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<h3>
Andreas Tille pushed to branch upstream
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/69dfa6ed8b3dd0484d099a4a885356cc40636149">69dfa6ed</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-06T09:05:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 02.18</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
<span class="new-file">
+
CMakeLists.txt
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</a>
</li>
<li class="file-stats">
<a href="#fdaa912923a515a3fa3ee8601db5625a2e205318">
atomprops.h
</a>
</li>
<li class="file-stats">
<a href="#a495e6ed6e5efde72d06b99d535e2ce219f2c7b2">
autobondrot.c
</a>
</li>
<li class="file-stats">
<a href="#88983560358e4b68192cf98b467d75b80c156b22">
probe.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/king-probe/-/commit/69dfa6ed8b3dd0484d099a4a885356cc40636149#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 3.10.0<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>probe<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="4" 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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>WIN32<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span>-D_CRT_SECURE_NO_WARNINGS<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>probe_SOURCES</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cmake"> abin.c</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cmake"> atomprops.c</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"> autobondrot.c</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"> dots.c</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cmake"> geom3d.c</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cmake"> hybrid_36_c.c</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cmake"> readPDBrecs.c</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cmake"> parse.c</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"> select.c</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cmake"> stdconntable.c</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cmake"> utility.c</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake"> probe.c</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cmake"><span class="p">)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>probe_HEADERS</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cmake"> abin.h</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cmake"> atomprops.h</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cmake"> autobondrot.h</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cmake"> dots.h</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cmake"> geom3d.h</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cmake"> hybrid_36_c.h</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cmake"> parse.h</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cmake"> readPDBrecs.h</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cmake"> select.h</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cmake"> stdconntable.h</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cmake"> utility.h</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cmake"><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>probe <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">probe_SOURCES</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">probe_HEADERS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT WIN32<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>probe m<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span></pre>
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<li id="fdaa912923a515a3fa3ee8601db5625a2e205318">
<a href="https://salsa.debian.org/med-team/king-probe/-/commit/69dfa6ed8b3dd0484d099a4a885356cc40636149#fdaa912923a515a3fa3ee8601db5625a2e205318"><strong>atomprops.h</strong></a>
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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">@@ -93,6 +93,9 @@ enum atomIdentifiers {</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define METALIC_ATOM_FLAG (1 << 0) </span><span class="cm" style="color: #998; font-style: italic;">/*atomProp AtomTbl flags: element features*/</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define IONIC_ATOM_FLAG (1 << 1) </span><span class="cm" style="color: #998; font-style: italic;">/*dcr041007 partial, now on halides*/</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Explicit vdW radius of carbonyl (C=O, atomC) entry. */</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define ATOMC_EXPLICIT_VDW (1.70)</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef INIT_ATOM_TABLE</span></span>
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97
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* For non-metals, explicit VDW radii from */</span></span>
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98
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Gavezzotti, J. Am. Chem. Soc. (1983) 105, 5220-5225. */</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -120,7 +123,7 @@ atomProp AtomTbl[NUMATOMTYPES] = { /* noAtom must be first */</td>
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120
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="p">{</span><span class="n" style="color: #333;">atomHarom</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"Har"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mo" style="color: #099;">00</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">00</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="s" style="color: #d14;">"grey"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>
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121
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"> <span class="p">{</span><span class="n" style="color: #333;">atomHpolar</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"Hpol"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mo" style="color: #099;">00</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">00</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="s" style="color: #d14;">"grey"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>
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122
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> <span class="p">{</span><span class="n" style="color: #333;">atomHOd</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"HOd"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mo" style="color: #099;">00</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">00</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="s" style="color: #d14;">"grey"</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;">/*hb-only-dummy*/</span></span>
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<td class="old_line diff-line-num old" data-linenumber="123" 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">
123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c"> <span class="p">{</span><span class="n" style="color: #333;">atomC</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">70</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">70</span></span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">90</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">77</span><span class="p">,</span> <span class="s" style="color: #d14;">"white"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="p">{</span><span class="n" style="color: #333;">atomC</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ATOMC_EXPLICIT_VDW</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ATOMC_EXPLICIT_VDW</span></span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">90</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">77</span><span class="p">,</span> <span class="s" style="color: #d14;">"white"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>
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124
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="p">{</span><span class="n" style="color: #333;">atomCarom</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="s" style="color: #d14;">"Car"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">75</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">75</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">90</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">77</span><span class="p">,</span> <span class="s" style="color: #d14;">"white"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>
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125
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"> <span class="p">{</span><span class="n" style="color: #333;">atomN</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="s" style="color: #d14;">"N"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">55</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">55</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">70</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">70</span><span class="p">,</span> <span class="s" style="color: #d14;">"sky"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>
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126
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"> <span class="p">{</span><span class="n" style="color: #333;">atomO</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="s" style="color: #d14;">"O"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">66</span><span class="p">,</span> <span class="s" style="color: #d14;">"red"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,7 +140,7 @@ void scanXDBinputText(xformDatabase* xdb, FILE *inf, FILE *outf,</td>
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140
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"> <span class="p">}</span></span>
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141
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141
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<pre style="margin: 0;"> <span id="LC141" 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;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'@'</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* include file */</span></span>
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142
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142
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<pre style="margin: 0;"> <span id="LC142" 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;">if2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="n" style="color: #333;">if2</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;">s</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;">"r"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="n" style="color: #333;">if2</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;">s</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;">"r<span class="idiff left right">b</span>"</span><span class="p">);</span></span>
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">if2</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* recursive call */</span></span>
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<pre style="margin: 0;"> <span id="LC145" 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;">"%s%s</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;">cch</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/king-probe/-/commit/69dfa6ed8b3dd0484d099a4a885356cc40636149#88983560358e4b68192cf98b467d75b80c156b22"><strong>probe.c</strong></a>
