Revision history for Perl extension Chemistry::Mol. 0.37 May 10 2009 - Parse non-integer formulas (Daniel Scott). - Fixed some typos. - Fixed bug in Chemistry::File, where $self->mols wasn't updated during the read loop. - Fixed bug where $atom->symbol tried to modify the symbol given (which crashed when the symbol was a constant!) - Added an undocumented "next_id" method (Liliana Felix Avila). - Documented the descriptor methods that existed since 0.36 but were undocumented. 0.36 Sep 20 2005 - Sort formulas in Hill order. - Fixed calc_implicit_hydrogens for halides. 0.35 May 20 2005 - Added formal_radical atom property. - Compatibility with Storable-2.14, which already takes care of weak references. - calc_implicit_hydrogens, add_implicit_hydrogens 0.34 May 16 2005 - Fixed $atom->bonds duplication on $mol->separate (bug 1173237) - New method: safe_clone 0.33 Mar 29 2005 - Fixed spurious warnings in sprout_hydrogens (bug 1157393) - Added a test for incompatible Chemistry::File::SMILES versions. 0.32 Feb 24 2005 - Fixed spurious warnings in separate(). - Fixed division by zero for ill-defined angles. - Fixed bond deletion/addition bug #1076503. 0.31 Nov 10 2004 - Fixed an error in t/zlib.t (forgot to create t/tmp directory) - Fixed some typos in the documentation 0.30 Nov 9 2004 - New Chemistry::File interface - Added gzip support for reading and writing - New Atom methods: sprout_hydrogens, collapse_hydrogens, mass_number - New Mol methods: sprout_hydrogens, collapse_hydrogens - Added support for Chemistry::Isotope - Extended the Chemistry::Obj::attr method - New Obj methods: new() - Fixed backward compatibility bug in File/Dumper.pm - Fixed inconsistency when an object id was changed - Improved the testing suite 0.26 Aug 6 2004 - Added %S option to $mol->printf - Atom.pm: added total_hydrogens, implicit_hydrogens, explicit_valence, and deprecated hydrogens. 0.25 Jun 30 2004 - Fixed Chemistry::File :auto so that it looks in every @INC directory. - Added internal coordinates for atoms. - Updated the tutorial a little bit. 0.24 Jun 16 2004 - Mol:: _weaken, sort_atoms, atom_class, bond_class - Atom:: sprintf, printf, hydrogens, valence - Added the Chemistry::File::Dumper module. 0.23 May 19 2004 - New methods: Mol::printf, sprintf, charge; Atom::aromatic, formal_charge; Bond::aromatic - Fixed POD bug. 0.22 May 17 2004 - Fixed bug in bonds($from) - Added add_atom_np, add_bond_np, bonds_neighbors - Fixed another memory leak - Added Atom::formal_charge 0.21 May 13 2004 - Fixed bug where $/ was undef'ed in a nonlocal way in File.pm. - Added formula parser contributed by Brent Gregersen. - Added %j and %% formats to Formula.pm. 0.20 May 06 2004 - Use Scalar::Util::weaken to avoid strong cyclic references and ensure garbage collection. - New methods for Chemistry::Mol: delete_atom, delete_bond, clone, combine, separate, distance - New methods for Chemistry::Atom: angle, dihedral, angle_deg, dihedral_deg, delete - New methods for Chemistry::Bond: delete - Chemistry::Mol can export read_mol - Chemistry::Atom can export distance, angle, dihedral 0.11 Feb 22 2004 - New methods for Chemistry::Mol: mass, formula, formula_hash - New methods for Chemistry::Atom: mass - New module: Chemistry::File::Formula 0.10 Nov 03 2003 - New methods for Chemistry::Atom: distance - New methods for Chemistry::Obj: del_attr - New subroutines for Chemistry::Mol: read_mol, register_format - New class method for Mol, Atom, and Bond: reset_id - Incompatible changes: - Changed File I/O API. It should be more stable now, but it's certainly not frozen yet. - Chemistry::Mol->atoms() and bonds() now use 1-based indexing instead of zero-based. - Now Chemistry::Obj overloads cmp instead of ==. Note that this overloading behavior was undocumented, so it shouldn't cause a problem. 0.06 Sep 26 2003 - New methods for Chemistry::Mol - atoms() - bonds() - by_id() - atoms_by_name() 0.05 Sep 23 2003 - First release