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<h3>

Andrius Merkys pushed to branch master

at <a href="https://salsa.debian.org/med-team/pdb2pqr">Debian Med / pdb2pqr</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/-/commit/1305c081bd2f81a95c0fb0f0ac08dd12a6980189">1305c081</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-02-23T06:57:37-05:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing dependency on xmlto and outdated manpages (will be built using help2man).

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/-/commit/e4e99bb71fc23e0a0f0d6d5d238685d24e759adf">e4e99bb7</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-02-23T06:58:56-05:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Does not depend on openbabel anymore.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/-/commit/4af989fc018e6998de6f327b0f7a798a5e4b9687">4af989fc</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-02-23T08:05:47-05:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Creating manpages using help2man.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/-/commit/157df156942622c11a1496b79aac32c1e659bcbd">157df156</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-02-23T08:14:49-05:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing a symlink to old executable name, pdb2pqr.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/-/commit/faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0">faaa68ce</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-02-23T08:15:59-05:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjusting dependencies of pdb2pqr.

</pre>

</li>

</ul>

<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">

<span class="new-file">

+

debian/clean

</span>

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#27a7894397a58c8e90cc6d3f10355d3fa529ea90">

<span class="deleted-file">

−

debian/pdb2pqr.1.xml

</span>

</a>

</li>

<li class="file-stats">

<a href="#2ff4ccf502c1ef38d81c98e9c6951963dfac01d1">

<span class="new-file">

+

debian/pdb2pqr.links

</span>

</a>

</li>

<li class="file-stats">

<a href="#0505dbb2e6849d1dd6b51a3ccd9f23e05c968386">

<span class="new-file">

+

debian/pdb2pqr.manpages

</span>

</a>

</li>

<li class="file-stats">

<a href="#77ef61f516a77c54daf4b3788783bd7a9d8ef39f">

<span class="deleted-file">

−

debian/psize.1.xml

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="f5f51601866c86e59a004bd93fa415f5675be8c5">

<a href="https://salsa.debian.org/med-team/pdb2pqr/-/compare/d0bc9318aade2fd9f88843c66b36f0b975e2684b...faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0#f5f51601866c86e59a004bd93fa415f5675be8c5"><strong>debian/clean</strong></a>

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<td class="new_line diff-line-num new" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">dx2cube.1</span>

</pre>

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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="plaintext">inputgen.1</span>

</pre>

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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="plaintext">pdb2pqr30.1</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/pdb2pqr/-/compare/d0bc9318aade2fd9f88843c66b36f0b975e2684b...faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(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="8" style="width: 35px; color: rgba(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">@@ -8,8 +8,7 @@ Priority: optional</td>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               dh-sequence-sphinxdoc,</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="11" 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">

11

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<td class="new_line diff-line-num old" data-linenumber="11" 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="LC11" class="line" lang="plaintext">               xmlto,</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="12" 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">

12

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<td class="new_line diff-line-num old" data-linenumber="11" 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="LC12" class="line" lang="plaintext">               openbabel,</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="13" 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="11" 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">

11

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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="LC11" class="line" lang="plaintext">               help2man,</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="plaintext">               python3-dev,</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(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="LC13" class="line" lang="plaintext">               python3-numpy,</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">               python3-pandas <!nocheck>,</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(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="25" style="width: 35px; color: rgba(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">@@ -26,11 +25,11 @@ Rules-Requires-Root: no</td>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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

<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Package: pdb2pqr</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Architecture: all</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="29" 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">

29

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<td class="new_line diff-line-num old" data-linenumber="28" 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="LC29" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="30" 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="28" 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">

28

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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="LC28" class="line" lang="plaintext">Depends: python3-numpy,</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="30" 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="29" 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">

29

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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="LC29" class="line" lang="plaintext">         python3-networkx,</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="30" 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="30" 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">

30

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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="LC30" class="line" lang="plaintext">         python3-pdb2pqr,</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

