ITUB / PerlMol-0.3500 / Changes

Revision history for PerlMol

0.3500
    NEW!!! Added an examples/ directory

    New distributions:
        Chemistry-File-VRML             0.10
        Chemistry-3DBuilder             0.10

    Changed versions:

        Chemistry-Mol                   0.35
            - Added formal_radical atom property.
            - Compatibility with Storable-2.14, which already takes care of
              weak references.
            - calc_implicit_hydrogens, add_implicit_hydrogens
            - Fixed $atom->bonds duplication on $mol->separate (bug 1173237)
            - New method: safe_clone
            - Fixed spurious warnings in sprout_hydrogens (bug 1157393)
            - Added a test for incompatible Chemistry::File::SMILES versions.

        Chemistry-Mok                   0.25
            - Read one molecule at a time using the Chemistry-Mol-0.30 
              interface.
            - New special variable $FH
            - Added support for Chemistry::3DBuilder (-3 command-line option)
            - Add #line to the generated code so that errors give more 
              meaningful line numbers.
            - Fixed parsing bug where the first block used an explicit pattern
              language
            - Restructured Chemistry::Mok to be more object-oriented: 
            - WARNING: the mok object is now a hash reference instead of an 
              array reference. This may affect derived classes.

        Chemistry-File-SMILES           0.44
            - Fixed memory leak that prevented the last atom from being garbage
              collected.

        Chemistry-File-SMARTS           0.22
            - Added the original SMARTS string as the $patt->name property.
            - Added support for atom mapping numbers

        Chemistry-File-PDB              0.21
            - Changed parse_file to read_mol
            - Read multi-model files (each model read as one molecule)
            - Read chain id and insertion code

        Chemistry-Pattern               0.26
            - Fixed mapping bug for overlap => 0

        Chemistry-MidasPattern          0.11
            - Chain support.
            - Be more lenient with whitespace.
            - Refactored parsing and execution.

        Chemistry-File-MDLMol           0.20
            - Added support for charges and radicals.
            - Add implicit hydrogens on read.
            - Support for some query properties: atom lists, bond topology, and
              bond types.

        Chemistry-Isotope               0.11
            - Added natural abundance table

    Unchanged versions:
        Chemistry-InternalCoords        0.18
        Chemistry-MacroMol              0.06
        Chemistry-Ring                  0.18
        Chemistry-Canonicalize          0.10
        Chemistry-Bond-Find             0.21
        Chemistry-File-SLN              0.10
        Chemistry-FormulaPattern        0.10
        Chemistry-File-Mopac            0.15
        Chemistry-File-XYZ              0.11
        Chemistry-Reaction              0.02
        Math-VectorReal                 1.02
        Statistics-Regression           0.15
        Parse-Yapp                      1.05

0.3200  Mar 04 2005
    New distributions:
        Chemistry-Reaction              0.02
        Chemistry-Isotope               0.10
    Changed versions:
        Chemistry-Mol                   0.32
        Chemistry-Mok                   0.24
        Chemistry-InternalCoords        0.18
        Chemistry-File-MDLMol           0.19
        Chemistry-File-SMILES           0.43
        Chemistry-File-SMARTS           0.21
    Unchanged versions:
        Chemistry-MacroMol              0.06
        Chemistry-Ring                  0.18
        Chemistry-Canonicalize          0.10
        Chemistry-Pattern               0.25
        Chemistry-Bond-Find             0.21
        Chemistry-File-SLN              0.10
        Chemistry-File-PDB              0.20
        Chemistry-FormulaPattern        0.10
        Chemistry-MidasPattern          0.10
        Chemistry-File-Mopac            0.15
        Chemistry-File-XYZ              0.11
        Math-VectorReal                 1.02
        Statistics-Regression           0.15
        Parse-Yapp                      1.05

0.2600  Aug 12 2004
    New distributions:
        Chemistry-File-SLN              0.10
        Chemistry-FormulaPattern        0.10
        Parse-Yapp                      1.05
    Changed versions:
        Chemistry-Mol                   0.26
        Chemistry-InternalCoords        0.17
        Chemistry-Ring                  0.18
        Chemistry-Pattern               0.25
        Chemistry-File-MDLMol           0.17
        Chemistry-File-SMILES           0.42
        Chemistry-File-SMARTS           0.20
        Chemistry-File-XYZ              0.11
        Chemistry-Mok                   0.23
    Unchanged versions:
        Chemistry-MacroMol              0.06
        Chemistry-Canonicalize          0.10
        Chemistry-Bond-Find             0.21
        Chemistry-File-PDB              0.20
        Chemistry-MidasPattern          0.10
        Chemistry-File-Mopac            0.15
        Math-VectorReal                 1.02
        Statistics-Regression           0.15


0.2500  Jul 03 2004
    New distributions:
        Chemistry-File-XYZ              0.10
        Chemistry-MidasPattern          0.10
    Changed versions:
        Chemistry-File-MDLMol           0.16
        Chemistry-File-Mopac            0.15
        Chemistry-File-PDB              0.20
        Chemistry-File-SMARTS           0.11
        Chemistry-File-SMILES           0.41
        Chemistry-InternalCoords        0.16
        Chemistry-MacroMol              0.06
        Chemistry-Mok                   0.22
        Chemistry-Mol                   0.25
        Chemistry-Ring                  0.15
    Unchanged versions:
        Chemistry-Bond-Find             0.21
        Chemistry-Canonicalize          0.10
        Chemistry-Pattern               0.21
        Math-VectorReal                 1.02
        Statistics-Regression           0.15



0.2400  Jun 18 2004
    Removed core modules from the bundle. New versions:
        Statistics-Regression           0.15
        Chemistry-Mol                   0.24
        Chemistry-Ring                  0.11
        Chemistry-Canonicalize          0.10
        Chemistry-Pattern               0.21
        Chemistry-Bond-Find             0.21
        Chemistry-File-SMILES           0.40
        Chemistry-File-PDB              0.15
        Chemistry-File-SMARTS           0.10
        Chemistry-Mok                   0.21

0.2300  Jun 11 2004
    First version, including the following modules:
        Test-Simple                 0.47
        Scalar-List-Utils           1.14
        Storable                    2.12
        Text-Balanced               1.95
        Math-VectorReal             1.02
        Chemistry-Mol               0.23
        Chemistry-MacroMol          0.05
        Chemistry-InternalCoords    0.11
        Chemistry-File-MDLMol       0.15
        Chemistry-File-SMILES       0.33
        Chemistry-File-PDB          0.10
        Chemistry-File-Mopac        0.10
        Chemistry-Pattern           0.20
        Chemistry-Bond-Find         0.20
        Chemistry-Mok               0.20



Hosting generously
sponsored by Bytemark