Fix parseMMCIF and fetchPDB to get CIF files #2126
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probably we need more tests for this |
jamesmkrieger
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This won't fix the pfam gzip error, but it will at least make things slightly less cryptic |
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@anupam-banerjee Does any of this conflict with your PR #2165 ? |
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It shouldn't do because it barely touches the actually parsing functions and it's a different one that is touched |
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Bug 1: parseMMCIF was taking .pdb files if they were found. This is solved by adding the format to the second run of findPDBFiles in fetchPDB.
Bug 2: non-pdb files couldn't be retrieved from the PDBe as the extension replacement wasn't being done. This is fixed by making the replacement from .ent as well as .pdb