v1.3.0

1.3.0 (2023-09-22)

Features

• automated_pypi_releases (deeaa91)

v1.2.1

1.2.1 (2023-07-13)

Bug Fixes

• add Copyright info and modify theme options (779dac0)
• only remove PIKAChU if it is there initially (caused crash) (3b5d3e0)

v1.2.0

1.2.0 (2023-07-05)

Features

• add Release-please for automated releases (cb8a74f)
• orderly enumeration of R group indices (0481aaa)

Bug Fixes

• Failing documentation theme issues (987db2c)

Documentation

• version bump: 1.1.8-->1.2.0 (9c54d7c)

1.1.8

What's Changed

• Explicite hydrogen inclusion by @OBrink in #41

Full Changelog: 1.1.7...1.1.8

1.1.7

• Major restructuring of the code (this addresses #5)
• 2D coordinate layouts generated with Indigo are now randomly rotated
• Users now can generate depictions along with cxSMILES strings that contain dimensionless coordinates that describe the positions of the atoms as they have been depicted
  • XY-shearing has been removed from the augmentation lists to not to influence the coordinates
  • Only the CDK, RDKit and Indigo are used here as PIKAChU re-generates coordinates during the depiction process

RanDepict 1.1.5

• the CDK depictions are generated using more fonts for labels
• alkyl chain abbreviations are more diverse (eg. an ethyl group is now also abbreviated as "C2H5" instead of just as "Et")
• "Y" has been added as an R group variable per default for generating Markush SMILES using the RandomMarkushStructureCreator. We are aware of the conflict with the element Yttrium, but it appears that the R group variable is a typical case, while the occurrence of Yttrium is very rare A user who does not want to use it can still exclude it.
• The RandomMarkushStructureCreator now also includes the lowercase characters a-f in R group labels. For example, labels like "R1a" can be generated.
• The RandomMarkushStructureCreator does not replace isotopes or charges atoms with R group labels anymore as the resulting SMILES are invalid (see #35).
• The JVM heap size has been set to 4GB. We hope that this helps with #25, but this needs to be validated. For now, it does not break anything.

RanDepict 1.1.4

• implemented a workaround for a bug in PIKAChU that leads to problems when depicting large molecules

RanDepict 1.1.3

• Fixed problem with Pillow's resampling method being accessed differently in different versions
• Avoid replacing chiral R groups in RandomMarkushStructureCreator as it leads to the generation of invalid SMILES

RanDepict 1.1.2

What's Changed

• Tm dev by @OBrink in #26:
  • Fixed broken tests
  • Updated to CDK 2.8
• enable configuring depictor styles by @tulay in #31
  • RandomDepictor objects can now be instantiated using a configuration
  • Configuration class added
  • Tests added

New Contributors

• @tulay made their first contribution in #31

Full Changelog: 1.1.1...1.1.2

RanDepict 1.1.1

• Depiction feature fingerprints are now implemented for the PIKAChU depictions
• A bug with path definitions of the backgrounds for the hand-drawn-like augmentations has been fixed.