78382ec622ba99e0ac2262317bdd7316"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#ga78382ec622ba99e0ac2262317bdd7316">VRNA_CONVERT_OUTPUT_MM_INT_23</a>   64U</td></tr>
+<tr class="memitem:gae67af9f1cdf7baf2865481282a5d1034"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#gae67af9f1cdf7baf2865481282a5d1034">VRNA_CONVERT_OUTPUT_MM_MULTI</a>   128U</td></tr>
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+<tr class="memitem:ga036ffd996d8c8a9acf631760dd1da24b"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#ga036ffd996d8c8a9acf631760dd1da24b">VRNA_CONVERT_OUTPUT_DANGLE5</a>   512U</td></tr>
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+<tr class="memitem:gacf770881d9034431ebe741642342a1f9"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#gacf770881d9034431ebe741642342a1f9">VRNA_CONVERT_OUTPUT_INT_21</a>   4096U</td></tr>
+<tr class="memitem:gaa307671e2631cdacad9cbe4c6583b05f"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#gaa307671e2631cdacad9cbe4c6583b05f">VRNA_CONVERT_OUTPUT_INT_22</a>   8192U</td></tr>
+<tr class="memitem:ga7092fe0be4de6f02cc0bf08e81af726a"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#ga7092fe0be4de6f02cc0bf08e81af726a">VRNA_CONVERT_OUTPUT_BULGE</a>   16384U</td></tr>
+<tr class="memitem:gac5c2289fdf8ff1b980976d1613ff943a"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#gac5c2289fdf8ff1b980976d1613ff943a">VRNA_CONVERT_OUTPUT_INT</a>   32768U</td></tr>
+<tr class="memitem:gaf2c8755d64eff3852aa45df9ac80a4fe"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#gaf2c8755d64eff3852aa45df9ac80a4fe">VRNA_CONVERT_OUTPUT_ML</a>   65536U</td></tr>
+<tr class="memitem:ga46d5b1535ae86060b6317565b7c6b40b"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#ga46d5b1535ae86060b6317565b7c6b40b">VRNA_CONVERT_OUTPUT_MISC</a>   131072U</td></tr>
+<tr class="memitem:gaa1ff48a79642d69579d1766561ec6db6"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#gaa1ff48a79642d69579d1766561ec6db6">VRNA_CONVERT_OUTPUT_SPECIAL_HP</a>   262144U</td></tr>
+<tr class="memitem:ga0d4e8a836bb4864ab5129c085dbf592d"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#ga0d4e8a836bb4864ab5129c085dbf592d">VRNA_CONVERT_OUTPUT_VANILLA</a>   524288U</td></tr>
+<tr class="memitem:ga2eb0462f16939ddacdaf751a88d675ce"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#ga2eb0462f16939ddacdaf751a88d675ce">VRNA_CONVERT_OUTPUT_NINIO</a>   1048576U</td></tr>
+<tr class="memitem:gac86976e9c2a55b3a6481ea60044f6098"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#gac86976e9c2a55b3a6481ea60044f6098">VRNA_CONVERT_OUTPUT_DUMP</a>   2097152U</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:gafbe538bc4eb2cf2a33326e1010005f8a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__energy__parameters__convert.html#gafbe538bc4eb2cf2a33326e1010005f8a">convert_parameter_file</a> (const char *iname, const char *oname, unsigned int options)</td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<p>Convert energy parameter files into the latest format. </p>
+<p>To preserve some backward compatibility the RNAlib also provides functions to convert energy parameter files from the format used in version 1.4-1.8 into the new format used since version 2.0 </p>
+<hr/><h2>Macro Definition Documentation</h2>
+<a class="anchor" id="ga8dc6aee5a806c49b71557152f9616bc4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_ALL   1U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of a complete parameter set </p>
+
+</div>
+</div>
+<a class="anchor" id="gaf66fe2cb11dfcfd32d791049c254a8a4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_HP   2U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of hairpin contributions </p>
+
+</div>
+</div>
+<a class="anchor" id="gad23522d63f8d4c50d5a5deee9bee3ef2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_STACK   4U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of base pair stack contributions </p>
+
+</div>
+</div>
