JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / doc / latex / group__energy__parameters__convert.aux
index fb41c6a..9290854 100644 (file)
@@ -1,60 +1,57 @@
 \relax 
-\@writefile{toc}{\contentsline {section}{\numberline {9.24}Converting energy parameter files}{69}{section.9.24}}
-\newlabel{group__energy__parameters__convert}{{9.24}{69}{Converting energy parameter files\relax }{section.9.24}{}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {9.24.1}Detailed Description}{69}{subsection.9.24.1}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {9.24.2}Macro Definition Documentation}{70}{subsection.9.24.2}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.1}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L}{70}{subsubsection.9.24.2.1}}
-\newlabel{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{{9.24.2.1}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L\relax }{subsubsection.9.24.2.1}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.2}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}{70}{subsubsection.9.24.2.2}}
-\newlabel{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{{9.24.2.2}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P\relax }{subsubsection.9.24.2.2}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.3}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K}{70}{subsubsection.9.24.2.3}}
-\newlabel{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{{9.24.2.3}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K\relax }{subsubsection.9.24.2.3}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.4}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}{70}{subsubsection.9.24.2.4}}
-\newlabel{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{{9.24.2.4}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P\relax }{subsubsection.9.24.2.4}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.5}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T}{70}{subsubsection.9.24.2.5}}
-\newlabel{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{{9.24.2.5}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\relax }{subsubsection.9.24.2.5}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.6}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}1\discretionary {-}{}{}N}{70}{subsubsection.9.24.2.6}}
-\newlabel{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{{9.24.2.6}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N\relax }{subsubsection.9.24.2.6}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.7}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}23}{70}{subsubsection.9.24.2.7}}
-\newlabel{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{{9.24.2.7}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23\relax }{subsubsection.9.24.2.7}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.8}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}T\discretionary {-}{}{}I}{70}{subsubsection.9.24.2.8}}
-\newlabel{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{{9.24.2.8}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I\relax }{subsubsection.9.24.2.8}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.9}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}X\discretionary {-}{}{}T}{70}{subsubsection.9.24.2.9}}
-\newlabel{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{{9.24.2.9}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T\relax }{subsubsection.9.24.2.9}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.10}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}L\discretionary {-}{}{}E5}{70}{subsubsection.9.24.2.10}}
-\newlabel{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{{9.24.2.10}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5\relax }{subsubsection.9.24.2.10}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.11}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}L\discretionary {-}{}{}E3}{70}{subsubsection.9.24.2.11}}
-\newlabel{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{{9.24.2.11}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3\relax }{subsubsection.9.24.2.11}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.12}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}11}{70}{subsubsection.9.24.2.12}}
-\newlabel{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{{9.24.2.12}{70}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11\relax }{subsubsection.9.24.2.12}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.13}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}21}{71}{subsubsection.9.24.2.13}}
-\newlabel{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{{9.24.2.13}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21\relax }{subsubsection.9.24.2.13}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.14}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}22}{71}{subsubsection.9.24.2.14}}
-\newlabel{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{{9.24.2.14}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22\relax }{subsubsection.9.24.2.14}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.15}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}G\discretionary {-}{}{}E}{71}{subsubsection.9.24.2.15}}
-\newlabel{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{{9.24.2.15}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E\relax }{subsubsection.9.24.2.15}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.16}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T}{71}{subsubsection.9.24.2.16}}
-\newlabel{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{{9.24.2.16}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\relax }{subsubsection.9.24.2.16}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.17}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}L}{71}{subsubsection.9.24.2.17}}
-\newlabel{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{{9.24.2.17}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L\relax }{subsubsection.9.24.2.17}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.18}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C}{71}{subsubsection.9.24.2.18}}
-\newlabel{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{{9.24.2.18}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C\relax }{subsubsection.9.24.2.18}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.19}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}C\discretionary {-}{}{}I\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}{71}{subsubsection.9.24.2.19}}
-\newlabel{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{{9.24.2.19}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P\relax }{subsubsection.9.24.2.19}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.20}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}L\discretionary {-}{}{}A}{71}{subsubsection.9.24.2.20}}
-\newlabel{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{{9.24.2.20}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A\relax }{subsubsection.9.24.2.20}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.21}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}O}{71}{subsubsection.9.24.2.21}}
-\newlabel{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{{9.24.2.21}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O\relax }{subsubsection.9.24.2.21}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.22}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}U\discretionary {-}{}{}M\discretionary {-}{}{}P}{71}{subsubsection.9.24.2.22}}
-\newlabel{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{{9.24.2.22}{71}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P\relax }{subsubsection.9.24.2.22}{}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {9.24.3}Function Documentation}{71}{subsection.9.24.3}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.3.1}convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}{71}{subsubsection.9.24.3.1}}
-\newlabel{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{{9.24.3.1}{71}{convert\-\_\-parameter\-\_\-file\relax }{subsubsection.9.24.3.1}{}}
-\gdef \LT@liii {\LT@entry 
-    {1}{78.18367pt}\LT@entry 
-    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {section}{\numberline {9.24}Converting energy parameter files}{88}{section.9.24}}
