Daniel Rademaker

Regarding the use of 'sets' instead of 'lists' to store nodes.

1

I discussed with @cbaakman today, and he believes that using lists should suffice, and there may not be a need for sets. He had initially considered using sets as a...

Using a pdb file containing only one chain gives unexpected results

14

Hello, I cannot generate correct edges. Not only are they not symmetrical (if there is an edge(0,1) there should also be an edge(1,0)), the edges calculates are completely different when...

Allow for >20 types in `AminoAcid` class

11

Hello, I am working with the AminoAcid class (deeprankcore/models/amino_acid.py) because the Residue class (deeprankcore/models/structure.py) requires it, and running into an issue. The common 20 amino-acids are nicely initialized in deeprankcore/domain/amino_acid.py,...