polyply_1.0
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marrink-lab
Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
Only parse files with known extensions in force field directory.
In this PR we add molecule.interactions dict to the temporary dict in applied links. With that also interactions within a residue can be modified if need be. Also we add...
In our latest preprint on carbohydrates is mentions that parameters are part of polyply which they sort of are. If you are looking for those parameters please read [this discussion](https://github.com/marrink-lab/polyply_1.0/discussions/254).
Unfortunately interactions within a residue cannot be modified, because of the handling of the interaction dict when making links.
in polyply edge attributes can be parsed as is the case for node attributes. In vermouth instead the attribute is set to the last node of the edge, which is...
polyply assumes all versions dict to start at 1 but martinize2 at 0. As long as this is done consistently it's fine, but should be taken care to streamline at...
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Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates