Comments (7)
If somebody can come up with a parser (one probably exists in a function in MDAnalysis or similar somewhere) that can parse the .ndx
files which provide the atom groups for GROMACS etc, then this can become at attribute on import and allow for inclusion of the atom groups inside of Molecular Nodes.
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Hi Brady! I've never contributed before, so I don't know how to do it necessarily. I did however find this other project that seems to accomplish what you need.
https://gist.github.com/jbarnoud/09a22ac41fbd5969af51458eb89317e7
If you'd like, you can give me a little more specific guidance and I can try to add this, or else it looks like it has all the info you might need to do it yourself.
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oooh thanks for pointing this out! I hadn't looked into it deeply yet, but it seems like this should be straightforward to implement.
Happy to support a PR, if you'd like to have a go at implementing it. I'd like to prioritise encouraging community contributions over doing everything myself.
from molecularnodes.
In terms of contributing, I've got some minor details in the README about how to do it in terms of building your own Molecular Nodes. You'll want VSCode and a couple of specific addons for Blender addon development.
The function that does the MDAnalysis importing is here:
MolecularNodes/MolecularNodes/md.py
Lines 65 to 246 in 7979e38
For this to be used, I imagine adding an extra argument to the function maybe file_idx
which defaults to None
. If a file is given, then use the code above to create a list of boolean selections, each of which can be applied as attributes, similarly to:
MolecularNodes/MolecularNodes/md.py
Lines 206 to 218 in 7979e38
The function is called in this operator:
MolecularNodes/MolecularNodes/ui.py
Line 78 in 7979e38
so it will need to be updated, along with adding a new bpy.context.scene.*
property for the file, and displaying that in the UI.
If it's a bit much, then I'm happy to go about it as well. The code base I think still requires a bit of a refactor, and blender addons can be a bit overwhelming if you haven't worked with them before as well.
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I'll give it a go as well. This isn't top priority for me at the moment, but I really like this project, and it's getting me to learn some more git and Blender, which I'm super happy about!
from molecularnodes.
If you have questions about approach to take, please let me know! As a brief outline, you'll want to:
- Fork the repo into your github account.
- Download your fork onto you local computer.
- Tinker around with making the changes.
- Push your changes back to your fork of the repo.
- When you are ready to get some feedback on code / ideas, create a pull request to merge your fork back into my repo. That will allow me to do code review & give feedback.
- You can continue to make changes on your fork, which will be reflected in the pull request.
- Once it's all good, I'll merge it in to main and it's part of the package!
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Brady thanks for the generous guide! I should have some time next week to start poking at this.
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Related Issues (20)
- Molecule class implementation HOT 6
- Use an MDA Universe as a "data twin" to the blender objects HOT 3
- Usage of a missing attribute in the Molecule class HOT 2
- Introducing a Dev branch HOT 2
- Load local PDB File using the python API. HOT 11
- Install MN via pip HOT 1
- Extend requirements file in a manner, that we can run the tests locally HOT 4
- Optimize molecule class HOT 14
- Defaul Materials HOT 2
- Missing VDW radius values for rarely used elements HOT 1
- Side packages install correctly but are not detected HOT 4
- 'Live' MDAnlaysis session loses connection upon object name change
- Blender 4.1 import density broken
- Blender 4.1 custom nodes broken
- change pytest-snapshot to use syrupy
- v4.0.11 surface HOT 3
- TypeError: unsupported operand type(s) for *: 'NoneType' and 'float' HOT 17
- BUG: ValueError in npyio.py loading oxdna topology and trajectory HOT 5
- Can these four formats be imported? If so, which one should I choose? HOT 2
- Un-centered object import broken HOT 1
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