simularium / simulariumio

Python package that converts simulation outputs to the format consumed by the Simularium viewer website

Apache License 2.0

5 stars 3 forks source link

Include option to draw bonds from MD trajectory #180

Closed advaitathreya closed 6 months ago

advaitathreya commented 6 months ago

Time estimate or Size

Small

Problem

Allows visualizing bonds present in MDAnalysis Universe using Fiber types.

Solution

What I/we did to solve this problem Added code to _read_universe function in MdConverter.

Type of change

New feature (non-breaking change which adds functionality)
This change requires a documentation update

Change summary:

Include option to draw bonds from MD trajectory

Steps to Verify:

Screenshots (optional):

Keyfiles (delete if not relevant):

Thanks for contributing!

blairlyons commented 6 months ago

@advaitathreya thanks for the PR! If you check CONTRIBUTING.md there's instructions to run the tests and fix the lint issues using just install and just build. If you update from main, you can get the fixes I just merged for the issues causing the tests to fail. It would be great if you can also add a test to simulariumio/tests/converters/test_md_converter.py. Let us know if we can help with this, we'd like to get your code changes in soon.

advaitathreya commented 6 months ago

@blairlyons I should have read CONTRIBUTING.md first, sorry. Not used to contributing to projects 😅. I'm stumbling around trying to clean up stuff I've already done and looks like I messed up this pull request. Let me start over and open a new one once I get that fixed.

blairlyons commented 6 months ago

@advaitathreya no problem! We're happy you're contributing. I can help you with the tests etc on Monday, I'll base on your new PR