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primaryodors / primarydock

PrimaryOdors.org molecular docker.
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Unit tests. #263

Closed electronicsbyjulie closed 1 year ago

electronicsbyjulie commented 1 year ago

Created a master unit test that runs the big 3 tests. TODO: Check output of docks.

Plenty more work to be done on this. See #257 .

primaryodors commented 1 year ago

Any new progress on this? @ssepeq

electronicsbyjulie commented 1 year ago

Going to be afk for several days this week and next. Want to get protein coupling working reliably and then have coupled PDBs ready and docking running on a cron on the local server, that way there'll be docks ready for analysis on my return.

primaryodors commented 1 year ago

Going to want to include test/motif_test.pepd in the master unit test.

primaryodors commented 1 year ago

While the server is performing large numbers of docks, now would be a great time to resume the unit tests.

electronicsbyjulie commented 1 year ago

Molecular assembly is a crazy bizarre funhouse right now! Here's one example:

image

Another bug is saturated rings (cyclohexane etc) aren't working. It makes a straight chain hydrocarbon and then bonds the ends together, but doesn't curl it into a ring. I think that one might be a not too difficult fix in order to get mol_assem_test working.

primaryodors commented 1 year ago

Don't worry too much right now about the molecule assembly tests that are failing; recall that some SMILES strings have never worked in the classes and that's why we integrated with OpenBabel.

Any tests that are failing should be left commented out for now. If a test can be fixed with just one or two lines of code, that's fine to include, but anything more than that is out of scope for this PR.

electronicsbyjulie commented 1 year ago

☹️

Turning off debugging and checking in molecule assembly changes so far...

primaryodors commented 1 year ago

These tests are looking good. If you can think of anything else to add, go for it, otherwise this master test looks good enough to start with.

The express test can include everything except the TAAR8 and OR1A1 tests. Once that is ready, feel free to mark this for review.

electronicsbyjulie commented 1 year ago

Even the protein test and motif test? They each take a moment to run.

primaryodors commented 1 year ago

The protein test, motif test, and molecule assembly tests can be omitted from the express test.

primaryodors commented 1 year ago

The Big Three test is now obsolete; all future PRs will be required to pass unit_test_master (i.e. it should not output any red text) before merge.