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0.12.3 2025-11-28
- Introduce 'write_atom_sub' option to write_SMILES().
0.12.2 2025-11-19
- Introduce 'report_unnecessary_dot_usage' parser option.
0.12.1 2025-10-22
- Do not remove square brackets from atom if its normal valence is
ambiguous.
- Fix a bug in handling of disconnected molecular entities in
parentheses.
- Warn about 2 aromatic atoms in a cycle not having an aromatic bond
between them.
- Warn about aromatic atoms with less than 2 aromatic bonds.
0.12.0 2025-04-25
- Ceasing to output aromatic bonds, excess parentheses and explicit
hydrogen atoms by default. These features can be re-enabled by
writer options.
- Reusing ring bond numbers immediately after their closure. The
old behavior can be brought back via an option.
0.11.6 2025-02-14
- Restoring incompatibility with Perl Graph package versions before
v0.9727 which have a bug in bridges().
- Limiting the set of allowed aromatic elements.
0.11.5 2025-02-13
- Fixing a bug failing to recognise @TB10.
- Forbidding unknown chemical elements.
- Forbidding ring bonds to self.
- Accepting order subroutine in kekulise() in order to make the
algorithm stable.
- Supporting octahedral chirality in chirality_to_pseudograph().
- Introducing Chemistry::OpenSMILES::is_aromatic_bond().
- Reporting aromatic bonds outside aromatic rings in _validate().
0.11.4 2025-02-04
- Reducing false-positive cis/trans conflicts detected in _validate().
- Fixing a bug causing allene systems to be validated more times than
needed in _validate().
0.11.3 2025-02-03
- Respecting and validating allene systems in _validate().
- Better validation of cis/trans and chirality settings in _validate().
0.11.2 2025-01-16
- Fixing nondeterminism in relative cis/trans marker placement.
0.11.1 2025-01-14
- Recognising unimportant anomer chiral centers.
0.11.0 2025-01-06
- Fixing handling of octahedral chirality.
- Implementing an alternative method to mark cis/trans settings by
giving their list instead of providing a callback.
0.10.0 2024-11-28
- Reworking the logic of marking atoms with nonstandard valences.
- Introducing Chemistry::OpenSMILES::valence().
- Changing the API of Chemistry::OpenSMILES::Writer::write_SMILES() to
accept option hash as the second parameter. Backwards compatibility
for old calls is retained.
0.9.2 2024-11-26
- Fix a pair of bugs in valence calculation.
0.9.1 2024-11-26
- Handling trigonal bipyramidal centers.
- Exporting all Chemistry::OpenSMILES::is_chiral_*() subroutines.
- Fixing a bug where H atom counts of 0 given in square brackets were
not preserved.
0.9.0 2023-10-25
- Handling square planar chirality.
0.8.6 2023-06-19
- Implementing is_ring_atom().
- No longer removing chiral centers from atoms in rings.
- Accepting coloring subroutine references in
is_unimportant_double_bond() and mark_all_double_bonds().
- Returning false instead of undefined value.
- Exporting %bond_order_to_symbol and %bond_symbol_to_order to simplify
conversion between bond symbols and orders.
0.8.5 2023-01-26
- Fixing incorrect chirality handling code as it did not consider all
ring bonds up to now.
0.8.4 2022-11-29
- Ceasing to mark unimportant double bonds in
Chemistry::OpenSMILES::Stereo.
0.8.3 2022-11-03
- Exporting %Chemistry::OpenSMILES::normal_valence.
0.8.2 2022-09-20
- Adding Chemistry::OpenSMILES::Aromaticity and
Chemistry::OpenSMILES::Stereo from smiles-scripts project v0.2.0.
- Fixing prototypes of recently added functions.
- Introducing Chemistry::OpenSMILES::is_double_bond().
- Introducing Chemistry::OpenSMILES::is_ring_bond().
0.8.1 2022-05-11
- Fixing a bug with incomplete cis/trans markers on ring bonds.
- Introducing Chemistry::OpenSMILES::toggle_cistrans().
- Introducing two functions for bond type determination.
0.8.0 2022-05-05
- Implementing support for tetrahedral chiral centers having lone
pairs.