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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">@@ -51,7 +51,8 @@</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"></span>
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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>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"></span>
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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 2.16.160404, Copyright 1996-2016, J. Michael Word"</span><span class="p">;</span></span>
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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>
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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>
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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>
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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>
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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>
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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">@@ -70,7 +71,8 @@ static char *versionString = "probe: version 2.16.160404, Copyright 1996-2016, J</td>
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<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>
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71
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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>
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73
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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>
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<pre style="margin: 0;">-<span id="LC73" 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.2.16.160404"</span><span class="p">;</span></span>
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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>
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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>
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74
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76
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<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>
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75
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77
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<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>
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78
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<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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(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="151" style="width: 35px; color: rgba(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">@@ -149,7 +151,7 @@ static float Min_regular_hb_cutoff=0.6; /* globals controling hbond cutoff */</td>
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149
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151
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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>
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150
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152
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<pre style="margin: 0;"> <span id="LC152" 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>
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151
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153
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<pre style="margin: 0;"> <span id="LC153" 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>
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152
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<pre style="margin: 0;">-<span id="LC152" 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="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">75</span></span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* global VDW radius scale Factor for C=O */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="154" 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">
154
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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;"><span class="idiff left right">ATOMC_EXPLICIT_VDW</span></span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* global VDW radius scale Factor for C=O */</span></span>
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153
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155
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<pre style="margin: 0;"> <span id="LC155" 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>
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154
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156
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<pre style="margin: 0;"> <span id="LC156" 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>
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155
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157
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<pre style="margin: 0;"> <span id="LC157" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="297" style="width: 35px; color: rgba(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="299" style="width: 35px; color: rgba(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">@@ -297,7 +299,7 @@ int mainProbeProc(int argc, char **argv, FILE *outf)</td>
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297
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"> <span class="n" style="color: #333;">note</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">);</span></span>
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298
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"> <span class="p">}</span></span>
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299
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="s" style="color: #d14;">"C=O carbon VDW scaled by %.3f to a radius of %g A"</span><span class="p">,</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="c"> <span class="n" style="color: #333;">CORadScale</span><span class="p">,</span> <span class="n" style="color: #333;">CORadScale</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">75</span></span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="302" 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">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="c"> <span class="n" style="color: #333;">CORadScale</span><span class="p">,</span> <span class="n" style="color: #333;">CORadScale</span><span class="o" style="font-weight: 600;">*</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">ATOMC_EXPLICIT_VDW</span></span><span class="p">);</span></span>
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301
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c"> <span class="n" style="color: #333;">note</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">);</span></span>
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302
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rawOutput</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">countDots</span><span class="p">)</span> <span class="p">{</span></span>
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303
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="s" style="color: #d14;">"Score Weights: gapWt=%g, bumpWt=%g, HBWt=%g"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1899" style="width: 35px; color: rgba(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="1901" style="width: 35px; color: rgba(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">@@ -1899,7 +1901,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,</td>
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1899
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1901
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<pre style="margin: 0;"> <span id="LC1901" class="line" lang="c"> <span class="p">}</span></span>
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1900
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1902
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<pre style="margin: 0;"> <span id="LC1902" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1901
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1903
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<pre style="margin: 0;"> <span id="LC1903" class="line" lang="c"> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1902
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<pre style="margin: 0;">-<span id="LC1902" class="line" lang="c"> <span class="n" style="color: #333;">inf</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;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*p holds autobondrot input file name*/</span></span>
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1904
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<pre style="margin: 0;">+<span id="LC1904" class="line" lang="c"> <span class="n" style="color: #333;">inf</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;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"r<span class="idiff left right">b</span>"</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*p holds autobondrot input file name*/</span></span>
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1903
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1905
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<pre style="margin: 0;"> <span id="LC1905" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">inf</span><span class="p">)</span> <span class="p">{</span></span>
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1904
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1906
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<pre style="margin: 0;"> <span id="LC1906" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mabip</span><span class="p">)</span> <span class="p">{</span></span>
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1905
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1907
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<pre style="margin: 0;"> <span id="LC1907" class="line" lang="c"> <span class="n" style="color: #333;">mabip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filenum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1965" style="width: 35px; color: rgba(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="1967" style="width: 35px; color: rgba(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">@@ -1965,7 +1967,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,</td>
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1965
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1967
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<pre style="margin: 0;"> <span id="LC1967" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1966
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1968
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<pre style="margin: 0;"> <span id="LC1968" class="line" lang="c"> <span class="p">{</span></span>
