[BioRuby] Preparing for 1.1 release
Mikael Borg
mikael.borg at utoronto.ca
Mon Jul 9 20:00:47 UTC 2007
On Mon, 2007-09-07 at 20:57 +0900, Toshiaki Katayama wrote:
> Hi all,
>
> Finally, I'm preparing for the BioRuby 1.1 release.
>
> Developers, are you ready for the next release?
>
> * If you have modules still working on, please let me know ASAP.
> - Which module should be excluded in the next release?
> - When will you finish and commit the final version?
>
> * If you have not filled the ChangeLog file, please document it now.
>
> I hope to pack this weekend.
>
> Regards,
> Toshiaki
>
>
> _______________________________________________
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> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
There are still a few bugs in the pdb parser. I have tried to correct
the ones I've found (see below), but as I find the original code
difficult to understand, I might have introduced new bugs. Maybe you can
have a look and either use my suggested changes, or come up with other
solutions?
Cheers,
Mikael
1. empty records causes parser to crash through
Bio::PDB::Record.Pdb_LString(nil).
Solution: if empty record, make empty string String.new('').
2. if calling method sheet (Bio::PDB) for a Bio::PDB structure that
doesn't contain any sheets, the parser crashes.
Solution: return nil if there are no sheets in structure
# diff -u ~mborg/tmp/bioruby-1.1.0-pre4/lib/bio/db/pdb/pdb.rb pdb.rb
--- /home/mborg/tmp/bioruby-1.1.0-pre4/lib/bio/db/pdb/pdb.rb
2007-04-19 09:59:29.000000000 -0400
+++ pdb.rb 2007-07-09 14:44:01.000000000 -0400
@@ -119,7 +119,11 @@
m
end
def self.new(str)
- String.new(str)
+ if str.nil?
+ String.new('')
+ else
+ String.new(str)
+ end
end
end
@@ -1755,6 +1759,7 @@
# If <em>sheetID</em> is given, it returns an array of
# <code>Bio::PDB::Record::SHEET</code> instances.
def sheet(sheetID = nil)
+ return nil unless @sheet
unless defined?(@sheet)
@sheet = make_grouping(self.record('SHEET'), :sheetID)
end
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