Refactor StructureSimilarity

DeepRank / pdb2sql

Fast and versatile biomolecular structure PDB file parser using SQL queries

https://pdb2sql.readthedocs.io

Apache License 2.0

24 stars 12 forks source link

Refactor StructureSimilarity #86

Open NicoRenaud opened 1 year ago

NicoRenaud commented 1 year ago

StructureSimilarity is a bit of a mess now. We have different ways of computing the metrics and they don't all have the same features and internal checks :

Some routines check for residue and atom matching some don't
Some routines accept multiple chains some don't

We want a unified API for all metrics such as :

def compute_x(self, chain_pairs=None, xzone=None, method='svd', check=True, name=['CA','C','N','O'] ):

github-actions[bot] commented 1 year ago

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cbaakman commented 4 months ago

I would like to have the option to select the chain IDs in. https://github.com/DeepRank/pdb2sql/blob/76d7b684b6921261436e2656d9ecd8be86148199/pdb2sql/StructureSimilarity.py#L531

Right now, it always picks the first two.