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GitLab

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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>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/9a897e6e5f74de6e6f0a68c05ab9b23036f757cc">9a897e6e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-01-28T16:54:31+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup watch file

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/0b94e5e42ba2934bfe53f8543066b5e1a0f0ac47">0b94e5e4</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-01-28T16:54:48+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 02.21</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/c1fa8080abada736ac29d4fa22df6aa4172aaa9f">c1fa8080</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-01-28T16:54:48+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/fb29eaf3fa89a50b0b720c189d9328b780c5b4f4">fb29eaf3</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-01-28T16:54:49+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/02.21'

Update to upstream version '02.21'

with Debian dir ef09dce3d690371cf8d56b411d75a57aaadf5f46</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/9e95fd7149540bbe218862af5b8a7bfbaa09b35b">9e95fd71</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-01-28T16:55:36+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>3 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">

debian/watch

</a>

</li>

<li class="file-stats">

<a href="#88983560358e4b68192cf98b467d75b80c156b22">

probe.c

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/king-probe/-/compare/8a4396a191eae197f387e007c4c8355a73b70c46...9e95fd7149540bbe218862af5b8a7bfbaa09b35b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">king-probe (02.21-1) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Cleanup watch file</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Fri, 28 Jan 2022 16:54:59 +0100</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre>

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1

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">king-probe (02.18-2) unstable; urgency=medium</span>

</pre>

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2

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9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

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3

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * Fix autopkgtest to reflect the result of using the proper radius for</span>

</pre>

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<br>

</li>

<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/king-probe/-/compare/8a4396a191eae197f387e007c4c8355a73b70c46...9e95fd7149540bbe218862af5b8a7bfbaa09b35b#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" 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="2" 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">@@ -2,10 +2,3 @@ version=4</td>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

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3

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<td class="new_line diff-line-num" data-linenumber="3" 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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4" 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">

4

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<td class="new_line diff-line-num" data-linenumber="4" 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">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">   https://github.com/rlabduke/probe/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz</span></pre>

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5

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">#opts="mode=git,pretty=2.16.160404+git%cd.%h" \</span>

</pre>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">#    https://github.com/rlabduke/probe.git HEAD</span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># asked for release tags in</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">#   https://github.com/rlabduke/probe/issues/4</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># closed. :-)</span></pre>

</td>

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</table>

<br>

</li>

<li id="88983560358e4b68192cf98b467d75b80c156b22">

<a href="https://salsa.debian.org/med-team/king-probe/-/compare/8a4396a191eae197f387e007c4c8355a73b70c46...9e95fd7149540bbe218862af5b8a7bfbaa09b35b#88983560358e4b68192cf98b467d75b80c156b22"><strong>probe.c</strong></a>

<hr>

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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">@@ -51,43 +51,8 @@</td>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define INLINE_FOR_SPEED 1</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="53" 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">

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">versionString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"probe: version 2.18.211005, Copyright 1996-2016, J. Michael Word; 2021 Richardson Lab"</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *versionString = "probe: version 2.16.160404, Copyright 1996-2016, J. Michael Word";*/</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *versionString = "probe: version 2.16.130520, Copyright 1996-2013, J. Michael Word";*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.15.130427, merged probeVector, Copyright 1996-2013, J. Michael Word";*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.14.130116, Copyright 1996-2013, J. Michael Word";*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.13.120907, Copyright 1996-2012, J. Michael Word";*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.14.120109, Copyright 1996-2011, J. Michael Word";probeVector version*/</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.13.110909, Copyright 1996-2011, J. Michael Word";*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.13.110830, Copyright 1996-2011, J. Michael Word";*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.12.110413, Copyright 1996-2007, J. Michael Word";*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.12.070821, Copyright 1996-2007, J. Michael Word";*/</span></span>

</pre>

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</td>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.11.061018, Copyright 1996-2006, J. Michael Word";*/</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

66

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.11.060831, Copyright 1996-2006, J. Michael Word";*/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

67

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*minor work: 2.11.060212*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

68

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.11.060129, Copyright 1996-2006, J. Michael Word";*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

69

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.11.050121, Copyright 1996-2005, J. Michael Word";*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

70

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.11.041112, Copyright 1996-2004, J. Michael Word";*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

71

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.10.031014dcr041101, Copyright 1996-2004, J. Michael Word";*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

72

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*"probe: version 2.10  10/14/2003, Copyright 1996-2003, J. Michael Word";*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

73

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*jmw & dcr agreement on version name and maintenance by dcr 041110*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

74

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">shortVersionStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"probe.2.18.211005"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

75

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.16.160404";*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

76

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.16.130520";*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

77

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.15.130427";*/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

78

</td>

<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.14.130116";*/</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

79

</td>

<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.13.120907"; gjk changed %s for OUTCOLor to make -OUT work again*/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

80

</td>

<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.14.120109";probeVector version*/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

81

</td>

<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.13.110909";*/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

82

</td>

<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.13.110830";*/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

83

</td>

<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.12.110413";*/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

84

</td>

<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC84" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.11.061018";*/</span></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "probe.2.11.060831";*/</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "Probe V2.11.060129";*/</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "Probe V2.11.050121";*/</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "Probe V2.11.041112";*/</span> <span class="cm" style="color: #998; font-style: italic;">/*041112 version change*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "Probe V2.10.031014dcr041101";*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*static char *shortVersionStr = "Probe V2.9 ( 10/14/2003)";*/</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">versionString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"probe: version 2.21.211221, Copyright 1996-2016, J. Michael Word; 2021 Richardson Lab"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">shortVersionStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"probe.2.21.211221"</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="56" 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">

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">referenceString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Word, et. al. (1999) J. Mol. Biol. 285, 1711-1733."</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">electronicReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http://kinemage.biochem.duke.edu/"</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="58" 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">

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" 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="112" 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">@@ -147,21 +112,21 @@ static int OutputVDWs    = TRUE; /* global controling display of contact categor</td>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">OnlyBadOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* global controling display of contact categories dcr041010*/</span></span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ContactSUMMARY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* global controling output of contact summaries dcr041101*/</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">Min_regular_hb_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">6</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* globals controling hbond cutoff */</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">Min_charged_hb_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">8</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* defaults set in processCommandline() */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">Min_regular_hb_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">6</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* globals controling hbond cutoff */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">Min_charged_hb_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">8</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* defaults set in processCommandline() */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="152" 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">

152

</td>

<td class="new_line diff-line-num" data-linenumber="117" 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">

117

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">RadScaleFactor</span>       <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* global VDW radius scale Factor r*f */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="153" 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">

