New Topology Format - Githubissues

lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings

https://dna.physics.ox.ac.uk/

GNU General Public License v3.0

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New Topology Format #69

Closed ErikPoppleton closed 12 months ago

ErikPoppleton commented 1 year ago

This pull request includes the following major updates to all systems:

The new topology format with correct DNA strand orientation
Updates to oat to work with the new topology format

And the following minor update to oxDNA:

Implement rate for stiff as well as for r0 for mutual_trap

And the following minor updates to oxDNA_analysis_tools:

Update external force system to work with the rate parameters above
Fixed bug in oxDNA2PDB CLI parser
Updates to typing and docstrings

ErikPoppleton commented 1 year ago

Note that update_pybind was already merged into this branch, so maybe I should wait until that's merged in and resubmit this.

lorenzo-rovigatti commented 1 year ago

I have added an example and some documentation. Can you have a look when you have some spare time? If you like it we can merge the branch (and maybe make a new release?)

ErikPoppleton commented 1 year ago

I haven't looked at the example yet, but I just took a pass at the documentation and added a bunch more of my own to the oat subdirectory.