30

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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">         ${misc:Depends},</span>

</pre>

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31

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<td class="new_line diff-line-num old" data-linenumber="32" 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="LC31" class="line" lang="plaintext">         ${python3:Depends},</span>

</pre>

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32

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<td class="new_line diff-line-num old" data-linenumber="32" 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="LC32" class="line" lang="plaintext">         python3-numpy,</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="33" 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">

33

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<td class="new_line diff-line-num old" data-linenumber="32" 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="LC33" class="line" lang="plaintext">         python3-networkx</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="34" 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="32" 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">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">         ${python3:Depends}</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Suggests: apbs</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

35

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Enhances: autodocktools</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

35

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Description: Preparation of protein structures for electrostatics calculations</span>

</pre>

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<br>

</li>

<li id="27a7894397a58c8e90cc6d3f10355d3fa529ea90">

<a href="https://salsa.debian.org/med-team/pdb2pqr/-/compare/d0bc9318aade2fd9f88843c66b36f0b975e2684b...faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0#27a7894397a58c8e90cc6d3f10355d3fa529ea90"><strong>debian/pdb2pqr.1.xml</strong>

deleted

</a>

<hr>

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1

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC1" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><?xml version="1.0"?></span></span>

</pre>

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2

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC2" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN" "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [</span></span>

</pre>

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3

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC3" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY pdb2pqr "<command></span>pdb2pqr<span class="nt" style="color: #000080;"></command></span>"></span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="xml">]></span>

</pre>

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5

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC5" class="line" lang="xml"><span class="nt" style="color: #000080;"><refentry></span></span>

</pre>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refentryinfo></span></span>

</pre>

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7

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC7" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>PDB2PQR Manual<span class="nt" style="color: #000080;"></title></span></span>

