schrodinger.livedesign.setup_reaction module

Users commonly sketch reactions that are not directly useable in reaction enumeration. This module includes tools that are needed to convert a reaction to a suitable format for use in reaction enumeration.

Here’s how LiveDesign calls the reaction enumeration tool:

seurat/TaskEngineTasks/python/schrodinger_enumerate/schrodinger_enumerate.py

This requires jaguar to be available to work.

schrodinger.livedesign.setup_reaction.map_reaction(reactants, products)

Call Jaguar’s reaction mapper.

Parameters

• reactants – list of schrodinger Structures

• products – list of schrodinger Structures

Returns

list of pairs of atoms that correspond

schrodinger.livedesign.setup_reaction.setup_reaction(rxn: rdkit.Chem.rdChemReactions.ChemicalReaction) → rdkit.Chem.rdChemReactions.ChemicalReaction

Converts display reaction into a reaction useable by core suite’s enumeration tool.

Users commonly sketch reactions without atom mappings, and that assume certain things.

Reaction enumeration requires that: - In reactants, hydrogens attached to aromatic nitrogens must be explicit - Reactants be aromatized rather than kekulized - Each R-group must be converted to ‘*’ (any atom) with a mapping number >100 - If there are R groups, that’s the only place the fragments should be allowed to connect - Atoms must be mapped from the reactant to the product.