153

</td>

<td class="new_line diff-line-num" data-linenumber="118" 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">

118

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">RadScaleOffset</span>       <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* global VDW radius scale Offset r+o */</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

154

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<td class="new_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">CORadScale</span>   <span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">65</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">ATOMC_EXPLICIT_VDW</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* global VDW radius scale Factor for C=O */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">CORadScale</span>   <span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">float</span></span><span class="p"><span class="idiff right">)(</span></span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">65</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">ATOMC_EXPLICIT_VDW</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* global VDW radius scale Factor for C=O */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="155" 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">

155

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<td class="new_line diff-line-num" data-linenumber="120" 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">

120

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">GAPweight</span>            <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">25</span><span class="p">;</span><span class="cm" style="color: #998; font-style: italic;">/* global raw GAP score weight */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="156" 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">

156

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<td class="new_line diff-line-num" data-linenumber="121" 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">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">BUMPweight</span>           <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="cm" style="color: #998; font-style: italic;">/* global raw BUMP score scale Factor */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="157" 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">

157

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<td class="new_line diff-line-num" data-linenumber="122" 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">

122

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">HBweight</span>             <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="cm" style="color: #998; font-style: italic;">/* global raw HBond score scale Factor */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="158" 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">

158

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<td class="new_line diff-line-num" data-linenumber="123" 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">

123

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">CHOHBfactor</span>          <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">;</span><span class="cm" style="color: #998; font-style: italic;">/* global CH..O HBond score scale Factor */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="159" 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">

159

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<td class="new_line diff-line-num" data-linenumber="124" 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">

124

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

160

</td>

<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">LowGoodCut</span>           <span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="p">;</span><span class="cm" style="color: #998; font-style: italic;">/* global cutoff for good bin */</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

125

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">LowGoodCut</span>           <span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span><span class="cm" style="color: #998; font-style: italic;">/* global cutoff for good bin */</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="161" 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">

161

</td>

<td class="new_line diff-line-num" data-linenumber="126" 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">

126

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">HighGoodCut</span>          <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">25</span><span class="p">;</span><span class="cm" style="color: #998; font-style: italic;">/* global cutoff for good bin */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="162" 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">

162

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<td class="new_line diff-line-num" data-linenumber="127" 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">

127

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">WorseBumpCut</span>         <span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* SJ 04/10/2015 - global cutoff for worse overlap*/</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">OccupancyCutoff</span>      <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">02</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* global occupancy below which atom has presence but no clashes */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">OccupancyCutoff</span>      <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">02</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* global occupancy below which atom has presence but no clashes */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="165" 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">

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<td class="new_line diff-line-num" data-linenumber="130" 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">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*unfortunately, one needs intervening atoms to avoid clashes between atoms*/</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="166" 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">

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<td class="new_line diff-line-num" data-linenumber="131" 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">

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*that are separated by <= Maxbonded, which thus needs to pass through any*/</span></span>

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<td class="old_line diff-line-num" data-linenumber="167" 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">

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<td class="new_line diff-line-num" data-linenumber="132" 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">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*atom no matter what it's own occupancy happens to be */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="200" 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="165" 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">@@ -200,6 +165,8 @@ static int  modelSrc  = 0; /*global model specified for source 041114*/</td>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span>  <span class="n" style="color: #333;">modelTarg</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*global model specified for target 041114*/</span></span>

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<td class="old_line diff-line-num" data-linenumber="201" 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">

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span>  <span class="n" style="color: #333;">modelToProcess</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*global model specified for processing 041114*/</span></span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dumpFileName</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>  <span class="cm" style="color: #998; font-style: italic;">/* global name of file to dump atom info to (default none) */</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="203" 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">

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<td class="new_line diff-line-num" data-linenumber="170" 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">

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define ATOMS_IN_THE_SAME_RES(aa, bb) IS_THE_SAME_RES((aa)->r, (bb)->r)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="171" 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">

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*041112 IS_THE_SAME_RES() cannot avoid modeltest, i.e. implied Lmodeltest==1*/</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="205" 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">

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<td class="new_line diff-line-num" data-linenumber="172" 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">

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define IS_THE_SAME_RES(ra, rb)  \</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="431" 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="398" 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">@@ -431,7 +398,27 @@ int mainProbeProc(int argc, char **argv, FILE *outf)</td>

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<td class="new_line diff-line-num" data-linenumber="398" 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">

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/*(returned param used on separate call for autobondrot processing)*/</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="399" 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">

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/*e.g. creates: newH->elem = atomHOd , dummy Hydrogen to make an H-Bond*/</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="c">         <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

434

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<td class="new_line diff-line-num old" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC434" class="line" lang="c">         <span class="cm" style="color: #998; font-style: italic;">/*now do the real work: */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC401" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

402

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* Dump the atom information if we've been asked to. */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

403

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dumpFileName</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

404

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="c">      <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dumpFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

405

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="c">      <span class="n" style="color: #333;">dumpFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">dumpFileName</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

406

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="c">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allMainAtoms</span><span class="p">;</span> <span class="n" style="color: #333;">a</span><span class="p">;</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

407

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="c">        <span class="cm" style="color: #998; font-style: italic;">/* Don't dump Phantom Hydrogen information. */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

408

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="c">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">elem</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">atomHOd</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

409

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC409" class="line" lang="c">          <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">dumpFile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s %s %3d %-4s %c %7.3f %7.3f %7.3f %5.2f %s %s %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

410

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="c">            <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">resname</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">resid</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">atomname</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

411

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="c">            <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">altConf</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">altConf</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

412

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="c">            <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">radius</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

413

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="c">            <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">props</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ACCEPTOR_PROP</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"isAcceptor"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"noAcceptor"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

414

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="c">            <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">props</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">DONOR_PROP</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"isDonor"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"noDonor"</span><span class="p">,</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

415

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="c">            <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">props</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">METAL_PROP</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"isMetallic"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"noMetallic"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

416

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="c">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

417

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="c">      <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

418

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC418" class="line" lang="c">      <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">dumpFile</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

419

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

420

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC420" class="line" lang="c"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

421

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*now do the real work: */</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="435" 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">

435

</td>

<td class="new_line diff-line-num" data-linenumber="422" 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">

422

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC422" class="line" lang="c">     <span class="n" style="color: #333;">doCommand</span><span class="p">(</span><span class="n" style="color: #333;">outf</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="436" 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">

436

</td>

<td class="new_line diff-line-num" data-linenumber="423" 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">