</pre>

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8

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="xml">    <span class="c" style="color: #998; font-style: italic;"><!-- "date" should be the date of the latest change --></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="xml">    <span class="nt" style="color: #000080;"><date></span>2008-06-04<span class="nt" style="color: #000080;"></date></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="xml">    <span class="nt" style="color: #000080;"><productname></span>pdb2pqr<span class="nt" style="color: #000080;"></productname></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="xml">    <span class="nt" style="color: #000080;"><authorgroup></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="xml">      <span class="nt" style="color: #000080;"><author></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="xml">   <span class="nt" style="color: #000080;"><firstname></span>Manuel<span class="nt" style="color: #000080;"></firstname><surname></span>Prinz<span class="nt" style="color: #000080;"></surname></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14" 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="0" 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="LC14" class="line" lang="xml">   <span class="nt" style="color: #000080;"><contrib></span>Wrote this manpage for the Debian System.<span class="nt" style="color: #000080;"></contrib></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="15" 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="0" 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="LC15" class="line" lang="xml">   <span class="nt" style="color: #000080;"><address><email></span>debian@pinguinkiste.de<span class="nt" style="color: #000080;"></email></address></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC16" class="line" lang="xml">      <span class="nt" style="color: #000080;"></author></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="xml">    <span class="nt" style="color: #000080;"></authorgroup></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="18" 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="0" 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="LC18" class="line" lang="xml">    <span class="nt" style="color: #000080;"><copyright><year></span>2008<span class="nt" style="color: #000080;"></year><holder></span>Manuel Prinz<span class="nt" style="color: #000080;"></holder></copyright></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC19" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refentryinfo></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC20" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refmeta></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC21" class="line" lang="xml">    <span class="nt" style="color: #000080;"><refentrytitle></span>pdb2pqr<span class="nt" style="color: #000080;"></refentrytitle></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC22" class="line" lang="xml">    <span class="nt" style="color: #000080;"><manvolnum></span>1<span class="nt" style="color: #000080;"></manvolnum></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC23" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refmeta></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refnamediv></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC25" class="line" lang="xml">    <span class="nt" style="color: #000080;"><refname></span>pdb2pqr<span class="nt" style="color: #000080;"></refname></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="26" 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="0" 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="LC26" class="line" lang="xml">    <span class="nt" style="color: #000080;"><refpurpose></span>Generate <span class="nt" style="color: #000080;"><acronym></span>PQR<span class="nt" style="color: #000080;"></acronym></span> files for use in electrostatics calculations<span class="nt" style="color: #000080;"></refpurpose></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refnamediv></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsynopsisdiv></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="xml">    <span class="nt" style="color: #000080;"><cmdsynopsis></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="xml">      <span class="nt" style="color: #000080;"><command></span>pdb2pqr<span class="nt" style="color: #000080;"></command></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--nodebump<span class="nt" style="color: #000080;"></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--noopt<span class="nt" style="color: #000080;"></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--chain<span class="nt" style="color: #000080;"></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--assign-only<span class="nt" style="color: #000080;"></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--clean<span class="nt" style="color: #000080;"></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--ffout=<span class="nt" style="color: #000080;"><replaceable></span>name<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--with-ph=<span class="nt" style="color: #000080;"><replaceable></span>ph<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--apbs-input<span class="nt" style="color: #000080;"></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--ligand=<span class="nt" style="color: #000080;"><replaceable></span>path<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="xml">      <span class="nt" style="color: #000080;"><group</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="xml">   <span class="nt" style="color: #000080;"><arg><option></span>--verbose<span class="nt" style="color: #000080;"></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="xml">   <span class="nt" style="color: #000080;"><arg><option></span>-v<span class="nt" style="color: #000080;"></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="xml">      <span class="nt" style="color: #000080;"></group></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;">><option></span>--ff=<span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>forcefield<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;">><option><replaceable></span>path<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;">><option><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="xml">    <span class="nt" style="color: #000080;"></cmdsynopsis></span></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="xml">    <span class="nt" style="color: #000080;"><cmdsynopsis></span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="xml">      <span class="nt" style="color: #000080;"><command></span>pdb2pqr<span class="nt" style="color: #000080;"></command></span></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="xml">      <span class="nt" style="color: #000080;"><group</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"req"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="xml">   <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;">><option></span>--help<span class="nt" style="color: #000080;"></option></arg></span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="xml">   <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;">><option></span>-h<span class="nt" style="color: #000080;"></option></arg></span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="xml">      <span class="nt" style="color: #000080;"></group></span></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="xml">    <span class="nt" style="color: #000080;"></cmdsynopsis></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsynopsisdiv></span></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsect1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"description"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>DESCRIPTION<span class="nt" style="color: #000080;"></title></span></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="xml">      <span class="ni" style="color: #800080;">&pdb2pqr;</span> automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a utility for converting protein files in <span class="nt" style="color: #000080;"><acronym></span>PDB<span class="nt" style="color: #000080;"></acronym></span> format (<span class="nt" style="color: #000080;"><replaceable></span>path<span class="nt" style="color: #000080;"></replaceable></span>) to <span class="nt" style="color: #000080;"><acronym></span>PQR<span class="nt" style="color: #000080;"></acronym></span> format (<span class="nt" style="color: #000080;"><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>). These tasks include:<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="xml">      <span class="nt" style="color: #000080;"><itemizedlist></span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem><para></span>Adding a limited number of missing heavy atoms to biomolecular structures<span class="nt" style="color: #000080;"></para></listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem><para></span>Determining side-chain pKas<span class="nt" style="color: #000080;"></para></listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem><para></span>Placing missing hydrogens<span class="nt" style="color: #000080;"></para></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem><para></span>Optimizing the protein for favorable hydrogen bonding<span class="nt" style="color: #000080;"></para></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem><para></span>Assigning charge and radius parameters from a variety of force fields<span class="nt" style="color: #000080;"></para></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="xml">      <span class="nt" style="color: #000080;"></itemizedlist></span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsect1></span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsect1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"options"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>OPTIONS<span class="nt" style="color: #000080;"></title></span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span><span class="ni" style="color: #800080;">&pdb2pqr;</span> accepts the following options:<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="xml">    <span class="nt" style="color: #000080;"><variablelist></span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--ff=<span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>forcefield<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>The <span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>forcefield<span class="nt" style="color: #000080;"></replaceable></span> to use. Current values are <span class="nt" style="color: #000080;"><option></span>amber<span class="nt" style="color: #000080;"></option></span>, <span class="nt" style="color: #000080;"><option></span>charm<span class="nt" style="color: #000080;"></option></span>, <span class="nt" style="color: #000080;"><option></span>parse<span class="nt" style="color: #000080;"></option></span> and <span class="nt" style="color: #000080;"><option></span>tyl06<span class="nt" style="color: #000080;"></option></span>.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--help<span class="nt" style="color: #000080;"></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>-h<span class="nt" style="color: #000080;"></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>Print a help message and exit.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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85

