📝 Notes

CReM database

Warning

For the tutorials, we will use the CReM database replacements02_sc2.db.gz. This is just because is a smaller one and therefore it has a fast download. For real problems consider reading first the CReM paper and also see the discussion on moldrug repo

Explicit hydrogens and RDKit library

Warning

Many RDKit functions, including the sascore, operate optimally when applied to molecules without explicit hydrogens. The sascore assigns a score ranging from 1 to 13, where 1 indicates an easily synthesizable molecule, and 13 signifies a challenging one. However, when explicit hydrogens are present, the function tends to yield higher scores, incorrectly suggesting a greater difficulty of synthesis. Detailed discussions on this issue can be found at SA_Score gives different values depending if the molecule has explicit hydrogens.

The moldrug-3.7.0 release has addressed this concern for all built-in fitness functions. Refer to moldrug’s CHANGELOG for a comprehensive overview of the fixes and improvements.