+<a class="anchor" id="gaa892c7b4957459090f3e08da298cc347"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_MM_HP   8U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of hairpin mismatch contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="ga4ff223fb1f9c62cd92d9ab811ad03d55"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_MM_INT   16U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of interior loop mismatch contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="gaf5d3743219f83c6348155cd81e755bbb"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_MM_INT_1N   32U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of 1:n interior loop mismatch contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="ga78382ec622ba99e0ac2262317bdd7316"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_MM_INT_23   64U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of 2:3 interior loop mismatch contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="gae67af9f1cdf7baf2865481282a5d1034"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_MM_MULTI   128U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of multi loop mismatch contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="gaf14ead7ef1fdbe725ade653750fc51e3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_MM_EXT   256U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of exterior loop mismatch contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="ga036ffd996d8c8a9acf631760dd1da24b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_DANGLE5   512U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of 5' dangle conctribution </p>
+
+</div>
+</div>
+<a class="anchor" id="ga34a8a5479ef885834ef32f3fb43d79bc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_DANGLE3   1024U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of 3' dangle contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="ga079aafefd5f8ab57ee5120099a34bd25"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_INT_11   2048U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of 1:1 interior loop contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="gacf770881d9034431ebe741642342a1f9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_INT_21   4096U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of 2:1 interior loop contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="gaa307671e2631cdacad9cbe4c6583b05f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_INT_22   8192U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of 2:2 interior loop contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="ga7092fe0be4de6f02cc0bf08e81af726a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_BULGE   16384U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of bulge loop contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="gac5c2289fdf8ff1b980976d1613ff943a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_INT   32768U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of interior loop contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="gaf2c8755d64eff3852aa45df9ac80a4fe"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_ML   65536U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of multi loop contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="ga46d5b1535ae86060b6317565b7c6b40b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_MISC   131072U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of misc contributions (such as terminalAU) </p>
+
+</div>
+</div>
+<a class="anchor" id="gaa1ff48a79642d69579d1766561ec6db6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_SPECIAL_HP   262144U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of special hairpin contributions (tri-, tetra-, hexa-loops) </p>
+
+</div>
+</div>
+<a class="anchor" id="ga0d4e8a836bb4864ab5129c085dbf592d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_VANILLA   524288U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of given parameters only<br/>
+</p>
+<dl class="section note"><dt>Note:</dt><dd>This option overrides all other output options, except <a class="el" href="group__energy__parameters__convert.html#gac86976e9c2a55b3a6481ea60044f6098">VRNA_CONVERT_OUTPUT_DUMP</a> ! </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="ga2eb0462f16939ddacdaf751a88d675ce"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_NINIO   1048576U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate printing of interior loop asymmetry contribution </p>
+
+</div>
+</div>
+<a class="anchor" id="gac86976e9c2a55b3a6481ea60044f6098"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_CONVERT_OUTPUT_DUMP   2097152U</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Flag to indicate dumping the energy contributions from the library instead of an input file </p>
+
+</div>