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC85" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="86" 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">

86

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC86" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--nodebump<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="87" 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">

87

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC87" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="88" 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">

88

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<td class="new_line diff-line-num old" data-linenumber="0" 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="xml">     <span class="nt" style="color: #000080;"><para></span>Do not perform debumping operation.<span class="nt" style="color: #000080;"></para></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">

89

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC89" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></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">

90

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC90" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="91" 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">

91

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC91" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="92" 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">

92

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC92" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--noopt<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="93" 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">

93

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC93" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="94" 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">

94

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC94" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>Do not perform hydrogen optimization.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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95

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC95" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="96" 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">

96

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC96" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="97" 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">

97

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC97" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="98" 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">

98

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC98" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--chain<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="99" 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">

99

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC99" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="100" 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">

100

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC100" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Keep the chain ID in the output PQR file.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="101" 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">

101

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC101" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="102" 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">

102

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC102" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="103" 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">

103

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC103" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="104" 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">

104

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC104" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--assign-only<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="105" 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="LC105" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Only assigns charges to add atoms, debump, or optimize.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--clean<span class="nt" style="color: #000080;"></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Do no optimization, atom addition, or parameter assignment, just return</span>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="xml">    the original <span class="nt" style="color: #000080;"><acronym></span>PDB<span class="nt" style="color: #000080;"></acronym></span> file in aligned format.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--ffout=<span class="nt" style="color: #000080;"><replaceable></span>name<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Instead of using the standard caninical naming scheme for</span>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="xml">    residue and atom names, use the names from the given forcefield.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--with-ph=<span class="nt" style="color: #000080;"><replaceable></span>ph<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Use <span class="nt" style="color: #000080;"><command></span>propka<span class="nt" style="color: #000080;"></command></span> to calculate pKas and apply</span>

</pre>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="xml">    them to the molecule given the pH value. Actual PropKa results will</span>

</pre>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="xml">    be output to <span class="nt" style="color: #000080;"><filename><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>.propka<span class="nt" style="color: #000080;"></filename></span>.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="xml">    <span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--apbs-input<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Create an APBS input file based on the generated</span>

</pre>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="xml">    PQR file. Also create a Python pickle for using these</span>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="xml">    parameters in other programs.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--ligand=<span class="nt" style="color: #000080;"><replaceable></span>path<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="143" 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="LC143" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Calculate the parameters for the ligand in MOL2 format at</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="144" 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="LC144" class="line" lang="xml">    the given <span class="nt" style="color: #000080;"><replaceable></span>path<span class="nt" style="color: #000080;"></replaceable></span>. Pdb2pka must be compiled.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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147

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="148" 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="LC148" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--verbose<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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149

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>-v<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></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">

151

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Print additional information to screen.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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