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1967
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1969
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<pre style="margin: 0;"> <span id="LC1969" class="line" lang="c"> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1968
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<pre style="margin: 0;">-<span id="LC1968" class="line" lang="c"> <span class="n" style="color: #333;">inf</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;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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1970
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<pre style="margin: 0;">+<span id="LC1970" class="line" lang="c"> <span class="n" style="color: #333;">inf</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;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"r<span class="idiff left right">b</span>"</span><span class="p">);</span></span>
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1969
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1971
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<pre style="margin: 0;"> <span id="LC1971" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">inf</span><span class="p">)</span></span>
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1970
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1972
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<pre style="margin: 0;"> <span id="LC1972" class="line" lang="c"> <span class="p">{</span></span>
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1971
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1973
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<pre style="margin: 0;"> <span id="LC1973" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">inputfilename</span><span class="p">,</span><span class="n" style="color: #333;">p</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*dcr041023*/</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1992" style="width: 35px; color: rgba(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="1994" style="width: 35px; color: rgba(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">@@ -1992,7 +1994,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,</td>
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1992
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1994
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<pre style="margin: 0;"> <span id="LC1994" class="line" lang="c"> <span class="n" style="color: #333;">DoMcMc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TRUE</span><span class="p">;</span></span>
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1993
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1995
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<pre style="margin: 0;"> <span id="LC1995" class="line" lang="c"> <span class="n" style="color: #333;">DoHet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TRUE</span><span class="p">;</span></span>
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1994
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1996
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<pre style="margin: 0;"> <span id="LC1996" class="line" lang="c"> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1995
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<pre style="margin: 0;">-<span id="LC1995" class="line" lang="c"> <span class="n" style="color: #333;">inf</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;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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1997
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<pre style="margin: 0;">+<span id="LC1997" class="line" lang="c"> <span class="n" style="color: #333;">inf</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;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"r<span class="idiff left right">b</span>"</span><span class="p">);</span></span>
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1996
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<td class="new_line diff-line-num" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1998
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<pre style="margin: 0;"> <span id="LC1998" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">inf</span><span class="p">)</span></span>
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1997
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1999
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<pre style="margin: 0;"> <span id="LC1999" class="line" lang="c"> <span class="p">{</span></span>
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1998
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2000
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<pre style="margin: 0;"> <span id="LC2000" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">inputfilename</span><span class="p">,</span><span class="n" style="color: #333;">p</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*dcr041023*/</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2242" style="width: 35px; color: rgba(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="2244" style="width: 35px; color: rgba(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">@@ -2242,7 +2244,7 @@ void ProcessResInfo(chainEndData_t *ed, atom *a)</td>
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2242
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2244
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<pre style="margin: 0;"> <span id="LC2244" 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;">strcmp</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 class="s" style="color: #d14;">" O "</span><span class="p">))</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* last Os[0-7] (cleared each res)*/</span></span>
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2243
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2245
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<pre style="margin: 0;"> <span id="LC2245" 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="mi" style="color: #099;">8</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>
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2244
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2246
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<pre style="margin: 0;"> <span id="LC2246" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ed</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ambigO</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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2245
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<pre style="margin: 0;">-<span id="LC2245" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ed</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ambig<span class="idiff left right">N</span></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;">1</span><span class="p">]</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;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="p">))</span> <span class="p">{</span></span>
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2247
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<pre style="margin: 0;">+<span id="LC2247" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ed</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ambig<span class="idiff left right">O</span></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;">1</span><span class="p">]</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;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r</span><span class="p">))</span> <span class="p">{</span></span>
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2246
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2248
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<pre style="margin: 0;"> <span id="LC2248" class="line" lang="c"> <span class="n" style="color: #333;">ed</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ambigO</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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2247
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2249
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<pre style="margin: 0;"> <span id="LC2249" class="line" lang="c"> <span class="p">}</span></span>
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2248
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2250
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<pre style="margin: 0;"> <span id="LC2250" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6516" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6516,6 +6518,8 @@ fprintf(outf,"2.15.130427 version number change for merged code! \n");</td>
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6516
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6518
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<pre style="margin: 0;"> <span id="LC6518" 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;">"2.16.130509 jjh added support for segid instead of chaind</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6517
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6519
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<pre style="margin: 0;"> <span id="LC6519" 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;">"2.16.130520 jjh fixed bug in segid handling</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6518
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6520
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<pre style="margin: 0;"> <span id="LC6520" 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>
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6521
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<pre style="margin: 0;">+<span id="LC6521" 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>
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<td class="old_line diff-line-num new" data-linenumber="6519" 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="6522" 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">
6522
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<pre style="margin: 0;">+<span id="LC6522" 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>
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<td class="old_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
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<td class="new_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
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<pre style="margin: 0;"> <span id="LC6523" class="line" lang="c"></span>
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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="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
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<pre style="margin: 0;"> <span id="LC6524" 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>
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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
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6525
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<pre style="margin: 0;"> <span id="LC6525" class="line" lang="c"></span>
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