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.)