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gruenewald-lab / CGsmiles

Coarse-Grained Smiles (CGsmiles) for representing abitrarily complex molecules using a compact line notation
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Sampler #17

Open fgrunewald opened 2 months ago

fgrunewald commented 2 months ago

Initial draft for a sampler class that takes fragments and makes random molecules according to bonding probabilities

fgrunewald commented 24 minutes ago

@pckroon All reactivities are probabilities. Reactivities is used when the decision is based on a bonding descriptor. I've added a clarification in the docs.

they should all be from_fragment_string but some examples were older from before

Not entirely because at the CG level branch termination cannot be determined by the bonding descriptor when no end-group is added. Otherwise, yes one could do as suggest. Of course one other option is to simply define an empty or fake terminal. But not sure that makes it easier.