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1. RDkit (http://www.rdkit.org/)
2. pandas (https://pandas.pydata.org/)

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1. GAMS (https://www.gams.com/)
2. CPLEX solver

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Description:

1. rePrime

• rePrime procedure identifies and captures as a reaction rule the molecular graph topological changes underpinning the substrate to product graph conversion.

2. novoStoic

• An MILP procedure to identifies a mass-balanced de novo biochemical network that converts a source metabolite to a target while satisfying a multitude of constraints and optimizing the objective function.

3. How to cite rePrime/novoStoic -"Kumar, Akhil, et al. "Pathway design using de novo steps through uncharted biochemical spaces." Nature communications 9.1 (2018): 184."

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