johnmay/mdk

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

mdk's Issues

Package Naming

Package name should be based on uk.ac.ebi.mdk

Artifact Naming

Artifact names should be changed to reflect the new project name

Code License

Code license/copyright should be normalised across project

Stereo center detection on hashing algorithm doesn't work as expected

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.

StoichiometricMatrix interface

There is no interface for Reaction matrices thus the Reconstruction interface allows setting of an Object which is cast to a matrix.

Annotation/Entity Version Tracking

Need to track/version annotation history, we can do this using a user-stamp and time-stamp on each annotation an entity.