graphein
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a-r-j
Protein Graph Library
**Is your feature request related to a problem? Please describe.** [Currently](https://github.com/a-r-j/graphein/blob/0e6f075e716ae10b8afebf47cc0d8eada46d4f08/graphein/cli.py#L54) the CLI uses the normal `construct_graphs` function. Once the `dataloaders` PR (#71) is merged we can change this to...
**Is your feature request related to a problem? Please describe.** Now that we have a CLI (#113), it would be nice to provide some default configs implementing graph construction schemes...
Hey @a-r-j, just pinging back here as promised yesterday with what probably could be considered a design doc for Graphein. I'm excited about this! I also know that my memory...
- [x] ProtVec Embeddings - [ ] High Scoring Pairs (HSP) - [ ] Disorder measurement (ANCHOR?) - [ ] Hydropathy index - [ ] Parse PSSMs - [ ]...
Hey @ericmjl, yep we’re getting there 😁 ! Docs are on the horizon. The plan for tomorrow is: 1. Docs coverage (as close 100% as sanity allows) 2. Feature Pre-processing...
I think you're right about `granularity` - it's doing too much. The idea is to have control over: 1. What the nodes are in a residue graph (e.g. a-Carbon "CA",...
Create good train/val/test sets based on SCOP/CATH classifications. Sequence-based approaches (e.g. identity thresholding or BLAST) are bad practice and should not be encouraged.
#### Reference Issues/PRs Fixes #210 #### What does this implement/fix? Explain your changes support for loading both local and downloading pdb files, and save at `self.raw_dir` #### What testing did...
On #208 @1511878618 mentioned he'd be interested in handling this.