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I forgot to mention, the mmCIF parser is fine with this and returns
the correct organism string. <br>
<br>
So the other solution is simply to use mmCIF files. To load a
structure from mmCIF with AtomCache you need something like this:<br>
<br>
AtomCache cache = new AtomCache(); <br>
StructureIO.setAtomCache(cache); <br>
cache.setUseMmCif(true);<br>
<br>
Structure struct = StructureIO.getStructure("4XCW");<br>
<br>
In general it is a good idea to use mmCIF, since they have more
complete and better structured information. Additionally, the PDB
has already stopped providing some large structures in the PDB
format, so the only way to cover the whole PDB is to use mmCIF.<br>
<br>
Good luck<br>
<br>
Jose<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 25.06.2015 17:16, Jose Manuel Duarte
wrote:<br>
</div>
<blockquote cite="mid:558C1B35.2040909@psi.ch" type="cite">
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charset=windows-1252">
Hi Guoying<br>
<br>
Thanks for reporting the problem. I've added the issue to github
and fixed it:<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://github.com/biojava/biojava/issues/289">https://github.com/biojava/biojava/issues/289</a><br>
<br>
The next release of biojava should then contain the fix. <br>
<br>
Note that you can also directly open issues in github to report
specific problems like this one.<br>
<br>
Cheers<br>
<br>
Jose<br>
<br>
<br>
<div class="moz-cite-prefix">On 25.06.2015 15:38, Guoying Qi
wrote:<br>
</div>
<blockquote
cite="mid:0B91117E-F086-40CC-8F5A-8D81244B6506@ebi.ac.uk"
type="cite">
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class="">For PDB 4xcw, only partial organism scientific name
returned by the following method:</div>
<div class=""><br class="">
</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class="">getOrganismScientific()</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class="">org.biojava.nbio.structure.Compound </div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class=""><br class="">
</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class="">HELICOBACTER PYLORI (STRAIN J99 / ATCC 7</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class=""><br class="">
</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class="">I traced back to PDBFileParser, it seems this PDB
file being treated in legacy format and the line length being
trimmed into 72.</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class=""><br class="">
</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class="">Can this problem be fixed somehow?</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class=""><br class="">
</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class="">Thanks.</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class=""><br class="">
</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;"
class="">Guoying Qi</div>
<br>
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