423

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC423" class="line" lang="c">        <span class="n" style="color: #333;">allMainAtoms</span><span class="p">,</span> <span class="n" style="color: #333;">abins</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="437" 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">

437

</td>

<td class="new_line diff-line-num" data-linenumber="424" 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">

424

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC424" class="line" lang="c">        <span class="n" style="color: #333;">dots</span><span class="p">,</span> <span class="n" style="color: #333;">probeRad</span><span class="p">,</span> <span class="n" style="color: #333;">density</span><span class="p">,</span> <span class="n" style="color: #333;">spikelen</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1328" 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="1315" 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">@@ -1328,6 +1315,7 @@ else { /*longlist option*/</td>

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<td class="old_line diff-line-num" data-linenumber="1328" 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">

1328

</td>

<td class="new_line diff-line-num" data-linenumber="1315" 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">

1315

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1315" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"  -OLDU        generate old style -u output: kissEdge2BullsEye, etc</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1329" 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">

1329

</td>

<td class="new_line diff-line-num" data-linenumber="1316" 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">

1316

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1316" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"  -VErbose     verbose mode (default)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1330" 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">

1330

</td>

<td class="new_line diff-line-num" data-linenumber="1317" 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">

1317

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1317" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"  -DOTDUMP     dump dot info while doing examineDots()</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1318

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1318" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"  -DUMPATOMS filename  dump atom information to filename for regression testing</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1331" 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">

1331

</td>

<td class="new_line diff-line-num" data-linenumber="1319" 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">

1319

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1319" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"  -REFerence   display reference string</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1332" 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">

1332

</td>

<td class="new_line diff-line-num" data-linenumber="1320" 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">

1320

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1320" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"  -CHANGEs     display a list of program changes</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1333" 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">

1333

</td>

<td class="new_line diff-line-num" data-linenumber="1321" 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">

1321

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1321" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"  -Quiet       quiet mode</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1496" 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="1484" 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">@@ -1496,6 +1484,13 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,</td>

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<td class="old_line diff-line-num" data-linenumber="1496" 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">

1496

</td>

<td class="new_line diff-line-num" data-linenumber="1484" 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">

1484

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<pre style="margin: 0;"> <span id="LC1484" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1497" 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">

1497

</td>

<td class="new_line diff-line-num" data-linenumber="1485" 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">

1485

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<pre style="margin: 0;"> <span id="LC1485" class="line" lang="c">     <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">compArgStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"DOTDUMP"</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">)){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1498" 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">

1498

</td>

<td class="new_line diff-line-num" data-linenumber="1486" 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">

1486

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1486" class="line" lang="c">        <span class="n" style="color: #333;">Ldotdump</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TRUE</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*111202dcr Ldotdump in examineOneDotEach() */</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1487

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1487" class="line" lang="c">     <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1488

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1488" class="line" lang="c">     <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">compArgStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"DUMPATOMS"</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">)){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1489

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1489" class="line" lang="c">       <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1490

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1490" class="line" lang="c">          <span class="n" style="color: #333;">dumpFileName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1491

</td>

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<pre style="margin: 0;">+<span id="LC1491" class="line" lang="c">       <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1492

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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="c">          <span class="n" style="color: #333;">halt</span><span class="p">(</span><span class="s" style="color: #d14;">"no filename after -DUMPATOMS flag"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1493

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1493" class="line" lang="c">       <span class="p">}</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="1499" 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">

1499

</td>

<td class="new_line diff-line-num" data-linenumber="1494" 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">

1494

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1494" class="line" lang="c">     <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1500" 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">

1500

</td>

<td class="new_line diff-line-num" data-linenumber="1495" 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">

1495

</td>

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<pre style="margin: 0;"> <span id="LC1495" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">compArgStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"QUIET"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)){</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1501" 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">

1501

</td>

<td class="new_line diff-line-num" data-linenumber="1496" 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">

1496

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1496" class="line" lang="c">       <span class="n" style="color: #333;">Verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1633" 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="1628" 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">@@ -1633,14 +1628,14 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,</td>

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<td class="old_line diff-line-num" data-linenumber="1633" 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">

1633

</td>

<td class="new_line diff-line-num" data-linenumber="1628" 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">

1628

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1628" class="line" lang="c">       <span class="n" style="color: #333;">argcnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1634" 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">

1634

</td>

<td class="new_line diff-line-num" data-linenumber="1629" 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">

1629

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1629" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">srcArg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"not water"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1635" 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">

1635

</td>

<td class="new_line diff-line-num" data-linenumber="1630" 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">

1630

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1630" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">keepUnselected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1636

</td>

<td class="new_line diff-line-num old" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1636" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probeRad</span>      <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1631

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<pre style="margin: 0;">+<span id="LC1631" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probeRad</span>      <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1637" 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">

1637

</td>

<td class="new_line diff-line-num" data-linenumber="1632" 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">

1632

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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">groupLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"SCS"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1638" 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">

1638

</td>

<td class="new_line diff-line-num" data-linenumber="1633" 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">

1633

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<pre style="margin: 0;"> <span id="LC1633" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1639" 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">

1639

</td>

<td class="new_line diff-line-num" data-linenumber="1634" 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">

1634

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<pre style="margin: 0;"> <span id="LC1634" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">compArgStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"EXPOSED"</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">)){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1640" 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">

1640

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<td class="new_line diff-line-num" data-linenumber="1635" 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">

1635

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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">EXTERNALSURFACE</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1641" 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">

1641

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<td class="new_line diff-line-num" data-linenumber="1636" 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">

1636

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<pre style="margin: 0;"> <span id="LC1636" class="line" lang="c">       <span class="n" style="color: #333;">nargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1642" 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">

1642

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<td class="new_line diff-line-num" data-linenumber="1637" 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">

1637

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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">keepUnselected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1643

</td>

<td class="new_line diff-line-num old" data-linenumber="1638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1643" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probeRad</span>      <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1638

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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probeRad</span>      <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1644" 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">

1644

</td>

<td class="new_line diff-line-num" data-linenumber="1639" 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">

1639

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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">groupLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"SCS"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1645" 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">

1645

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<td class="new_line diff-line-num" data-linenumber="1640" 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">

1640

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<pre style="margin: 0;"> <span id="LC1640" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1646" 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">

1646

</td>

<td class="new_line diff-line-num" data-linenumber="1641" 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">

1641

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<pre style="margin: 0;"> <span id="LC1641" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">compArgStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"ASURFACE"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)){</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1649" 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="1644" 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">@@ -1649,7 +1644,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,</td>

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<td class="old_line diff-line-num" data-linenumber="1649" 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">