152

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="xml">    <span class="nt" style="color: #000080;"></variablelist></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="155" 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="LC155" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsect1></span></span>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsect1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"extensions"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>EXTENSIONS<span class="nt" style="color: #000080;"></title></span></span>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Extensions add functionality to PDB2PQR and are called by passing a parameter</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="159" 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="LC159" class="line" lang="xml">    to <span class="ni" style="color: #800080;">&pdb2pqr;</span>. They put their results into files located in <span class="nt" style="color: #000080;"><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>The following extensions can be used by <span class="ni" style="color: #800080;">&pdb2pqr;</span>:<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="xml">    <span class="nt" style="color: #000080;"><variablelist></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="162" 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="LC162" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="163" 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="LC163" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--phi<span class="nt" style="color: #000080;"></option></term></span></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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<pre style="margin: 0;">-<span id="LC164" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="165" 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="LC165" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Print the per-residue backbone phi angle to </span>

</pre>

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166

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="xml">    <span class="nt" style="color: #000080;"><filename><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>.phi<span class="nt" style="color: #000080;"></filename></span>.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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167

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="168" 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">

168

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="169" 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">

169

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC169" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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

170

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC170" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--psi<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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

171

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC171" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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

172

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC172" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Print the per-residue backbone psi angle to</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="173" 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">

173

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="xml">    <span class="nt" style="color: #000080;"><filename><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>.phi<span class="nt" style="color: #000080;"></filename></span>.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="174" 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">

174

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC174" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="175" 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">

175

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC175" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="176" 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">

176

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="177" 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">

177

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--hbond<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="178" 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">

178

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC178" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="179" 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">

179

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC179" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Print a list of hygrogen bonds to</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="180" 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">

180

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC180" class="line" lang="xml">    <span class="nt" style="color: #000080;"><filename><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>.hbond<span class="nt" style="color: #000080;"></filename></span>.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="181" 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">

181

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC181" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="182" 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">

182

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC182" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="183" 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">

183

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</td>

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

<pre style="margin: 0;">-<span id="LC183" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="184" 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">

184

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC184" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--chi<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="185" 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">

185

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</td>

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

<pre style="margin: 0;">-<span id="LC185" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="186" 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">

186

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<pre style="margin: 0;">-<span id="LC186" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Print the per-residue backbone chi angle to</span>

</pre>

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187

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="xml">    <span class="nt" style="color: #000080;"><filename><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>.chi<span class="nt" style="color: #000080;"></filename></span>.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="188" 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">

188

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="189" 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">

189

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<pre style="margin: 0;">-<span id="LC189" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="190" 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">

190

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC190" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="191" 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">

191

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--contact<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="192" 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">

192

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="193" 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">

193

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Print a list of contacts to</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="194" 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">

194

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="xml">    <span class="nt" style="color: #000080;"><filename><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>.con<span class="nt" style="color: #000080;"></filename></span>.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="195" 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">

195

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="196" 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">

196

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="197" 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">

197

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="198" 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">

198

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--hbondwhatif<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="199" 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">

199

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="200" 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">

200

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC200" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Print a list of hydrogen bonds to</span>

</pre>

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

201

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="xml">    <span class="nt" style="color: #000080;"><filename><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>.hbo<span class="nt" style="color: #000080;"></filename></span>.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="202" 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">

202

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC202" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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

203

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC203" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="204" 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">

204

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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="LC204" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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

205

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--salt<span class="nt" style="color: #000080;"></option></term></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="206" 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">

206

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Print a list of salt bridges to</span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="xml">    <span class="nt" style="color: #000080;"><filename><replaceable></span>output-path<span class="nt" style="color: #000080;"></replaceable></span>.salt<span class="nt" style="color: #000080;"></filename></span>.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--rama<span class="nt" style="color: #000080;"></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Print the per-residue phi and psi angles to</span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="xml">    <span class="nt" style="color: #000080;"><filename><replaceable></span>outpath-path<span class="nt" style="color: #000080;"></replaceable></span>.rama<span class="nt" style="color: #000080;"></filename></span>.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="xml">    <span class="nt" style="color: #000080;"></variablelist></span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsect1></span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsect1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"citing"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>CITING PDB2PQR<span class="nt" style="color: #000080;"></title></span></span>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Please acknowledge your use of <span class="ni" style="color: #800080;">&pdb2pqr;</span> by citing:<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research, 32, W665-W667 (2004).<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsect1></span></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsect1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"seealso"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>SEE ALSO<span class="nt" style="color: #000080;"></title></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para><citerefentry><refentrytitle></span>psize<span class="nt" style="color: #000080;"></refentrytitle><manvolnum></span>1<span class="nt" style="color: #000080;"></manvolnum></citerefentry></para></span></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsect1></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="xml"><span class="nt" style="color: #000080;"></refentry></span></span></pre>

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<br>

</li>

<li id="2ff4ccf502c1ef38d81c98e9c6951963dfac01d1">

<a href="https://salsa.debian.org/med-team/pdb2pqr/-/compare/d0bc9318aade2fd9f88843c66b36f0b975e2684b...faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0#2ff4ccf502c1ef38d81c98e9c6951963dfac01d1"><strong>debian/pdb2pqr.links</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/bin/pdb2pqr30 usr/bin/pdb2pqr</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">usr/share/man/man1/pdb2pqr30.1.gz usr/share/man/man1/pdb2pqr.1.gz</span></pre>

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<br>

</li>

<li id="0505dbb2e6849d1dd6b51a3ccd9f23e05c968386">

<a href="https://salsa.debian.org/med-team/pdb2pqr/-/compare/d0bc9318aade2fd9f88843c66b36f0b975e2684b...faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0#0505dbb2e6849d1dd6b51a3ccd9f23e05c968386"><strong>debian/pdb2pqr.manpages</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">dx2cube.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">inputgen.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">pdb2pqr30.1</span></pre>

