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a-r-j / graphein

Protein Graph Library
https://graphein.ai/
MIT License
1.03k stars 131 forks source link

Atom Graph Construction #41

Closed a-r-j closed 2 years ago

a-r-j commented 3 years ago

Currently, we are not distinguishing bond order. We also do not check for over-connected atoms. Further checks and balances to be implemented from: https://www.daylight.com/meetings/mug01/Sayle/m4xbondage.html

https://pubs.acs.org/doi/10.1021/ci300358c

JoshuaMeyers commented 3 years ago

Hey @a-r-j, nice library! I've been experimenting with graphein this morning and noticed that the atom graph construction currently isn't working (following the atom granularity tutorial), I think this is because these two lines should be uncommented (otherwise the graph has 0 nodes): https://github.com/a-r-j/graphein/blob/master/graphein/protein/graphs.py#L270-L271

Happy to create a new ticket if you like

a-r-j commented 3 years ago

Hey @JoshuaMeyers! Thanks for the heads up. I'm away for the next few days but will check this out next week. You can try installing in editable mode and uncommenting (really not sure why those lines have been commented out). Otherwise, you could try using the low-level API as per https://graphein.ai/notebooks/residue_graphs.html#Low-Level-API

JoshuaMeyers commented 3 years ago

Hey @a-r-j thanks for the quick reply, yep I'm working in editable mode for the time being so no rush, just thought I'd flag this 👍

a-r-j commented 3 years ago

@JoshuaMeyers Heya, going to check this out in the next few days. Did uncommenting get things working for you? Thanks again for flagging this.

JoshuaMeyers commented 2 years ago

Hey @a-r-j yep it did from my limited testing – I was able to get valid graphs with nodes and edges.