1649

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<td class="new_line diff-line-num" data-linenumber="1644" 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">

1644

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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="c">       <span class="n" style="color: #333;">argcnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1650" 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">

1650

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<td class="new_line diff-line-num" data-linenumber="1645" 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">

1645

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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">srcArg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"not water"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1651" 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">

1651

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<td class="new_line diff-line-num" data-linenumber="1646" 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">

1646

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1646" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">keepUnselected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1652

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<td class="new_line diff-line-num old" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1652" class="line" lang="c">       <span class="n" style="color: #333;">RadScaleOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1647

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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="c">       <span class="n" style="color: #333;">RadScaleOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1653" 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">

1653

</td>

<td class="new_line diff-line-num" data-linenumber="1648" 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">

1648

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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probeRad</span>      <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1654" 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">

1654

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<td class="new_line diff-line-num" data-linenumber="1649" 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">

1649

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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">groupLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"AS"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1655" 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">

1655

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<td class="new_line diff-line-num" data-linenumber="1650" 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">

1650

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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1657" 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="1652" 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">@@ -1657,7 +1652,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,</td>

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<td class="old_line diff-line-num" data-linenumber="1657" 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">

1657

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<td class="new_line diff-line-num" data-linenumber="1652" 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">

1652

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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">EXTERNALSURFACE</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1658" 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">

1658

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<td class="new_line diff-line-num" data-linenumber="1653" 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">

1653

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<pre style="margin: 0;"> <span id="LC1653" class="line" lang="c">       <span class="n" style="color: #333;">nargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1659" 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">

1659

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<td class="new_line diff-line-num" data-linenumber="1654" 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">

1654

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<pre style="margin: 0;"> <span id="LC1654" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">keepUnselected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1660

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<td class="new_line diff-line-num old" data-linenumber="1655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1660" class="line" lang="c">       <span class="n" style="color: #333;">RadScaleOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1655" class="line" lang="c">       <span class="n" style="color: #333;">RadScaleOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1661" 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">

1661

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<td class="new_line diff-line-num" data-linenumber="1656" 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">

1656

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<pre style="margin: 0;"> <span id="LC1656" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probeRad</span>      <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1662" 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">

1662

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<td class="new_line diff-line-num" data-linenumber="1657" 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">

1657

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<pre style="margin: 0;"> <span id="LC1657" class="line" lang="c">       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">groupLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"AS"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1663" 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">

1663

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<td class="new_line diff-line-num" data-linenumber="1658" 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">

1658

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<pre style="margin: 0;"> <span id="LC1658" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2412" 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="2407" 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">@@ -2412,7 +2407,7 @@ atomBins* binAtoms(atom *theAtoms, region *boundingBox, char serialNum,</td>

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<td class="old_line diff-line-num" data-linenumber="2412" 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">

2412

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<td class="new_line diff-line-num" data-linenumber="2407" 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">

2407

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<pre style="margin: 0;"> <span id="LC2407" class="line" lang="c">   <span class="n" style="color: #333;">atomBins</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2413" 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">

2413

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<td class="new_line diff-line-num" data-linenumber="2408" 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">

2408

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2408" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2414" 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">

2414

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<td class="new_line diff-line-num" data-linenumber="2409" 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">

2409

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2409" class="line" lang="c">   <span class="n" style="color: #333;">bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">initBins</span><span class="p">(</span><span class="n" style="color: #333;">serialNum</span><span class="p">,</span> <span class="n" style="color: #333;">boundingBox</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2415

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<td class="new_line diff-line-num old" data-linenumber="2410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2415" class="line" lang="c">       <span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">getMaxRadius</span><span class="p">(</span><span class="n" style="color: #333;">ImplicitH</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">probeRad</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2410

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2410" class="line" lang="c">       <span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">getMaxRadius</span><span class="p">(</span><span class="n" style="color: #333;">ImplicitH</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">probeRad</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">2</span><span class="n" style="color: #333;"><span class="idiff right">f</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2416" 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">

2416

</td>

<td class="new_line diff-line-num" data-linenumber="2411" 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">

2411

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<pre style="margin: 0;"> <span id="LC2411" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2417" 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">

2417

</td>

<td class="new_line diff-line-num" data-linenumber="2412" 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">

2412

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<pre style="margin: 0;"> <span id="LC2412" class="line" lang="c">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theAtoms</span><span class="p">;</span> <span class="n" style="color: #333;">a</span><span class="p">;</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2418" 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">

2418

</td>

<td class="new_line diff-line-num" data-linenumber="2413" 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">

2413

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<pre style="margin: 0;"> <span id="LC2413" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">keepUnselected</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">selflags</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2708" 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="2703" 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">@@ -2708,7 +2703,7 @@ int atomsClose(atom *a, atom *b, float probeRad)</td>

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<td class="old_line diff-line-num" data-linenumber="2708" 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">

2708

</td>

<td class="new_line diff-line-num" data-linenumber="2703" 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">

2703

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2703" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2709" 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">

2709

</td>

<td class="new_line diff-line-num" data-linenumber="2704" 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">

2704

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<pre style="margin: 0;"> <span id="LC2704" class="line" lang="c">   <span class="n" style="color: #333;">lim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">radius</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">radius</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">probeRad</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">probeRad</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2710" 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">

2710

</td>

<td class="new_line diff-line-num" data-linenumber="2705" 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">

2705

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2705" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2711

</td>

<td class="new_line diff-line-num old" data-linenumber="2706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2711" class="line" lang="c">   <span class="n" style="color: #333;">dsq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v3distanceSq</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">));</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2706

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2706" class="line" lang="c">   <span class="n" style="color: #333;">dsq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">v3distanceSq</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">));</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2712" 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">

2712

</td>

<td class="new_line diff-line-num" data-linenumber="2707" 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">

2707

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2707" class="line" lang="c"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2713" 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">

2713

</td>

<td class="new_line diff-line-num" data-linenumber="2708" 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">

2708

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2708" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/* if too close they must be the same atom...dummy atom?? */</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2714" 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">

2714

</td>

<td class="new_line diff-line-num" data-linenumber="2709" 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">

2709

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2709" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3012" 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="3007" 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">@@ -3012,15 +3007,13 @@ void examineOneDotEach(atom *src, int type, atom *scratch,</td>

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<td class="old_line diff-line-num" data-linenumber="3012" 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">

3012

</td>

<td class="new_line diff-line-num" data-linenumber="3007" 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">

3007

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<pre style="margin: 0;"> <span id="LC3007" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*called from genDotIntersect() with same names except scratch==atomList2 */</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3013" 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">

