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Model Development Kit (MDK) - a library for managing metabolic information related to models. This code was created by members of the Cheminformatics and Metabolism group, EMBL-EBI
Package name should be based on uk.ac.ebi.mdk
There is no interface for Reaction matrices thus the Reconstruction interface allows setting of an Object which is cast to a matrix.
Code license/copyright should be normalised across project
Artifact names should be changed to reflect the new project name
The stereo-center handedness (parity) is not used the stereo hashing and instead whether the bond is up/down. To remedy this we could use an algorithm (see. Gillian's code sample) to match stereo centres regardless of up/down bonds.
Need to track/version annotation history, we can do this using a user-stamp and time-stamp on each annotation an entity.
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