[BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.12,1.13

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv8780/doc

Modified Files:
	Changes-0.7.rd 
Log Message:
Added/modified changes for PDB classes


Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** Changes-0.7.rd	18 Dec 2005 19:13:09 -0000	1.12
--- Changes-0.7.rd	15 Jan 2006 09:41:42 -0000	1.13
***************
*** 189,202 ****
  --- Bio::PDB
  
  * Bio::PDB::Atom is removed. Instead, please use Bio::PDB::Record::ATOM and
    Bio::PDB::Record::HETATM.
  * Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
!   changed. Now, Record is changed from hash to Struct, and
!   method_missing is no longer used.
  * In the "MODEL" record, model_serial is changed to serial.
  * In records, record_type is changed to record_name.
! * In any records, record_type is changed to record_name.
! * In most records contains real numbers, changed to return
!   float values instead of strings.
  * Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
    Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
--- 189,207 ----
  --- Bio::PDB
  
+ In 0.7.0:
+ 
  * Bio::PDB::Atom is removed. Instead, please use Bio::PDB::Record::ATOM and
    Bio::PDB::Record::HETATM.
  * Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
!   changed. Now, records is changed from hash to Struct objects.
!   (Note that method_missing is no longer used.)
! * In records, "do_parse" is now automatically called.
!   Users don't need to call do_parse explicitly.
!   (0.7.0 feature: "inspect" does not call do_parse.)
!   (0.7.1 feature: "inspect" calls do_parse.)
  * In the "MODEL" record, model_serial is changed to serial.
  * In records, record_type is changed to record_name.
! * In most records contains real numbers, return values are changed
!   to float instead of string.
  * Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
    Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
***************
*** 204,207 ****
--- 209,228 ----
    Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
    Bio::PDB::DataType.
+ * There are more and more changes to be written...
+ 
+ In 0.7.1:
+ 
+ * Heterogens and HETATMs are completely separeted from residues and ATOMs.
+   HETATMs (Bio::PDB::Record::HETATM objects) are stored in
+   Bio::PDB::Heterogen (which inherits Bio::PDB::Residue).
+ * Waters (resName=="HOH") are treated as normal heterogens.
+   Model#solvents is still available but it will be deprecated.
+ * In Bio::PDB::Chain, adding "LIGAND" to the heterogen id is no longer
+   available. Instead, please use Chain#get_heterogen_by_id method.
+   In addition, Bio::{PDB|PDB::Model::PDB::Chain}#heterogens, #each_heterogen,
+   #find_heterogen, Bio::{PDB|PDB::Model::PDB::Chain::PDB::Heterogen}#hetatms,
+   #each_hetatm, #find_hetatm methods are added.
+ * Bio::PDB#seqres returns Bio::Sequence::NA object if the chain seems to be
+   a nucleic acid sequence.
  * There are more and more changes to be written...