3013

</td>

<td class="new_line diff-line-num" data-linenumber="3008" 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">

3008

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3008" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*cloned and modified from examineDots to do only the OneDotEach option 111205*/</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3014" 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">

3014

</td>

<td class="new_line diff-line-num" data-linenumber="3009" 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">

3009

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3009" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*111013 switch to dump details... 111202 now input param: -dotdump */</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3015

</td>

<td class="new_line diff-line-num old" data-linenumber="3010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3015" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">neighborhoodsq</span><span class="p">,</span><span class="n" style="color: #333;">neighbor2dotsq</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3016" 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">

3016

</td>

<td class="new_line diff-line-num" data-linenumber="3010" 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">

3010

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3010" class="line" lang="c">   <span class="n" style="color: #333;">atom</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">holdsrc</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3017" 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">

3017

</td>

<td class="new_line diff-line-num" data-linenumber="3011" 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">

3011

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3011" class="line" lang="c">   <span class="n" style="color: #333;">atom</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">holdcause</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3018" 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">

3018

</td>

<td class="new_line diff-line-num" data-linenumber="3012" 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">

3012

</td>

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<pre style="margin: 0;"> <span id="LC3012" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">holdtype</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3019" 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">

3019

</td>

<td class="new_line diff-line-num" data-linenumber="3013" 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">

3013

</td>

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<pre style="margin: 0;"> <span id="LC3013" class="line" lang="c">   <span class="n" style="color: #333;">point3d</span> <span class="n" style="color: #333;">holddotloc</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3020" 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">

3020

</td>

<td class="new_line diff-line-num" data-linenumber="3014" 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">

3014

</td>

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<pre style="margin: 0;"> <span id="LC3014" class="line" lang="c">   <span class="n" style="color: #333;">point3d</span> <span class="n" style="color: #333;">holdspikeloc</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3021

</td>

<td class="new_line diff-line-num old" data-linenumber="3015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3021" class="line" lang="c">   <span class="n" style="color: #333;">dotNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">holdresults</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3022" 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">

3022

</td>

<td class="new_line diff-line-num" data-linenumber="3015" 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">

3015

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3015" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">holdovrlaptype</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3023

</td>

<td class="new_line diff-line-num old" data-linenumber="3016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3023" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">holdmingap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">999</span><span class="p">.</span><span class="mi" style="color: #099;">9</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3016

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3016" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">holdmingap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">999</span><span class="p">.</span><span class="mi" style="color: #099;">9</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3024" 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">

3024

</td>

<td class="new_line diff-line-num" data-linenumber="3017" 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">

3017

</td>

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<pre style="margin: 0;"> <span id="LC3017" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">holdptmaster</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3025" 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">

3025

</td>

<td class="new_line diff-line-num" data-linenumber="3018" 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">

3018

</td>

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<pre style="margin: 0;"> <span id="LC3018" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Lholdingdot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*111021dcr src and targ can have diff patterns*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3026" 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">

3026

</td>

<td class="new_line diff-line-num" data-linenumber="3019" 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">

3019

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<pre style="margin: 0;"> <span id="LC3019" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Lbetweenatoms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*111202dcr*/</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3036" 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="3029" 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">@@ -3036,13 +3029,12 @@ void examineOneDotEach(atom *src, int type, atom *scratch,</td>

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<td class="old_line diff-line-num" data-linenumber="3036" 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">

3036

</td>

<td class="new_line diff-line-num" data-linenumber="3029" 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">

3029

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3029" class="line" lang="c">   <span class="n" style="color: #333;">point3d</span> <span class="n" style="color: #333;">targetloc</span><span class="p">,</span> <span class="n" style="color: #333;">dotloc</span><span class="p">,</span> <span class="n" style="color: #333;">dotvect</span><span class="p">,</span> <span class="n" style="color: #333;">exploc</span><span class="p">,</span> <span class="n" style="color: #333;">spikeloc</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3037" 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">

3037

</td>

<td class="new_line diff-line-num" data-linenumber="3030" 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">

3030

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3030" class="line" lang="c">   <span class="n" style="color: #333;">point3d</span> <span class="n" style="color: #333;">gapvect</span><span class="p">,</span> <span class="n" style="color: #333;">gaploc</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="3038" 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">

3038

</td>

<td class="new_line diff-line-num" data-linenumber="3031" 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">

3031

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3031" class="line" lang="c">   <span class="n" style="color: #333;">point3d</span> <span class="n" style="color: #333;">perploc</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*LOneDotEach occluder perpendicular to src-targ 111018*/</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3039

</td>

<td class="new_line diff-line-num old" data-linenumber="3032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3039" class="line" lang="c">   <span class="n" style="color: #333;">point3d</span> <span class="n" style="color: #333;">distalloc</span><span class="p">,</span><span class="n" style="color: #333;">distalvec</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*point across gap from source dot 111024dcr*/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3040" 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">

3040

</td>

<td class="new_line diff-line-num" data-linenumber="3032" 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">

3032

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3032" class="line" lang="c">   <span class="n" style="color: #333;">pointSet</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">srcDots</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3041" 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">

3041

</td>

<td class="new_line diff-line-num" data-linenumber="3033" 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">

3033

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3033" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ptmaster</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">' '</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*pointmaster character  dcr041009*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3042" 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">

3042

</td>

<td class="new_line diff-line-num" data-linenumber="3034" 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">

3034

</td>

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<pre style="margin: 0;"> <span id="LC3034" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*dcr041020*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3043" 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">

3043

</td>

<td class="new_line diff-line-num" data-linenumber="3035" 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">

3035

</td>

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<pre style="margin: 0;"> <span id="LC3035" class="line" lang="c">   <span class="n" style="color: #333;">atom</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*dcr20120120*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3044" 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">

3044

</td>

<td class="new_line diff-line-num" data-linenumber="3036" 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">

3036

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3036" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*int LXHvector = TRUE;*/</span>  <span class="cm" style="color: #998; font-style: italic;">/*dcr20120120  eventually commandline param*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3045

</td>

<td class="new_line diff-line-num old" data-linenumber="3037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3045" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">XHdistance</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">99</span><span class="p">.</span><span class="mi" style="color: #099;">9</span><span class="p">;</span>  <span class="cm" style="color: #998; font-style: italic;">/*dcr20120120*/</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3037

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3037" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">XHdistance</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">99</span><span class="p">.</span><span class="mi" style="color: #099;">9</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span>  <span class="cm" style="color: #998; font-style: italic;">/*dcr20120120*/</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3046" 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">

