Change Log

v3.0.3 (2023-06-19)

Now compatible with python 3.11

v3.0.2 (2023-02-23)

Now try to find largest component with multiple compounds separated via . in SMILES
Added langchain for text explanations

v3.0.1 (2023-02-02)

Removed ~ any bonds from SMILES strings coming from synspace

v3.0.0 (2023-01-24)

Added synspace method to generate synthetically feasible space
Added drug-like filter by default for counterfactuals

v2.2.1 (2022-12-7)

Fixed bug in sorting for text explanations
Fixed empty plot names saying None
Added priority for naming and removed invalid names
Added more names (metyhl, ethyl, butyl, etc)
Fixed sample_space to accept partials or objects
Added openai prompting
Added name_morgan_bit as external facing

v2.2.0 (2022-11-3)

Added natural language explanation method

v2.1.1 (2022-6-03)

Fixed plotting bug in plot_descriptors

v2.1.0 (2022-6-03)

plot_descriptors will no longer save to file without filename

v2.0.1 (2022-5-31)

Made default run_stoned argument use basic instead of semantically robust alphabet, as
claimed in documentation

v2.0.0 (2022-5-31)

Added surrogate model explanation method
Added support for attributing ECFP, MACCS fingerprints, rdkit descriptors and plotting them
Example notebooks for new method
Fixed chirality stripping in sanitize
Made it possible to use multiple base molecules for ECFP descriptors

v1.1.0 (2022-5-2)

Made it possible to have model function that only takes one argument instead of SMILES and SELFIES

v1.0.2 (2022-5-2)

Switched to bulk Tanimoto to improve speed
Tightened chemed api limit

v1.0.1 (2022-4-4)

Added quiet mode

v1.0.0 (2022-1-21)

Switched to SELFIES v2.0 release, which has a different token list
Removed “experimental” tag from Chemed and Custom methods
Type annotations now pass mypy
Paper models now generate SVGs correctly and fixed token issues

v0.6.0 (2022-1-17)

Changed behavior of num_samples so that it is not affected by mutation count in STONED

v0.5.2 (2022-1-4)

Fixed SMILES escaping in URL in chemed

v0.5.1 (2021-11-16)

Fixed similarity float vs int in chemed

v0.5.0 (2021-10-26)

Added custom lists for counterfactual source (contributed by @maclandrol)

v0.4.1 (2021-09-27)

Fixed randint usage in stoned.py

v0.4.0 (2021-09-17)

Refactored code into files
Added SVG rewrite so mol structures are SVGs
SVGs are handled with skunks
Added cartoon style for scatter plot in plot_space

v0.3.2 (2021-09-02)

Added SMILES sanitization before generating sample space

v0.3.1 (2021-08-26)

Fixed num_samples not passed correctly
Fixed unparsable simles coming from pubchem

v0.3.0 (2021-08-25)

Added CHEMED method and progress bar

v0.2.0 (2021-08-14)

Initial package release