<html>
<head>
<style>
body {
font-family: Verdana, sans-serif;
font-size: 0.8em;
color:#484848;
}
h1, h2, h3 { font-family: "Trebuchet MS", Verdana, sans-serif; margin: 0px; }
h1 { font-size: 1.2em; }
h2, h3 { font-size: 1.1em; }
a, a:link, a:visited { color: #2A5685;}
a:hover, a:active { color: #c61a1a; }
a.wiki-anchor { display: none; }
fieldset.attachments {border-width: 1px 0 0 0;}
hr {
width: 100%;
height: 1px;
background: #ccc;
border: 0;
}
span.footer {
font-size: 0.8em;
font-style: italic;
}
</style>
</head>
<body>
Issue #2948 has been updated by Lenna Peterson.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15370?detail_id=1677">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Resolved</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>Applied to master here (can't find a corresponding issue or pull request):</p>
<p><a class="external" href="https://github.com/biopython/biopython/commit/cc9da03002ae90a3b8eedae69a8adae7216506b8">https://github.com/biopython/biopython/commit/cc9da03002ae90a3b8eedae69a8adae7216506b8</a></p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2948#change-15370">Bug #2948: _parse_pdb_header_list: bug in TITLE handling</a></h1>
<ul><li>Author: Anonymous</li>
<li>Status: Resolved</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: 1.52</li>
<li>URL: </li></ul>
<p>parse_pdb_header.py<br />_parse_pdb_header_list</p>
<p>Hi,</p>
<p>1. If the TITLE in a PDB begins with a number, the parse_pdb_header_list method is stripping the prefixed number from the title, I believe because the regex written did not expect this. So the TITLE line:<br />TITLE 3D STRUCTURE OF ALZHEIMER'S <abbr title="1-42">ABETA</abbr> FIBRILS <br />becomes:<br />" D STRUCTURE OF ALZHEIMER'S <abbr title="1-42">ABETA</abbr> FIBRILS"</p>
<p>2. ... or it should, but it doesn't. This is because for some reason the title is converted to lower case. So it actually becomes:<br />" d structure of alzheimer's abeta(1-42) fibrils"</p>
<p>This is fixed by changing the line of code:<br />name=_chop_end_codes(tail).lower()<br />to:<br />name=_chop_end_codes(tail)</p>
<p>I don't have a solution for problem <a class="issue tracker-1 status-5 priority-3 priority-lowest closed" title="this is a test (Closed)" href="https://redmine.open-bio.org/issues/1">#1</a>. Frankly, I think the (whole, or most all of the) method should be re-written to use positional stripping, ie, line[X:Y].strip().</p>
<p>Paul</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1463/bug2948.patch">bug2948.patch</a>
(914 Bytes)<br />
<a href="https://redmine.open-bio.org/attachments/download/1464/0001-modified-parse_pdb_header.py.patch">0001-modified-parse_pdb_header.py.patch</a>
(1.01 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1465/0001-modified-parse_pdb_header.py.patch">0001-modified-parse_pdb_header.py.patch</a>
(1.01 KB)<br />
</fieldset>
<hr />
<span class="footer"><p>You have received this notification because you have either subscribed to it, or are involved in it.<br />To change your notification preferences, please click here and login: <a class="external" href="http://redmine.open-bio.org">http://redmine.open-bio.org</a></p></span>
</body>
</html>