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marrink-lab / polyply_1.0

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
Apache License 2.0
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Load topology from JSON file #319

Open jan-stevens opened 1 year ago

jan-stevens commented 1 year ago

Adding support for loading molecule topologies from JSON files. For large and simple systems, JSON-based topology files are easily created and speed up the generation of the topology object tremendously. (i.e., for the 500Kb chromosome)

An initial idea for implementing this would be simply using the from_json function of the MetaMolecule class in order to add all the molecules iteratively to an empty topology object.

fgrunewald commented 1 year ago

to add to this we could also directly generate a tpr file. This way we save the grompp step ...