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<br>

</li>

<li id="77ef61f516a77c54daf4b3788783bd7a9d8ef39f">

<a href="https://salsa.debian.org/med-team/pdb2pqr/-/compare/d0bc9318aade2fd9f88843c66b36f0b975e2684b...faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0#77ef61f516a77c54daf4b3788783bd7a9d8ef39f"><strong>debian/psize.1.xml</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><?xml version="1.0"?></span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN" "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY psize "<command></span>psize<span class="nt" style="color: #000080;"></command></span>"></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="xml">]></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="xml"><span class="nt" style="color: #000080;"><refentry></span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refentryinfo></span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>PDB2PQR Manual<span class="nt" style="color: #000080;"></title></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="xml">    <span class="c" style="color: #998; font-style: italic;"><!-- "date" should be the date of the latest change --></span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="xml">    <span class="nt" style="color: #000080;"><date></span>2008-06-04<span class="nt" style="color: #000080;"></date></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="xml">    <span class="nt" style="color: #000080;"><productname></span>psize<span class="nt" style="color: #000080;"></productname></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="xml">    <span class="nt" style="color: #000080;"><authorgroup></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="xml">      <span class="nt" style="color: #000080;"><author></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="xml">   <span class="nt" style="color: #000080;"><firstname></span>Manuel<span class="nt" style="color: #000080;"></firstname><surname></span>Prinz<span class="nt" style="color: #000080;"></surname></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14" 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="0" 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="LC14" class="line" lang="xml">   <span class="nt" style="color: #000080;"><contrib></span>Wrote this manpage for the Debian System.<span class="nt" style="color: #000080;"></contrib></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="15" 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="0" 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="LC15" class="line" lang="xml">   <span class="nt" style="color: #000080;"><address><email></span>debian@pinguinkiste.de<span class="nt" style="color: #000080;"></email></address></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC16" class="line" lang="xml">      <span class="nt" style="color: #000080;"></author></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="xml">    <span class="nt" style="color: #000080;"></authorgroup></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC18" class="line" lang="xml">    <span class="nt" style="color: #000080;"><copyright><year></span>2008<span class="nt" style="color: #000080;"></year><holder></span>Manuel Prinz<span class="nt" style="color: #000080;"></holder></copyright></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC19" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refentryinfo></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC20" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refmeta></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC21" class="line" lang="xml">    <span class="nt" style="color: #000080;"><refentrytitle></span>psize<span class="nt" style="color: #000080;"></refentrytitle></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="xml">    <span class="nt" style="color: #000080;"><manvolnum></span>1<span class="nt" style="color: #000080;"></manvolnum></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refmeta></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC24" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refnamediv></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC25" class="line" lang="xml">    <span class="nt" style="color: #000080;"><refname></span>psize<span class="nt" style="color: #000080;"></refname></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="26" 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="0" 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="LC26" class="line" lang="xml">    <span class="nt" style="color: #000080;"><refpurpose></span>Get dimensions and other information from <span class="nt" style="color: #000080;"><acronym></span>PQR<span class="nt" style="color: #000080;"></acronym></span> files<span class="nt" style="color: #000080;"></refpurpose></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC27" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refnamediv></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC28" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsynopsisdiv></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" 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="0" 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="LC29" class="line" lang="xml">    <span class="nt" style="color: #000080;"><cmdsynopsis></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="xml">      <span class="nt" style="color: #000080;"><command></span>psize<span class="nt" style="color: #000080;"></command></span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--cfact=<span class="nt" style="color: #000080;"><replaceable></span>value<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--fadd=<span class="nt" style="color: #000080;"><replaceable></span>value<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--space=<span class="nt" style="color: #000080;"><replaceable></span>value<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--gememfac=<span class="nt" style="color: #000080;"><replaceable></span>value<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--gememceil=<span class="nt" style="color: #000080;"><replaceable></span>value<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--ofrac=<span class="nt" style="color: #000080;"><replaceable></span>value<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"opt"</span><span class="nt" style="color: #000080;">><option></span>--redfac=<span class="nt" style="color: #000080;"><replaceable></span>value<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="xml">      <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"req"</span><span class="nt" style="color: #000080;">><option><replaceable></span>pqrfile<span class="nt" style="color: #000080;"></replaceable></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="xml">    <span class="nt" style="color: #000080;"></cmdsynopsis></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="xml">    <span class="nt" style="color: #000080;"><cmdsynopsis></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="xml">      <span class="nt" style="color: #000080;"><command></span>psize<span class="nt" style="color: #000080;"></command></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="xml">      <span class="nt" style="color: #000080;"><group</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"req"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="xml">   <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;">><option></span>--help<span class="nt" style="color: #000080;"></option></arg></span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="xml">   <span class="nt" style="color: #000080;"><arg</span> <span class="na" style="color: #008080;">choice=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;">><option></span>-h<span class="nt" style="color: #000080;"></option></arg></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="xml">      <span class="nt" style="color: #000080;"></group></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="xml">    <span class="nt" style="color: #000080;"></cmdsynopsis></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsynopsisdiv></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsect1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"description"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>DESCRIPTION<span class="nt" style="color: #000080;"></title></span></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="xml">      <span class="ni" style="color: #800080;">&psize;</span> derives information from <span class="nt" style="color: #000080;"><acronym></span>PQR<span class="nt" style="color: #000080;"></acronym></span> files to preprare the models of proteins and chemicals for electrostatics calculations. The tool calculates dimensions for coarse and fine grids, grid spacings, box size and estimates the memory required to perform an electrostatics calculation.