Draft: Feature/reaction side cpds

Objectives of this MR:

• Compute Reaction Specific Side compounds
• Overload the getReactionGraph method to take into account reaction-wise cofactors

Work in progress:

• Optimisation/Architecture
• Unit tests

The side compound identification strategy is up to discussion because to be able to also consider compounds implicated in spurious edges I had to turn the problem upside down: 1: For each reaction, identify the compounds implicated in Main edges as Main compounds 2: Consider all other compounds of this reaction as Side compounds (All compounds - Main compounds)

requested review from @clement.frainay

assigned to @louison.fresnais

changed target branch from master to develop

added 1 commit

• bf9cc47b - remove debugging verbose in getReactionSideCompounds

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added 1 commit

• e2e09890 - Add a globalsidecompound feature (to remove CoA)

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added 3 commits

• b32ea655 - add getReactionMainCompounds
• 17aaaeeb - Add getSimplifiedReactionGraph option
• 5080ce64 - Add write reaction main compounds

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We need to discuss the CarbonSkeletonNet app and some features I implemented that might not be very useful.