[BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb,1.18,1.19

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory dev.open-bio.org:/tmp/cvs-serv6337/lib/bio/db/pdb

Modified Files:
	pdb.rb 
Log Message:
In justify_atomname, changed to determine HETATM, and P is added to the
1-letter atoms when ATOM.


Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** pdb.rb	27 Mar 2007 16:37:33 -0000	1.18
--- pdb.rb	28 Mar 2007 10:25:17 -0000	1.19
***************
*** 1039,1043 ****
              end
            end
!           if self.class == HETATM then
              if /\A(B[^AEHIKR]|C[^ADEFLMORSU]|F[^EMR]|H[^EFGOS]|I[^NR]|K[^R]|N[^ABDEIOP]|O[^S]|P[^ABDMORTU]|S[^BCEGIMNR]|V|W|Y[^B])/ =~
                  atomname then
--- 1039,1043 ----
              end
            end
!           if self.kind_of?(HETATM) then
              if /\A(B[^AEHIKR]|C[^ADEFLMORSU]|F[^EMR]|H[^EFGOS]|I[^NR]|K[^R]|N[^ABDEIOP]|O[^S]|P[^ABDMORTU]|S[^BCEGIMNR]|V|W|Y[^B])/ =~
                  atomname then
***************
*** 1047,1051 ****
              end
            else # ATOM
!             if /\A[CHONS]/ =~ atomname then
                return sprintf(' %-3s', atomname)
              else
--- 1047,1051 ----
              end
            else # ATOM
!             if /\A[CHONSP]/ =~ atomname then
                return sprintf(' %-3s', atomname)
              else