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PDB 3NH3 HIS:244 breaks parser with occupancy of -1.0. Changed initia…
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…l last_occupancy of DisorderedAtom to -99.
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João Rodrigues committed May 12, 2011
1 parent 40298a6 commit c177210
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2 changes: 1 addition & 1 deletion Bio/PDB/Atom.py
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Expand Up @@ -301,7 +301,7 @@ def __init__(self, id):
Arguments: Arguments:
o id - string, atom name o id - string, atom name
""" """
self.last_occupancy=-1 self.last_occupancy=-99
DisorderedEntityWrapper.__init__(self, id) DisorderedEntityWrapper.__init__(self, id)


# Special methods # Special methods
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2 comments on commit c177210

@etal
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@etal etal commented on c177210 May 12, 2011

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So this is a magic number now? Can you add a comment to make that clear?

Also consider these alternatives (for choosing the highest-occupancy atom in disordered_add, if I'm reading that correctly):

float("-Inf")
-inf
max(None, -1)
-1
max(float("-Inf"), None)
-inf

@JoaoRodrigues
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-1 was a magic number already, which apparently didn't work for this case. I never saw a negative occupancy, but apparently they might exist (under some very dubious pretense though..). I chose -99 because I doubt that that will be a valid number, since occupancy is (usually) between 0 and 1. Peter however, suggested to use None and I agree. It seems a safer option indeed.

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