++ed by:

1 non-PAUSE user(s).

Ivan Tubert-Brohman

Modules

  • PerlMol - Perl modules for molecular chemistry

Changes for version 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