+\newlabel{group__energy__parameters__convert}{{9.24}{88}{Converting energy parameter files\relax }{section.9.24}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {9.24.1}Detailed Description}{89}{subsection.9.24.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {9.24.2}Define Documentation}{89}{subsection.9.24.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.1}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}{89}{subsubsection.9.24.2.1}}
+\newlabel{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{{9.24.2.1}{89}{VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL\relax }{subsubsection.9.24.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.2}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}{89}{subsubsection.9.24.2.2}}
+\newlabel{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{{9.24.2.2}{89}{VRNA\_\-CONVERT\_\-OUTPUT\_\-HP\relax }{subsubsection.9.24.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.3}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}{89}{subsubsection.9.24.2.3}}
+\newlabel{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{{9.24.2.3}{89}{VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK\relax }{subsubsection.9.24.2.3}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.4}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}{89}{subsubsection.9.24.2.4}}
+\newlabel{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{{9.24.2.4}{89}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP\relax }{subsubsection.9.24.2.4}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.5}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}{89}{subsubsection.9.24.2.5}}
+\newlabel{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{{9.24.2.5}{89}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\relax }{subsubsection.9.24.2.5}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.6}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}{89}{subsubsection.9.24.2.6}}
+\newlabel{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{{9.24.2.6}{89}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N\relax }{subsubsection.9.24.2.6}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.7}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}{89}{subsubsection.9.24.2.7}}
+\newlabel{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{{9.24.2.7}{89}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23\relax }{subsubsection.9.24.2.7}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.8}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}{89}{subsubsection.9.24.2.8}}
+\newlabel{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{{9.24.2.8}{89}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI\relax }{subsubsection.9.24.2.8}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.9}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}{89}{subsubsection.9.24.2.9}}
+\newlabel{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{{9.24.2.9}{89}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT\relax }{subsubsection.9.24.2.9}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.10}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}{90}{subsubsection.9.24.2.10}}
+\newlabel{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{{9.24.2.10}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5\relax }{subsubsection.9.24.2.10}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.11}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}{90}{subsubsection.9.24.2.11}}
+\newlabel{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{{9.24.2.11}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3\relax }{subsubsection.9.24.2.11}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.12}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}{90}{subsubsection.9.24.2.12}}
+\newlabel{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{{9.24.2.12}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11\relax }{subsubsection.9.24.2.12}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.13}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}{90}{subsubsection.9.24.2.13}}
+\newlabel{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{{9.24.2.13}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21\relax }{subsubsection.9.24.2.13}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.14}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}{90}{subsubsection.9.24.2.14}}
+\newlabel{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{{9.24.2.14}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22\relax }{subsubsection.9.24.2.14}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.15}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}{90}{subsubsection.9.24.2.15}}
+\newlabel{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{{9.24.2.15}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE\relax }{subsubsection.9.24.2.15}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.16}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}{90}{subsubsection.9.24.2.16}}
+\newlabel{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{{9.24.2.16}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\relax }{subsubsection.9.24.2.16}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.17}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}{90}{subsubsection.9.24.2.17}}
+\newlabel{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{{9.24.2.17}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-ML\relax }{subsubsection.9.24.2.17}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.18}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}{90}{subsubsection.9.24.2.18}}
+\newlabel{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{{9.24.2.18}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC\relax }{subsubsection.9.24.2.18}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.19}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}{90}{subsubsection.9.24.2.19}}
+\newlabel{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{{9.24.2.19}{90}{VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP\relax }{subsubsection.9.24.2.19}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.20}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}{91}{subsubsection.9.24.2.20}}
+\newlabel{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{{9.24.2.20}{91}{VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA\relax }{subsubsection.9.24.2.20}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.21}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}{91}{subsubsection.9.24.2.21}}
+\newlabel{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{{9.24.2.21}{91}{VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO\relax }{subsubsection.9.24.2.21}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.2.22}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}{91}{subsubsection.9.24.2.22}}
+\newlabel{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{{9.24.2.22}{91}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP\relax }{subsubsection.9.24.2.22}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {9.24.3}Function Documentation}{91}{subsection.9.24.3}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {9.24.3.1}convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}{91}{subsubsection.9.24.3.1}}
+\newlabel{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{{9.24.3.1}{91}{convert\_\-parameter\_\-file\relax }{subsubsection.9.24.3.1}{}}
 \@setckpt{group__energy__parameters__convert}{
-\setcounter{page}{73}
+\setcounter{page}{93}
 \setcounter{equation}{0}
 \setcounter{enumi}{0}
 \setcounter{enumii}{0}
 \setcounter{paragraph}{0}
 \setcounter{subparagraph}{0}
 \setcounter{figure}{0}
-\setcounter{table}{53}
-\setcounter{NAT@ctr}{0}
+\setcounter{table}{0}
 \setcounter{float@type}{8}
+\setcounter{lstlisting}{0}
 \setcounter{lstnumber}{1}
 \setcounter{Item}{0}
 \setcounter{Hfootnote}{0}
-\setcounter{bookmark@seq@number}{168}
-\setcounter{lofdepth}{1}
-\setcounter{lotdepth}{1}
-\setcounter{LT@tables}{53}
-\setcounter{LT@chunks}{1}
-\setcounter{PWSTtable}{0}
-\setcounter{lstlisting}{0}
 \setcounter{section@level}{3}
 }