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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/king-probe">Debian Med / king-probe</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/c37c8dbafc87edc181f3a7ebe39afe71b2478e06">c37c8dba</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-10-06T16:40:24+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix autopkgtest to reflect the result of using the proper radius for C=O carbonyl atoms
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<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/8a4396a191eae197f387e007c4c8355a73b70c46">8a4396a1</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-10-06T16:41:13+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/king-probe/-/compare/429b9ff70c0d74dacb87585ae53310332b1edb65...8a4396a191eae197f387e007c4c8355a73b70c46#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">king-probe (02.18-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix autopkgtest to reflect the result of using the proper radius for</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> C=O carbonyl atoms (see https://github.com/rlabduke/probe/issues/9)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 06 Oct 2021 16:40:30 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">king-probe (02.18-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Upstream is now using release tags - adapt watch file</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/king-probe/-/compare/429b9ff70c0d74dacb87585ae53310332b1edb65...8a4396a191eae197f387e007c4c8355a73b70c46#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,10 +19,13 @@ cd "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>data</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># For change of results see here: https://github.com/rlabduke/probe/issues/9</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 1</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell">king-probe 6ins.pdb1 <span class="o" style="font-weight: 600;">>></span> 6ins.kin</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tail</span> +2 6ins.kin <span class="o" style="font-weight: 600;">></span> 6ins.kin.head</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">2e8e38fca908f21e53f47bd3a9411219</span> 6ins.kin.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">e6f6d229b1a5d3a73fcb841dd26a1096</span> 6ins.kin.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksum</span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +33,7 @@ echo</td>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 2</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell">king-probe <span class="nt" style="color: #000080;">-count</span> <span class="nt" style="color: #000080;">-self</span> all 6ins.pdb1 <span class="o" style="font-weight: 600;">></span> 6ins.dotinfo.table</span>
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tail</span> +2 6ins.dotinfo.table <span class="o" style="font-weight: 600;">></span> 6ins.dotinfo.table.head</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">23e6de91706f44a691ab0571ea50bcbb</span> 6ins.dotinfo.table.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">173ae675328752a3e2d6ac693c5870cf</span> 6ins.dotinfo.table.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksum</span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +41,7 @@ echo</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 3</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell">king-probe <span class="nt" style="color: #000080;">-unformated</span> <span class="nt" style="color: #000080;">-self</span> <span class="s2" style="color: #d14;">"all"</span> 6ins.pdb1 <span class="o" style="font-weight: 600;">></span> 6ins.rawinfo.table</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tail</span> +2 6ins.rawinfo.table <span class="o" style="font-weight: 600;">></span> 6ins.rawinfo.table.head</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">2a063119f359eb3ac5728788b372c8db</span> 6ins.rawinfo.table.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">40815736c8cd023fd1a2854d9e66e3d9</span> 6ins.rawinfo.table.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksum</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +49,7 @@ echo</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 4</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell">king-probe <span class="nt" style="color: #000080;">-out</span> all 6ins.pdb1 <span class="o" style="font-weight: 600;">>></span> 6ins.surfacedots.kin</span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tail</span> +2 6ins.surfacedots.kin <span class="o" style="font-weight: 600;">></span> 6ins.surfacedots.kin.head</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">bcea879aa884d7686e5213a9e9c935b4</span> 6ins.surfacedots.kin.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">1aff859a65fc961274f6db4ea499ca25</span> 6ins.surfacedots.kin.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksum</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,7 +57,7 @@ echo</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 5</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell">king-probe <span class="nt" style="color: #000080;">-both</span> chainE chainF 6ins.pdb1 <span class="o" style="font-weight: 600;">>></span> 6insEF.kin</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tail</span> +2 6insEF.kin <span class="o" style="font-weight: 600;">></span> 6insEF.kin.head</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">29f07cd1e66b932f66db395264a6160a</span> 6insEF.kin.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">42433d0201ba33d134be0a312930ca20</span> 6insEF.kin.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksum</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,7 +65,7 @@ echo</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 6</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell">king-probe <span class="nt" style="color: #000080;">-once</span> all all 6ins.pdb1 1zni.pdb1 <span class="o" style="font-weight: 600;">>></span> 6ins_1zni.kin</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tail</span> +2 6ins_1zni.kin <span class="o" style="font-weight: 600;">></span> 6ins_1zni.kin.head</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">b14361cd9e8fe621e74174bc24042adb</span> 6ins_1zni.kin.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">e3cacbc705b23c3acfb233c5f19c8e58</span> 6ins_1zni.kin.head"</span> <span class="o" style="font-weight: 600;">></span> checksum</span>
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66
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksum</span>
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67
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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68
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span></pre>
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