3046

</td>

<td class="new_line diff-line-num" data-linenumber="3038" 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">

3038

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3038" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">XHTangle</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span>  <span class="cm" style="color: #998; font-style: italic;">/*dcr20120120*/</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3047" 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">

3047

</td>

<td class="new_line diff-line-num" data-linenumber="3039" 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">

3039

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3039" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3048" 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">

3048

</td>

<td class="new_line diff-line-num" data-linenumber="3040" 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">

3040

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3040" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">elem</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ignoreAtom</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3117" 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="3109" 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">@@ -3117,7 +3109,7 @@ void examineOneDotEach(atom *src, int type, atom *scratch,</td>

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<td class="old_line diff-line-num" data-linenumber="3117" 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">

3117

</td>

<td class="new_line diff-line-num" data-linenumber="3109" 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">

3109

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3109" class="line" lang="c">           <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"[src %s %s %s] DOT [%s %s %s] dotloc:%7.3f,%7.3f,%7.3f DOT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">atomname</span><span class="p">,</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">resname</span><span class="p">,</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Hy36resno</span><span class="p">,</span><span class="n" style="color: #333;">extratarg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">atomname</span><span class="p">,</span><span class="n" style="color: #333;">extratarg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">resname</span><span class="p">,</span><span class="n" style="color: #333;">extratarg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Hy36resno</span><span class="p">,</span><span class="n" style="color: #333;">dotloc</span><span class="p">.</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">dotloc</span><span class="p">.</span><span class="n" style="color: #333;">y</span><span class="p">,</span><span class="n" style="color: #333;">dotloc</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3118" 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">

3118

</td>

<td class="new_line diff-line-num" data-linenumber="3110" 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">

3110

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3110" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* */</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3119" 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">

3119

</td>

<td class="new_line diff-line-num" data-linenumber="3111" 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">

3111

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3111" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3120

</td>

<td class="new_line diff-line-num old" data-linenumber="3112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3120" class="line" lang="c">      <span class="n" style="color: #333;">mingap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">999</span><span class="p">.</span><span class="mi" style="color: #099;">9</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3112

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3112" class="line" lang="c">      <span class="n" style="color: #333;">mingap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">999</span><span class="p">.</span><span class="mi" style="color: #099;">9</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3121" 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">

3121

</td>

<td class="new_line diff-line-num" data-linenumber="3113" 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">

3113

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3113" class="line" lang="c">      <span class="n" style="color: #333;">isaHB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tooCloseHB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3122" 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">

3122

</td>

<td class="new_line diff-line-num" data-linenumber="3114" 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">

3114

</td>

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<pre style="margin: 0;"> <span id="LC3114" class="line" lang="c">      <span class="n" style="color: #333;">hbondbumpgap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3123" 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">

3123

</td>

<td class="new_line diff-line-num" data-linenumber="3115" 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">

3115

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3115" class="line" lang="c">      <span class="n" style="color: #333;">ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*expect dot to be rejected*/</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3463" 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="3455" 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">@@ -3463,8 +3455,8 @@ fprintf(stderr," NEIGHBOR [%s %s %s] BENIGN for src---targ interaction\n",targ-></td>

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<td class="old_line diff-line-num" data-linenumber="3463" 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">

3463

</td>

<td class="new_line diff-line-num" data-linenumber="3455" 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">

3455

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3455" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3464" 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">

3464

</td>

<td class="new_line diff-line-num" data-linenumber="3456" 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">

3456

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3456" class="line" lang="c">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nearpt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/*disasterously near, i.e. on top of each other*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3465" 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">

3465

</td>

<td class="new_line diff-line-num" data-linenumber="3457" 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">

3457

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3457" class="line" lang="c">         <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3466

</td>

<td class="new_line diff-line-num old" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3466" class="line" lang="c">            <span class="n" style="color: #333;">sl</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="p">((</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">radius</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span>  <span class="p">(</span><span class="n" style="color: #333;">extratarg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">radius</span><span class="p">))</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3467

</td>

<td class="new_line diff-line-num old" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3467" class="line" lang="c">            <span class="n" style="color: #333;">mingap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">LowGoodCut</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*force arbitrary bad clash*/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3458

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3458" class="line" lang="c">            <span class="n" style="color: #333;">sl</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="p">((</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">radius</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span>  <span class="p">(</span><span class="n" style="color: #333;">extratarg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">radius</span><span class="p">))</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3459

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3459" class="line" lang="c">            <span class="n" style="color: #333;">mingap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">LowGoodCut</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*force arbitrary bad clash*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3468" 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">

3468

</td>

<td class="new_line diff-line-num" data-linenumber="3460" 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">

3460

</td>

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<pre style="margin: 0;"> <span id="LC3460" class="line" lang="c">            <span class="n" style="color: #333;">ovrlaptype</span> <span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*disaster overlap == clash!! */</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3469" 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">

3469

</td>

<td class="new_line diff-line-num" data-linenumber="3461" 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">

3461

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3461" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/*spikeloc calc from src->radius + sl, sl=spikelen*mingap,*/</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3470" 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">

3470

</td>

<td class="new_line diff-line-num" data-linenumber="3462" 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">

3462

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3462" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/*spikelen = 0.50 OR input param*/</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3680" 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="3672" 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">@@ -3680,7 +3672,7 @@ fprintf(stderr," NEIGHBOR [%s %s %s] BENIGN for src---targ interaction\n",targ-></td>

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<td class="old_line diff-line-num" data-linenumber="3680" 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">

3680

</td>

<td class="new_line diff-line-num" data-linenumber="3672" 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">

3672

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<pre style="margin: 0;"> <span id="LC3672" class="line" lang="c">               <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">XHdistance</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">XHdistance</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3681" 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">

3681

</td>

<td class="new_line diff-line-num" data-linenumber="3673" 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">

3673

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<pre style="margin: 0;"> <span id="LC3673" class="line" lang="c">               <span class="p">{</span><span class="cm" style="color: #998; font-style: italic;">/*parent atom for this Hydrogen*/</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3682" 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">

3682

</td>

<td class="new_line diff-line-num" data-linenumber="3674" 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">

3674

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<pre style="margin: 0;"> <span id="LC3674" class="line" lang="c">                  <span class="n" style="color: #333;">XHTangle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v3angle</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">holdcause</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3683

</td>

<td class="new_line diff-line-num old" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3683" class="line" lang="c">                  <span class="n" style="color: #333;">XHTangle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">XHTangle</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">360</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">3</span><span class="p">.</span><span class="mi" style="color: #099;">14159265</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3675

