Jan Stevens
Jan Stevens
Only parse files with known extensions in force field directory.
As the name suggest, there is a broken link in the [Single stranded circular DNA tutorial](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-Single-stranded-circular-DNA). We use the `amber14-parmbsc1` force field, which are no long online available from "official"...
Adding new functionality to Polyply in the form of a DNA backmapping procedure.
In this pull request, the frame-based backmapping protocol's first version will be implemented. The most basic idea is that users provide internal reference frames for each residue, which will be...
This PR prepares the code to support multiple backmapping protocols with small changes. The main goal is to take out Polyply's default backmapping protocol from the 'Backmap' class and make...
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....
This PR implements a file parser of oxDNA configuration files to read in rotational frames for residues. The initial goal is to use the file parser to implement a frame-based...