- Safeguarding against infinite cycles in
Chemistry::OpenSMILES::Writer::_permutation_order().
- Fixing mistake in Chemistry::OpenSMILES::Parser::parse()
documentation.
0.7.0 2021-10-30
- Fixing important issue with representing tetrahedral chiral centers
by introducing 'chirality_neighbours' key to atom hashes.
0.6.0 2021-10-18
- Allowing multi-digit hydrogen counts if enabled via parser option.
- Standardizing chiral markers for allenal carbons.
- Not standardizing chiral markers in raw output.
- Reporting '@' and '@@' chiralities with other than 4 neighbours as
they cannot be processed right now.
0.5.2 2021-10-11
- Creating explicitly refvertexed Graph objects to get around all the
problems caused by interpreting them as scalar values.
0.5.1 2021-08-29
- Working around an incompatibility with Graph v0.9721.
0.5.0 2021-08-26
- Handling raw parsing output in
Chemistry::OpenSMILES::clean_chiral_centers().
- Fixing a bug in position counting due to $1 pollution.
- Detecting and reporting disconnected parts of moieties.
- Introducing Chemistry::OpenSMILES::is_chiral() to detect both chiral
atoms and moieties.
- Fixing bug in Chemistry::OpenSMILES::clean_chiral_centers() which
caused removal of all chiral centers, not just tetrahedral.
- Introducing Chemistry::OpenSMILES::mirror() to invert chiral centers,
currently only tetrahedral.
- Fixing bug in printing of chiral centers, previously only tetrahedral
centers were printed.
0.4.6 2021-04-14
- Fixing reading/writing of cis/trans ring bonds.
0.4.5 2021-03-25
- Fixing a bug in aromatic bond detection.
0.4.4 2021-03-09
- Introducing Chemistry::OpenSMILES::clean_chiral_centers() to remove
unnecessary tetrahedral chiral settings.
0.4.3 2021-01-25
- Supporting tetrahedral chirality in
Chemistry::OpenSMILES::Writer::write_SMILES().
- Chiralities @TH1 and @TH2 are the same as @ and @@, respectively.
- Specifying the requirement of Graph v0.97 or later.
- Fixing issue with homepage.
0.4.2 2021-01-20
- Exporting Chemistry::OpenSMILES::Writer::write_SMILES().
- Removing chirality information from written SMILES, as code to
write this reliably is not yet available.
- Fixing writing of cis/trans bonds.
0.4.1 2021-01-12
- Fixing an issue with 'scalar %hash' in t/01_atoms.t.
- Listing a dependency on Graph::Traversal::DFS.
0.4.0 2021-01-11
- Adding Chemistry::OpenSMILES::Writer, implementing a SMILES writer
for the data structures built by Chemistry::OpenSMILES::Parser.
- Converting 'charge' atom field to integer.
- Exporting Chemistry::OpenSMILES::is_aromatic().
0.3.2 2020-10-05
- Explicitly setting bond order to ':' on bonds between aromatic
atoms.
0.3.1 2020-09-17
- Establishing deterministic order while generating graph vertices
for implicit hydrogen atoms.
0.3.0 2020-09-16
- Deriving counts of implicit hydrogen atoms.
- Default number of attached hydrogen atoms for atoms in square
brackets is 0.
- Supporting bracketless '*' atom.
0.2.1 2020-08-13
- Adding 'number' atom field to store atom positions in the initial
SMILES string.
- Making 'class' atom field mandatory.
- Making 'isotope' atom field an integer.
0.2.0 2020-05-20
- Fixing an issue with graph merging.
- Unifying the representation of single bonds.
- Extending POD documentation.
0.1.3 2020-05-19
- Detecting and reporting unbalanced parentheses.
- Detecting and reporting unclosed ring bonds.
- Fixing position pointers in error messages, removing line numbers.
- Adding versioned dependency on Module::Build::Parse::Yapp v0.1.2.
- Declaring minimum Perl version.
- Fixing the POD.
0.1.2 2020-05-17
- Turning hydrogen counts into real vertices. If 'raw' option is
present, hydrogen counts are left as integers instead.
0.1.1 2020-05-14
- Adding missing dependency on Graph::Undirected.
- Adding POD.
0.1.0 2020-05-13
- Initial release.
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