[Biopython-dev] [Bug 3171] New: inconsistent representation of missing elements PDB.PDBIO.PDBIO and PDB.Atom.Atom
anaryin at gmail.com
Wed Jan 26 11:55:46 UTC 2011
This being "my" problem, how do I fix this in Bugzilla? The problem is
already solved and pushed to Github since a few weeks.
João [...] Rodrigues
On Wed, Jan 26, 2011 at 12:08 PM, <bugzilla-daemon at portal.open-bio.org>wrote:
> Summary: inconsistent representation of missing elements
> PDB.PDBIO.PDBIO and PDB.Atom.Atom
> Product: Biopython
> Version: 1.56
> Platform: Macintosh
> OS/Version: Mac OS
> Status: NEW
> Severity: normal
> Priority: P2
> Component: Main Distribution
> AssignedTo: biopython-dev at biopython.org
> ReportedBy: edvin.fuglebakk at gmail.com
> There seems to be an inconsistency in the way missing elements are
> in PDB.PDBIO.PDBIO and PDB.Atom.Atom.
> The constructor of Atom sets the attribute element to '?' if this is
> while PDBIO raises a value error if it encouters atoms with the element set
> '?'. PDBIO._get_atom_line checks if Atom.element is falsish (None, False, 0
> ...) and chanhes the value of Atom.element to " " if it is.
> So it seems Atom represents missing elements by "?", while PDBIO represents
> them by falsish values, presumably None.
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