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structure/caching.md

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@@ -48,21 +48,35 @@ class is the main place to influence the level of detail and as a consequence th
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This example turns on the use of chemical components when loading a structure. (See also the [next chapter](chemcomp.md))
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<pre>
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AtomCache cache = new AtomCache();
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AtomCache cache = new AtomCache();
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cache.setPath("/tmp/");
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cache.setPath("/tmp/");
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FileParsingParameters params = cache.getFileParsingParams();
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FileParsingParameters params = cache.getFileParsingParams();
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params.setLoadChemCompInfo(true);
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params.setLoadChemCompInfo(true);
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StructureIO.setAtomCache(cache);
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StructureIO.setAtomCache(cache);
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Structure structure = StructureIO.getStructure("4hhb");
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Structure structure = StructureIO.getStructure("4hhb");
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</pre>
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## Caching of other SCOP, CATH
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The AtomCache not only provides access to PDB, it can also fetch Structure representations of protein domains, as defined by SCOP and CATH.
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<pre>
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// uses a SCOP domain definition
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Structure domain1 = StructureIO.getStructure("d4hhba_");
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// Get a specific protein chain, note: chain IDs are case sensitive, PDB IDs are not.
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Structure chain1 = StructureIO.getStructure("4HHB.A");
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</pre>
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There are quite a number of external database IDs that are supported here. See the
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<a href="http://www.biojava.org/docs/api/org/biojava/bio/structure/align/util/AtomCache.html#getStructure(java.lang.String)">AtomCache documentation</a> for more details on the supported options.
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