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smiles-scripts (unreleased)
* Added:
- cml-to-smi:
- warning about unsupported wedge/hatch stereochemistry.
- sdf-to-smi:
- command line option to turn off charge adjustment after type-8
bond conversion.
- handling of attached hydrogen atoms.
- handling of radicals.
- the '--remove-alkali-bonds' command line option.
- the '--remove-excess-stereochemistry' command line option.
- the '--no-estimate-attached-hydrogens' command line option.
- removal of superfluous cis/trans settings.
- marking of square planar stereochemistry.
- marking of trigonal bipyramidal stereochemistry.
- handling of chiral molecules in non-Sohncke space groups.
- smi_canonicalise:
- the '--ignore-class' command line option.
- the '--canonicalise-nitro-groups' command line option.
- the '--canonicalise-haloanions' command line option (on by
default).
- smi_isomorphism:
- the '--print-side-of-superfluous-moieties' command line option.
- the 'cdksdf2inchi' program.
- the 'smi_check' program.
- the 'smi_check_racemate' program.
- the 'smi_chemical_formula' program.
- the SmilesScripts::Isomorphism module.
- the SmilesScripts::OPSIN module.
- dependency installers for Ubuntu 22.04, Ubuntu 24.04, Debian 11 and
Debian 12.
* Changed:
- switched to Chemistry::OpenSMILES v0.11.6: Perl modules
Chemistry::OpenSMILES::Aromaticity and Chemistry::OpenSMILES::Stereo
have been moved to Chemistry::OpenSMILES in v0.8.2, thus they are
removed from the project.
- cml-to-smi:
- disable network access by default.
- sdf-to-smi:
- preserving original valences for atoms participating in type-8
bonds;
- converting [C-]#[O+] to [C]#[O].
- smi_canonicalise:
- using canonical atom order during kekulisation.
- smi_isomorphism:
- doubling nauty worksize.
- switched to a more conservative method of passing cis/trans settings
to SMILES writer, resulting in a smaller amount of warnings.
* Fixed:
- cml-to-smi:
- incorrect attached hydrogen estimation for atoms with nonstandard
valency.
- sdf-to-smi:
- handling of unusual valences.
- accidental removal of ring closing bonds in aromatic rings.
- smi_isomorphism:
- restoring compatibility with Graph v0.9722 and earlier.
* Removed:
- dependency installer for LinuxMint 19.3.
smiles-scripts (0.2.0)
* Added:
- the 'cml-to-smi' script.
- the 'completalowz' script.
- the 'sdf-to-smi' script.
- the 'smi_canonicalise' script.
- the 'smi_parse' script.
- fixalot:
- handling of a couple more compounds.
* Changed:
- fixalot:
- handling more compounds.
- fixhighz:
- improving the user interface.
* Fixed:
- dependencies of Java classes.
- cdkcif2xyz:
- set a fixed locale to avoid unexpected number formatting
under different system locales.
- cdkdepict:
- fixed a typo in the help message.
smiles-scripts (0.1.0)
* Initial release.
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