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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

Make the format of the PDB flexible so that we can read ZDOCK file #81

Closed NicoRenaud closed 1 year ago

NicoRenaud commented 2 years ago

I'm not sure if that's something we really want to do, but since pdb files are not all the time in the exact format we would like them to be, this PR tries to make pdb2sql a bit more flexible so that we can read more pdb files. See #74

There is now a flexible_format arg in the constructor of pdb2sql that if turned to true allow to only read the data up to the xyz coordinates. The default value is false and will therefore crash when trying to open a non ideal pdb files

NicoRenaud commented 2 years ago

We can now read zdock files (and most likely other format that complies with the PDB format up to the xyz coordinate). I don't know if that's a feature we want nor if that would be the best way of implementing it though

github-actions[bot] commented 2 years ago

This PR is stale because it has been open for 14 days with no activity. Remove stale label or comment or this will be closed in 7 days.

github-actions[bot] commented 2 years ago

This PR is stale because it has been open for 14 days with no activity. Remove stale label or comment or this will be closed in 7 days.

github-actions[bot] commented 1 year ago

This PR was closed because it has been inactive for 7 days since being marked as stale.