Release 2025.2.1

Release Notes

Refactoring of the code:

• Re-structured the data_source package to include more descriptive sub-packages: compound, compound_pattern, reaction, and reaction_pattern.
• Re-named the base classes.
• Removed the #noinspection comments.
• Updated the docstrings.
• Fixed small bugs.

Refactoring of the resources:

• Updated the data directory.
• Updated the figures directory.
• Updated the references directory.
• Updated the scripts directory.
• Updated the auxiliary files.

Addition of data sources:

• Chemical Compounds:
  • COCONUT 2.0 by (20241126, Chandrasekhar, V. et al.):
    • v_2_0_by_20241126_chandrasekhar_v_et_al
    • v_2_0_complete_by_20241126_chandrasekhar_v_et_al
• Chemical Compound Patterns:
  • RDKit:
    • v_brenk_by_20080307_brenk_r_et_al by (20080307, Brenk, R. et al.)
    • v_pains_by_20100204_baell_j_b_and_holloway_g_a by (20100204, Baell, J.B. and Holloway, G.A.)
• Chemical Reactions:
  • CRD:
    • v_reaction_smiles_1976_to_2024 by (20250118, van der Lingen, R.)
• Chemical Reaction Patterns:
  • Miscellaneous:
    • v_auto_template_by_20240627_chen_l_and_li_y by (20240627, Chen, L. and Li, Y.)

Release 2025.1.1

Release Notes

Restructured the data_source package to remove chemical reaction rules as a category. Now, there are only the chemical compound and chemical reaction categories to avoid redundancy.

Release 2024.8.1

Release Notes

Re-structured the data_source package.

Added the following computer-assisted chemical synthesis data sources:

• Chemical Reactions:
  • United States Patent and Trademark Office (USPTO):
    • USPTO (1976 to 2013) RSMI by (20121009, Lowe, D.M.)
    • USPTO (50k) by (20141226, Schneider, N. et al.)
    • USPTO (1976 to 2016) CML by (20121009, Lowe, D.M.)
    • USPTO (1976 to 2016) RSMI by (20121009, Lowe, D.M.)
    • USPTO (50k) by (20160905, Liu, B. et al.)
    • USPTO (LEF) by (20181221, Bradshaw, J. et al.)
    • USPTO (Mech 31k) by (20240810, Chen, S. et al.)

Modified the following computer-assisted chemical synthesis data sources:

• Chemical Compounds:
  • Miscellaneous
• Chemical Reactions:
  • Miscellaneous:
    • ORDerly by (20240422, Wigh, D.S. et al.)

Release 2024.7.4

Release Notes

Final release for the month of July.

Added the following computer-assisted chemical synthesis data sources:

• Chemical Reactions:
  • United States Patent and Trademark Office (USPTO):
    • USPTO (1976-2016) by (20210407, Schwaller, P. et al.)
    • USPTO (1976-2016) by (20240313, Chen, S. et al.)
    • USPTO (50k) by (20240313, Chen, S. et al.)
  • Miscellaneous:
    • (20211102, Lin, A. et al.)
    • (20240422, Wigh, D.S. et al.)

Removed the following computer-assisted chemical synthesis data sources:

• Chemical Compounds:
  • Miscellaneous:
    • (20190701, Button, A. et al.)

Modified the following computer-assisted chemical synthesis data sources:

• Chemical Compounds:
  • Miscellaneous:
    • (20180421, Avramova, S. et al.)
• Chemical Reactions:
  • Miscellaneous:
    • (20200508, Grambow, C.A. et al.)
    • (20220718, Spiekermann, K. et al.)

Release 2024.7.3

Release Notes

Fix the initial release so the 'setup.cfg' file references the correct version. Supports the following computer-assisted chemical synthesis data sources:

• Chemical Compounds:

  • ChEMBL
  • ZINC20
  • Miscellaneous Chemical Compound Data Sources

• Chemical Reactions:

  • United States Patent and Trademark Office (USPTO)
  • Open Reaction Database (ORD)
  • Chemical Reaction Database (CRD)
  • Rhea
  • Miscellaneous Chemical Reaction Data Sources

• Chemical Reaction Rules:

  • RetroRules
  • Miscellaneous Chemical Reaction Rule Data Sources

Release 2024.7.2

Release Notes

Fix the initial release to reference the correct commit. Supports the following computer-assisted chemical synthesis data sources:

• Chemical Compounds:

  • ChEMBL
  • ZINC20
  • Miscellaneous Chemical Compound Data Sources

• Chemical Reactions:

  • United States Patent and Trademark Office (USPTO)
  • Open Reaction Database (ORD)
  • Chemical Reaction Database (CRD)
  • Rhea
  • Miscellaneous Chemical Reaction Data Sources

• Chemical Reaction Rules:

  • RetroRules
  • Miscellaneous Chemical Reaction Rule Data Sources

Release 2024.7.1

Release Notes

The initial release. Supports the following computer-assisted chemical synthesis data sources:

• Chemical Compounds:

  • ChEMBL
  • ZINC20
  • Miscellaneous Chemical Compound Data Sources

• Chemical Reactions:

  • United States Patent and Trademark Office (USPTO)
  • Open Reaction Database (ORD)
  • Chemical Reaction Database (CRD)
  • Rhea
  • Miscellaneous Chemical Reaction Data Sources

• Chemical Reaction Rules:

  • RetroRules
  • Miscellaneous Chemical Reaction Rule Data Sources