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>The calculation of this information can be influenced by giving constraints to <span class="ni" style="color: #800080;">&psize;</span> as parameters.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsect1></span></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsect1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"options"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>OPTIONS<span class="nt" style="color: #000080;"></title></span></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span><span class="ni" style="color: #800080;">&psize;</span> accepts the following options:<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="xml">    <span class="nt" style="color: #000080;"><variablelist></span></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--help<span class="nt" style="color: #000080;"></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>-h<span class="nt" style="color: #000080;"></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>Print a help message and exit.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--cfact=<span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>value<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>Factor by which to expand the molecule dimensions to get the coarse grid dimensions<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--fadd=<span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>value<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>Amount to add to the molecule dimensions to get the fine grid dimensions.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--space=<span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>value<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>Desired fine mesh resolution.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--gememfac=<span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>value<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>Number of bytes per grid point required for sequential <span class="nt" style="color: #000080;"><acronym></span>MG<span class="nt" style="color: #000080;"></acronym></span> calculation.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--gememceil=<span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>value<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>Maximum <span class="nt" style="color: #000080;"><acronym></span>MB<span class="nt" style="color: #000080;"></acronym></span> allowed for sequential <span class="nt" style="color: #000080;"><acronym></span>MG<span class="nt" style="color: #000080;"></acronym></span> calculation. Adjust this to force the script to perform faster calculations (which require more parallelism).<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="xml">   <span class="nt" style="color: #000080;"><term><option></span>--ofrac=<span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>value<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="xml">   <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="xml">     <span class="nt" style="color: #000080;"><para></span>Overlap factor between mesh partitions.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="xml">   <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="xml">      <span class="nt" style="color: #000080;"><varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="xml">  <span class="nt" style="color: #000080;"><term><option></span>--redfac=<span class="nt" style="color: #000080;"><replaceable</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>value<span class="nt" style="color: #000080;"></replaceable></option></term></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="xml">  <span class="nt" style="color: #000080;"><listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="104" 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="LC104" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>Maximum factor by which a domain dimension can be reduced during focusing.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="xml">  <span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="xml">      <span class="nt" style="color: #000080;"></varlistentry></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="xml">    <span class="nt" style="color: #000080;"></variablelist></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsect1></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="xml">  <span class="nt" style="color: #000080;"><refsect1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"seealso"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="xml">    <span class="nt" style="color: #000080;"><title></span>SEE ALSO<span class="nt" style="color: #000080;"></title></span></span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para><citerefentry><refentrytitle></span>apbs<span class="nt" style="color: #000080;"></refentrytitle><manvolnum></span>1<span class="nt" style="color: #000080;"></manvolnum></citerefentry></span>, <span class="nt" style="color: #000080;"><citerefentry><refentrytitle></span>pdb2pqr<span class="nt" style="color: #000080;"></refentrytitle><manvolnum></span>1<span class="nt" style="color: #000080;"></manvolnum></citerefentry></para></span></span>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="xml">  <span class="nt" style="color: #000080;"></refsect1></span></span>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="xml"><span class="nt" style="color: #000080;"></refentry></span></span></pre>

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<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/pdb2pqr/-/compare/d0bc9318aade2fd9f88843c66b36f0b975e2684b...faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># -*- mode: makefile; coding: utf-8 -*-</span></span>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">include /usr/share/dpkg/pkg-info.mk</span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>

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

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(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">@@ -20,6 +21,12 @@ override_dh_auto_build:</td>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">     dh_auto_build</span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">     PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">override_dh_installman:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">     PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/dx2cube --no-info --version-string $(DEB_VERSION_UPSTREAM) > dx2cube.1</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">     PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/inputgen --no-info --version-string $(DEB_VERSION_UPSTREAM) > inputgen.1</span>

</pre>

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27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">     PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/pdb2pqr30 --no-info --version-string $(DEB_VERSION_UPSTREAM) > pdb2pqr30.1</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" 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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28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">     dh_installman</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" 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="29" 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">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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30

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">override_dh_installchangelogs_hide:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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31

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">     dh_installchangelogs ChangeLog.md</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

32

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>

</pre>

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