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