+</div>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="gafbe538bc4eb2cf2a33326e1010005f8a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">void convert_parameter_file </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>iname</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>oname</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">unsigned int </td>
+ <td class="paramname"><em>options</em> </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Convert/dump a Vienna 1.8.4 formatted energy parameter file</p>
+<p>The options argument allows to control the different output modes.<br/>
+ Currently available options are:<br/>
+ <a class="el" href="group__energy__parameters__convert.html#ga8dc6aee5a806c49b71557152f9616bc4">VRNA_CONVERT_OUTPUT_ALL</a>, <a class="el" href="group__energy__parameters__convert.html#gaf66fe2cb11dfcfd32d791049c254a8a4">VRNA_CONVERT_OUTPUT_HP</a>, <a class="el" href="group__energy__parameters__convert.html#gad23522d63f8d4c50d5a5deee9bee3ef2">VRNA_CONVERT_OUTPUT_STACK</a><br/>
+ <a class="el" href="group__energy__parameters__convert.html#gaa892c7b4957459090f3e08da298cc347">VRNA_CONVERT_OUTPUT_MM_HP</a>, <a class="el" href="group__energy__parameters__convert.html#ga4ff223fb1f9c62cd92d9ab811ad03d55">VRNA_CONVERT_OUTPUT_MM_INT</a>, <a class="el" href="group__energy__parameters__convert.html#gaf5d3743219f83c6348155cd81e755bbb">VRNA_CONVERT_OUTPUT_MM_INT_1N</a><br/>
+ <a class="el" href="group__energy__parameters__convert.html#ga78382ec622ba99e0ac2262317bdd7316">VRNA_CONVERT_OUTPUT_MM_INT_23</a>, <a class="el" href="group__energy__parameters__convert.html#gae67af9f1cdf7baf2865481282a5d1034">VRNA_CONVERT_OUTPUT_MM_MULTI</a>, <a class="el" href="group__energy__parameters__convert.html#gaf14ead7ef1fdbe725ade653750fc51e3">VRNA_CONVERT_OUTPUT_MM_EXT</a><br/>
+ <a class="el" href="group__energy__parameters__convert.html#ga036ffd996d8c8a9acf631760dd1da24b">VRNA_CONVERT_OUTPUT_DANGLE5</a>, <a class="el" href="group__energy__parameters__convert.html#ga34a8a5479ef885834ef32f3fb43d79bc">VRNA_CONVERT_OUTPUT_DANGLE3</a>, <a class="el" href="group__energy__parameters__convert.html#ga079aafefd5f8ab57ee5120099a34bd25">VRNA_CONVERT_OUTPUT_INT_11</a><br/>
+ <a class="el" href="group__energy__parameters__convert.html#gacf770881d9034431ebe741642342a1f9">VRNA_CONVERT_OUTPUT_INT_21</a>, <a class="el" href="group__energy__parameters__convert.html#gaa307671e2631cdacad9cbe4c6583b05f">VRNA_CONVERT_OUTPUT_INT_22</a>, <a class="el" href="group__energy__parameters__convert.html#ga7092fe0be4de6f02cc0bf08e81af726a">VRNA_CONVERT_OUTPUT_BULGE</a><br/>
+ <a class="el" href="group__energy__parameters__convert.html#gac5c2289fdf8ff1b980976d1613ff943a">VRNA_CONVERT_OUTPUT_INT</a>, <a class="el" href="group__energy__parameters__convert.html#gaf2c8755d64eff3852aa45df9ac80a4fe">VRNA_CONVERT_OUTPUT_ML</a>, <a class="el" href="group__energy__parameters__convert.html#ga46d5b1535ae86060b6317565b7c6b40b">VRNA_CONVERT_OUTPUT_MISC</a><br/>
+ <a class="el" href="group__energy__parameters__convert.html#gaa1ff48a79642d69579d1766561ec6db6">VRNA_CONVERT_OUTPUT_SPECIAL_HP</a>, <a class="el" href="group__energy__parameters__convert.html#ga0d4e8a836bb4864ab5129c085dbf592d">VRNA_CONVERT_OUTPUT_VANILLA</a>, <a class="el" href="group__energy__parameters__convert.html#ga2eb0462f16939ddacdaf751a88d675ce">VRNA_CONVERT_OUTPUT_NINIO</a><br/>
+ <a class="el" href="group__energy__parameters__convert.html#gac86976e9c2a55b3a6481ea60044f6098">VRNA_CONVERT_OUTPUT_DUMP</a></p>
+<p>The defined options are fine for bitwise compare- and assignment-operations, e. g.: pass a collection of options as a single value like this: </p>
+<pre class="fragment">convert_parameter_file(ifile, ofile, option_1 | option_2 | option_n) </pre><dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">iname</td><td>The input file name (If NULL input is read from stdin) </td></tr>
+ <tr><td class="paramname">oname</td><td>The output file name (If NULL output is written to stdout) </td></tr>
+ <tr><td class="paramname">options</td><td>The options (as described above) </td></tr>
+ </table>
+ </dd>
+</dl>
+
+</div>
+</div>
+</div><!-- contents -->
+</div><!-- doc-content -->
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+ <ul>
+ <li class="footer">Generated on Wed Jul 24 2013 13:38:59 for RNAlib-2.1.2 by
+ <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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