Elad Noor

Is it possible to update Jinja2 dependency to >= 3?

3

At the moment, the dependency requires [Jinja2=2.7.3](https://github.com/zakandrewking/escher/blob/364c482077df0930a5aae6ec1c4d926e7fe0f157/py/setup.py#L49). However, this is not compatible with python 3.10. Forcing Jinja2==3.1.2 seems to work on my system (tested on python 3.10).

Give new database IDs to the kegg_additions

1

Now, we issue "fake" IDs that look like KEGG, with high numbers (e.g. C80067). This is confusing and should be changed to something like COCO:C00001 (COCO for COmponent-COntribution).

Compound identifiers without InChI

3

The new main key for matching compounds is the InChIKey. This works very well across databases, but only when the compound has a structure. Unfortunately, we also have thermodynamic information...

Apparently, in the NIST database the compound 5-dehydroshikimate should be mapped to KEGG compound C02637, instead of C02652. The reason is that 5-dehydroshikimate belongs to an older nomenclature and is...

Allow the KEGG input file to contain "free" electrons (C05359) by creating a syntax for specifying their reduction potential. This can potentially replace having a long list of electron carriers...

Reactions that have 0 group change but shouldn't: 1) FMN(ox) = FMN(red) 2) FAD(ox) = FAD(red) 3) ATP + ADP = AMP + A-Tetra-P (in this case, it seems that...