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3675" class="line" lang="c">                  <span class="n" style="color: #333;">XHTangle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">XHTangle</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">360</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">3</span><span class="p">.</span><span class="mi" style="color: #099;">14159265</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3684" 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">

3684

</td>

<td class="new_line diff-line-num" data-linenumber="3676" 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">

3676

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<pre style="margin: 0;"> <span id="LC3676" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3685" 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">

3685

</td>

<td class="new_line diff-line-num" data-linenumber="3677" 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">

3677

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<pre style="margin: 0;"> <span id="LC3677" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Ldotdump</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3686" 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">

3686

</td>

<td class="new_line diff-line-num" data-linenumber="3678" 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">

3678

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3678" class="line" lang="c">                       <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"[src %s %s %s] :: [parent %s %s %s]*YES**about to saveDot:: mingap %8.3f, XHdistance: %8.3f, XHTangle: %8.3f HOLD</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">holdsrc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">atomname</span><span class="p">,</span><span class="n" style="color: #333;">holdsrc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">resname</span><span class="p">,</span><span class="n" style="color: #333;">holdsrc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Hy36resno</span><span class="p">,</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">atomname</span><span class="p">,</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">resname</span><span class="p">,</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Hy36resno</span><span class="p">,</span><span class="n" style="color: #333;">holdmingap</span><span class="p">,</span><span class="n" style="color: #333;">XHdistance</span><span class="p">,</span><span class="n" style="color: #333;">XHTangle</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3754" 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="3746" 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">@@ -3754,7 +3746,7 @@ void examineDots(atom *src, int type, atom *scratch,</td>

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<td class="old_line diff-line-num" data-linenumber="3754" 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">

3754

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<td class="new_line diff-line-num" data-linenumber="3746" 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">

3746

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<pre style="margin: 0;"> <span id="LC3746" class="line" lang="c">      <span class="n" style="color: #333;">v3add</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dotvect</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exploc</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3755" 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">

3755

</td>

<td class="new_line diff-line-num" data-linenumber="3747" 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">

3747

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3747" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3756" 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">

3756

</td>

<td class="new_line diff-line-num" data-linenumber="3748" 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">

3748

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<pre style="margin: 0;"> <span id="LC3748" class="line" lang="c">      <span class="n" style="color: #333;">ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3757

</td>

<td class="new_line diff-line-num old" data-linenumber="3749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3757" class="line" lang="c">      <span class="n" style="color: #333;">mingap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">999</span><span class="p">.</span><span class="mi" style="color: #099;">9</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3749

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3749" class="line" lang="c">      <span class="n" style="color: #333;">mingap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">999</span><span class="p">.</span><span class="mi" style="color: #099;">9</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3758" 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">

3758

</td>

<td class="new_line diff-line-num" data-linenumber="3750" 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">

3750

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3750" class="line" lang="c">      <span class="n" style="color: #333;">isaHB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tooCloseHB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3759" 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">

3759

</td>

<td class="new_line diff-line-num" data-linenumber="3751" 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">

3751

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<pre style="margin: 0;"> <span id="LC3751" class="line" lang="c">      <span class="n" style="color: #333;">hbondbumpgap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3760" 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">

3760

</td>

<td class="new_line diff-line-num" data-linenumber="3752" 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">

3752

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3752" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4670" 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="4662" 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">@@ -4670,7 +4662,6 @@ void freeResults(dotNode *results[][NODEWIDTH])</td>

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<td class="old_line diff-line-num" data-linenumber="4670" 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">

4670

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<td class="new_line diff-line-num" data-linenumber="4662" 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">

4662

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4662" class="line" lang="c"><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4671" 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">

4671

</td>

<td class="new_line diff-line-num" data-linenumber="4663" 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">

4663

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<pre style="margin: 0;"> <span id="LC4663" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4672" 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">

4672

</td>

<td class="new_line diff-line-num" data-linenumber="4664" 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">

4664

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4664" class="line" lang="c">   <span class="n" style="color: #333;">dotNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4673

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<td class="new_line diff-line-num old" data-linenumber="4665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4673" class="line" lang="c">   <span class="n" style="color: #333;">atom</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4674" 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">

4674

</td>

<td class="new_line diff-line-num" data-linenumber="4665" 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">

4665

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4665" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4675" 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">

4675

</td>

<td class="new_line diff-line-num" data-linenumber="4666" 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">

4666

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4666" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">NUMATOMTYPES</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4676" 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">

4676

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<td class="new_line diff-line-num" data-linenumber="4667" 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">

4667

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<pre style="margin: 0;"> <span id="LC4667" class="line" lang="c">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">NODEWIDTH</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4800" 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="4791" 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">@@ -4800,7 +4791,7 @@ void writeOutput(FILE *outf, char* groupname, dotNode *results[][NODEWIDTH], int</td>

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<td class="old_line diff-line-num" data-linenumber="4800" 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">

4800

</td>

<td class="new_line diff-line-num" data-linenumber="4791" 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">

4791

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<pre style="margin: 0;"> <span id="LC4791" class="line" lang="c"><span class="p">{</span><span class="sc" style="color: #d14;">'z'</span><span class="p">,</span><span class="sc" style="color: #d14;">'y'</span><span class="p">,</span><span class="sc" style="color: #d14;">'x'</span><span class="p">,</span><span class="sc" style="color: #d14;">'w'</span><span class="p">,</span><span class="sc" style="color: #d14;">'v'</span><span class="p">,</span><span class="sc" style="color: #d14;">'u'</span><span class="p">,</span><span class="sc" style="color: #d14;">'t'</span><span class="p">,</span><span class="sc" style="color: #d14;">'g'</span><span class="p">,</span><span class="sc" style="color: #d14;">'r'</span><span class="p">,</span><span class="sc" style="color: #d14;">'q'</span><span class="p">,</span><span class="sc" style="color: #d14;">'f'</span><span class="p">,</span><span class="sc" style="color: #d14;">'F'</span><span class="p">,</span><span class="sc" style="color: #d14;">'Q'</span><span class="p">,</span><span class="sc" style="color: #d14;">'R'</span><span class="p">,</span><span class="sc" style="color: #d14;">'G'</span><span class="p">,</span><span class="sc" style="color: #d14;">'T'</span><span class="p">,</span><span class="sc" style="color: #d14;">'U'</span><span class="p">,</span><span class="sc" style="color: #d14;">'V'</span><span class="p">,</span><span class="sc" style="color: #d14;">'W'</span><span class="p">,</span><span class="sc" style="color: #d14;">'X'</span><span class="p">,</span><span class="sc" style="color: #d14;">'Y'</span><span class="p">,</span><span class="sc" style="color: #d14;">'Z'</span><span class="p">};</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4801" 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">

