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 $mol->printf
- Atom.pm: added total_hydrogens, implicit_hydrogens, explicit_valence,
and deprecated hydrogens.
0.25 Jun 30 2004
- Fixed Chemistry::File :auto so that it looks in every @INC directory.
- Added internal coordinates for atoms.
- Updated the tutorial a little bit.
0.24 Jun 16 2004
- Mol:: weaken, sortatoms, atom_class, bond_class
- Atom:: sprintf, printf, hydrogens, valence
- Added the Chemistry::File::Dumper module.
0.23 May 19 2004
- New methods: Mol::printf, sprintf, charge; Atom::aromatic,
formal_charge; Bond::aromatic
- Fixed POD bug.
0.22 May 17 2004
- Fixed bug in bonds($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