[BioRuby-cvs] bioruby/lib/bio/db/pdb chain.rb, 1.9, 1.10 pdb.rb, 1.27, 1.28
Naohisa Goto
ngoto at dev.open-bio.org
Tue Apr 1 10:36:47 UTC 2008
Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory dev.open-bio.org:/tmp/cvs-serv9574/lib/bio/db/pdb
Modified Files:
chain.rb pdb.rb
Log Message:
* Fixed a bug that ArgumentError occurred in Bio::PDB::Chain#aaseq method
for nucleic acid chains. The same error might also be occurred in
Bio::PDB#seqres and also fixed.
* Fixed a bug that current residue/heterogen is not properly initialized when
current chain is changed.
Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** pdb.rb 28 Dec 2007 14:43:44 -0000 1.27
--- pdb.rb 1 Apr 2008 10:36:44 -0000 1.28
***************
*** 1498,1501 ****
--- 1498,1504 ----
chain = newChain
end
+ # chain might be changed, clearing cResidue and cLigand
+ cResidue = nil
+ cLigand = nil
end
end
***************
*** 1551,1554 ****
--- 1554,1559 ----
c_atom = nil
cChain = nil
+ cResidue = nil
+ cLigand = nil
if cModel.model_serial or cModel.chains.size > 0 then
self.addModel(cModel)
***************
*** 1810,1814 ****
#need to look up with Ala
aa = aa.capitalize
! (Bio::AminoAcid.three2one(aa) or 'X')
end
seq = Bio::Sequence::AA.new(a.to_s)
--- 1815,1823 ----
#need to look up with Ala
aa = aa.capitalize
! (begin
! Bio::AminoAcid.three2one(aa)
! rescue ArgumentError
! nil
! end || 'X')
end
seq = Bio::Sequence::AA.new(a.to_s)
***************
*** 1816,1820 ****
# nucleic acid sequence
a.collect! do |na|
! na = na.strip
na.size == 1 ? na : 'n'
end
--- 1825,1829 ----
# nucleic acid sequence
a.collect! do |na|
! na = na.delete('^a-zA-Z')
na.size == 1 ? na : 'n'
end
Index: chain.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/chain.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** chain.rb 18 Dec 2007 13:48:42 -0000 1.9
--- chain.rb 1 Apr 2008 10:36:44 -0000 1.10
***************
*** 190,194 ****
end
tlc = residue.resName.capitalize
! olc = (Bio::AminoAcid.three2one(tlc) or 'X')
string << olc
end
--- 190,198 ----
end
tlc = residue.resName.capitalize
! olc = (begin
! Bio::AminoAcid.three2one(tlc)
! rescue ArgumentError
! nil
! end || 'X')
string << olc
end
More information about the bioruby-cvs
mailing list