4801

</td>

<td class="new_line diff-line-num" data-linenumber="4792" 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">

4792

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4792" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*0 , 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 ,10 ,11 ,12 ,13 ,14 ,15 ,16 ,17 ,18 ,19 ,20 ,21*/</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4802" 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">

4802

</td>

<td class="new_line diff-line-num" data-linenumber="4793" 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">

4793

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4793" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/*std gapbins scope at least -.5 to +.5, wider if probeRad > 0.25 standard*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="4803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4803

</td>

<td class="new_line diff-line-num old" data-linenumber="4794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4803" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span>  <span class="n" style="color: #333;">gaplimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">probeRad</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">25</span><span class="o" style="font-weight: 600;">?</span><span class="n" style="color: #333;">probeRad</span><span class="o" style="font-weight: 600;">:</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">25</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">;</span>  <span class="cm" style="color: #998; font-style: italic;">/*20111220dcr*/</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4794

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<pre style="margin: 0;">+<span id="LC4794" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span>  <span class="n" style="color: #333;">gaplimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">probeRad</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">25</span><span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;">?</span><span class="n" style="color: #333;">probeRad</span><span class="o" style="font-weight: 600;">:</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">25</span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="n" style="color: #333;"><span class="idiff right">f</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">;</span>  <span class="cm" style="color: #998; font-style: italic;">/*20111220dcr*/</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4804" 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">

4804

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<td class="new_line diff-line-num" data-linenumber="4795" 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">

4795

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<pre style="margin: 0;"> <span id="LC4795" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gapcounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">gaplimit</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4805" 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">

4805

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<td class="new_line diff-line-num" data-linenumber="4796" 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">

4796

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<pre style="margin: 0;"> <span id="LC4796" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">maxgapcounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4806" 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">

4806

</td>

<td class="new_line diff-line-num" data-linenumber="4797" 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">

4797

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<pre style="margin: 0;"> <span id="LC4797" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span>  <span class="n" style="color: #333;">Lgotgapbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6210" 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="6201" 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">@@ -6210,7 +6201,7 @@ atom* updateHydrogenInfo(FILE *outf, atom *allMainAtoms,   atomBins *abins,</td>

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<td class="old_line diff-line-num" data-linenumber="6210" 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">

6210

</td>

<td class="new_line diff-line-num" data-linenumber="6201" 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">

6201

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<pre style="margin: 0;"> <span id="LC6201" class="line" lang="c">              <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6211" 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">

6211

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<td class="new_line diff-line-num" data-linenumber="6202" 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">

6202

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<pre style="margin: 0;"> <span id="LC6202" class="line" lang="c">                 <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">props</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ACCEPTOR_PROP</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6212" 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">

6212

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<td class="new_line diff-line-num" data-linenumber="6203" 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">

6203

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<pre style="margin: 0;"> <span id="LC6203" class="line" lang="c">                 <span class="p">{</span><span class="cm" style="color: #998; font-style: italic;">/* bgn: if acceptor_prop */</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="6213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6213

</td>

<td class="new_line diff-line-num old" data-linenumber="6204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6213" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">hbgap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapSize</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">orig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">),</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">radius</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="6214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="6204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6204

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<pre style="margin: 0;">+<span id="LC6204" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">hbgap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapSize</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">orig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">),</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">radius</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6214" 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">

6214

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<td class="new_line diff-line-num" data-linenumber="6205" 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">

6205

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<pre style="margin: 0;"> <span id="LC6205" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">int</span>   <span class="n" style="color: #333;">foundAromRingAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6215" 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">

6215

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<td class="new_line diff-line-num" data-linenumber="6206" 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">

6206

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<pre style="margin: 0;"> <span id="LC6206" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6216" 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">

6216

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<td class="new_line diff-line-num" data-linenumber="6207" 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">

6207

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<pre style="margin: 0;"> <span id="LC6207" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">props</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">AROMATIC_PROP</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6520" 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="6511" 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">@@ -6520,6 +6511,9 @@ fprintf(outf,"2.16.130520 jjh fixed bug in segid handling\n");</td>

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<td class="old_line diff-line-num" data-linenumber="6520" 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">

6520

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<td class="new_line diff-line-num" data-linenumber="6511" 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">

6511

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<pre style="margin: 0;"> <span id="LC6511" class="line" lang="c"><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outf</span><span class="p">,</span><span class="s" style="color: #d14;">"04/16/2015 - SJ added the -sepworse flag, if true will seperate the overlaps of >= 0.4 and overlaps of >=0.5. This is default by false. Had to change NODEWIDTH value (see probe.h)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> One can change the 0.5 cutoff for worse overlap by specifying the flag DIVWorse</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6521" 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">

6521

</td>

<td class="new_line diff-line-num" data-linenumber="6512" 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">

6512

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6512" class="line" lang="c"><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outf</span><span class="p">,</span><span class="s" style="color: #d14;">"09/24/2021 - RMT Version 2.17 Fixed crash when finding ambiguous Oxygens</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="6522" 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">

6522

</td>

<td class="new_line diff-line-num" data-linenumber="6513" 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">

6513

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6513" class="line" lang="c"><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outf</span><span class="p">,</span><span class="s" style="color: #d14;">"10/05/2021 - RMT Version 2.18 Makes default C=O radius scale depend on table value</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="6523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6514

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6514" class="line" lang="c"><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outf</span><span class="p">,</span><span class="s" style="color: #d14;">"12/09/2021 - RMT Version 2.19 Adds commend-line argument to dump atom info</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="6523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6515

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6515" class="line" lang="c"><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outf</span><span class="p">,</span><span class="s" style="color: #d14;">"12/21/2021 - RMT Version 2.20 Dumps atom information after hydrogens have been updated.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="6523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6516

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6516" class="line" lang="c"><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outf</span><span class="p">,</span><span class="s" style="color: #d14;">"12/21/2021 - RMT Version 2.21 Does not dump Phantom Hydrogen information.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="6523" 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">

6523

</td>

<td class="new_line diff-line-num" data-linenumber="6517" 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">

6517

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6517" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="6524" 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">

6524

</td>

<td class="new_line diff-line-num" data-linenumber="6518" 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">

6518

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6518" class="line" lang="c"><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="6525" 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">

6525

</td>

<td class="new_line diff-line-num" data-linenumber="6519" 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">

6519

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6519" class="line" lang="c"></span>

</pre>

</td>

</tr>

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