[Biopython-dev] [Bug 3171] New: inconsistent representation of missing elements PDB.PDBIO.PDBIO and PDB.Atom.Atom

[João Rodrigues]

This being "my" problem, how do I fix this in Bugzilla? The problem is
already solved and pushed to Github since a few weeks.

Cheers!

João [...] Rodrigues
http://doeidoei.wordpress.com



On Wed, Jan 26, 2011 at 12:08 PM, <bugzilla-daemon at portal.open-bio.org>wrote:

> http://bugzilla.open-bio.org/show_bug.cgi?id=3171
>
>           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
> represented
> in PDB.PDBIO.PDBIO and PDB.Atom.Atom.
>
> The constructor of Atom sets the attribute element to '?' if this is
> unkown,
> while PDBIO raises a value error if it encouters atoms with the element set
> to
> '?'. 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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