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CHANGELOG.md

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Changelog

v2.0.0-rc.1 - 18.10.2021

Changed:

  • Improved SMILES parsing (by using adjacencey lists internally), with tighter error handling (e.g. issues #62 and #60).
  • Faster and improved kekulization algorithm (issue #55 fixed).
  • Support for symbols that are constrained to 0 bonds (e.g., [CH4]) or >8 bonds (users can now specify custon bond constraints with over 8 bonds).
  • New strict=True flag to selfies.encoder, which raises an error if the input SMILES violates the current bond constraints. True by default, can be False for speed-up (if SMILES are guaranteed to be correct).
  • Added bond constraints for B (max. 3 bonds) to the default and preset constraints.
  • Updated the syntax of SELFIES symbols to be cleaner and more readable.
    • Removing expl from atomic symbols, e.g., [C@@Hexpl] becommes [C@@H]
    • Cleaner branch symbols, e.g., [BranchL_2] becomes [=BranchL]
    • Cleaner ring symbols, e.g., [Expl=RingL] becomes [=RingL]
    • If you want to use the old symbols, use the compatible=True flag to selfies.decoder, e.g., sf.decoder('[C][C][Expl=Ring1]',compatible=True) (not recommended!)
  • More logically consistent behaviour of [Ring] symbols.
  • Standardized SELFIES alphabet, i.e., no two symbols stand for the same atom/ion (issue #58), e.g., [N+1] and [N+] are equivalent now.
  • Indexing symbols are now included in the alphabet returned by selfies.get_semantic_robust_alphabet.

Removed

  • Removed constraints flag from selfies.decoder; please use selfies.set_semantic_constraints() and pass in "hypervalent" or "octet_rule" instead.
  • Removed print_error flag in selfies.encoder and selfies.decoder, which now raise errors selfies.EncoderError and selfies.DecoderError, respectively.

Bug Fixes

  • Potential chirality inversion of atoms making ring bonds (e.g. [C@@H]12CCC2CCNC1): fixed by inverting their chirality in selfies.encoder such that they are decoded with the original chirality preserved.
  • Failure to represent mismatching stereochemical specifications at ring bonds (e.g. F/C=C/C/C=C\C): fixed by adding new ring symbols (e.g. [-/RingL], [\/RingL], etc.).

v1.0.4 - 23.04.2021

Added:

  • decoder option for relaxed hypervalence rules, decoder(...,constraints='hypervalent')
  • decoder option for strict octet rules, decoder(...,constraints='octet_rule')

Bug Fix:

  • Fixed constraint for Phosphorus

v1.0.3 - 13.01.2021

Added:

  • Support for aromatic Si and Al (is not officially supported by Daylight SMILES, but RDKit supports it and examples exist in PubChem).

v1.0.2 - 14.10.2020

Added:

  • Support for aromatic Te and triple bonds.
  • Inbuild SELFIES to 1hot encoding, and 1hot encoding to SELFIES

Changed:

  • Added default semantic constraints for charged atoms (single positive/negative charge of [C], [N], [O], [S], [P])
  • Raised the bond capacity of P to 7 bonds (from 5 bonds).

Bug Fixes:

  • Fixed bug: selfies.decoder did not terminate for malformed SELFIES that are missing the closed bracket ']'.

v1.0.1 - 25.08.2020

Changed:

  • Code so that is compatible with python >= 3.5.
  • More descriptive error messages.

Bug Fixes:

  • Minor bug fixes in the encoder for SMILES ending in branches (e.g. C(Cl)(F)), and SMILES with ring numbers between branches (e.g. C(Cl)1(Br)CCCC1)
  • Minor bug fix with ring ordering in decoder (e.g. C1CC2CCC12 vs C1CC2CCC21).

v1.0.0 - 17.08.2020:

Added:

  • Added semantic handling of aromaticity / delocalization (by kekulizing SMILES with aromatic symbols before they are translated into SELFIES by selfies.encoder).
  • Added semantic handling of charged species (e.g. [CH+]1CCC1).
  • Added semantic handling of radical species ([CH]1CCC1) or any species with explicit hydrogens (e.g. CC[CH2]).
  • Added semantic handling of isotopes (e.g. [14CH2]=C or [235U]).
  • Improved semantic handling of explicit atom symbols in square brackets, e.g. Carbene ([C]=C).
  • Improved semantic handling of chirality (e.g. O=C[Co@@](F)(Cl)(Br)(I)S).
  • Improved semantic handling of double-bond configuration (e.g. F/C=C/C=C/C).
  • Added new functions to the library, such as selfies.len_selfies and selfies.split_selfies.
  • Added advanced-user functions to the library to customize the SELFIES semantic constraints, e.g. selfies.set_semantic_constraints. Allows to encode for instance diborane, [BH2]1[H][BH2][H]1.
  • Introduced new padding [nop] (no operation) symbol.

Changed:

  • Optimized the indexing alphabet (it is base-16 now).
  • Optimized the behaviours of rings and branches to fix an issue with specific non-standard molecules that could not be translated.
  • Changed behaviour of Ring/Branch, such that states X9991-X9993 are not necessary anymore.
  • Significantly improved encoding and decoding algorithms, it is much faster now.

v0.2.4 - 01.10.2019:

Added:

  • Function get_alphabet() which returns a list of 29 selfies symbols whose arbitrary combination produce >99.99% valid molecules.

Bug Fixes:

  • Fixed bug which happens when three rings start at one node, and two of them form a double ring.
  • Enabled rings with sizes of up to 8000 SELFIES symbols.
  • Bug fix for tiny ring to RDKit syntax conversion, spanning multiple branches.

We thank Kevin Ryan (LeanAndMean@github), Theophile Gaudin and Andrew Brereton for suggestions and bug reports.

v0.2.2 - 19.09.2019:

Added:

  • Enabled [C@],[C@H],[C@@],[C@@H],[H] to use in a semantic constrained way.

We thank Andrew Brereton for suggestions and bug reports.

v0.2.1 - 02.09.2019:

Added:

  • Decoder: added optional argument to restrict nitrogen to 3 bonds. decoder(...,N_restrict=False) to allow for more bonds; standard: N_restrict=True.
  • Decoder: added optional argument make ring-function bi-local (i.e. confirms bond number at target). decoder(...,bilocal_ring_function=False) to not allow bi-local ring function; standard: bilocal_ring_function=True. The bi-local ring function will allow validity of >99.99% of random molecules.
  • Decoder: made double-bond ring RDKit syntax conform.
  • Decoder: added state X5 and X6 for having five and six bonds free.

Bug Fixes:

  • Decoder + Encoder: allowing for explicit brackets for organic atoms, for instance [I].
  • Encoder: explicit single/double bond for non-canonical SMILES input issue fixed.
  • Decoder: bug fix for [Branch*] in state X1.

We thank Benjamin Sanchez-Lengeling, Theophile Gaudin and Zhenpeng Yao for suggestions and bug reports.

v0.1.1 - 04.06.2019:

  • initial release