Update d.ts

[adam-of-barot]

Added the following things mentioned in #389:

• Documented Reaction API (JSReaction)
• Documented for logging API (JSLog)
• Documented non-tetrahedral chirality control function
• Updated is_valid docstrings to be in-line with Release 2023_09_01

TODO:

• Add meaningful docstrings for JSLog related things

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[MichelML]

sorry for the delays here @adam-of-barot , this is a bit crazy at work since September, but I'll get to reviewing I promise 🤞