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docking-org / pydock3

Python package wrapping the DOCK Fortran program and providing several tools built on top of it.
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Undocked molecules despite complete OUTDOCK #32

Open gregorpatof opened 1 year ago

gregorpatof commented 1 year ago

Sometimes, the number of decoy molecules reported is lower than the number present in decoys.tgz. The explanation for that seems to be that the extraction of the decoys.tgz to scratch produces some corrupted db2 files, which DOCK then simply ignores.

ianscottknight commented 1 year ago

After discussing with @gregorpatof, it is worth noting that this is not a pydock3 issue per se but an issue with the strategy (used generally in the various instances of rundock.bash to date) of extracting multiple copies of the same tarball of molecules across multiple tasks. In the case of retrospective docking (e.g., in DockOpt), there only needs to be one copy of the extracted set of molecules, and all tasks can refer to that copy.

gregorpatof commented 1 year ago

Turns out that the uncompression to disk issue is already taken care of by Ben's newer scripts, so the fix is probably as simple as using them. Relevant documentation here: https://wiki.docking.org/index.php?title=SUBDOCK_DOCK3.8