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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



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