Q|Refinement
A set of unit tests to exercise specific parts of the qrefine codebase.
qr.test
Options available:
qr.test --nproc=8
Speed up the test set by running in parallel processes
qr.test --only=31
Run a single unit test, in this case only tst_31.py is exercised.
| Test ID | Test summary | Time (s) |
|---|---|---|
| tst_1 | Exercise standard (cctbx-based restraints) refinement with all defaults. | 7 |
| tst_2 | Exercise standard (cctbx-based restraints) optimization. | 19 |
| tst_3 | Exercise refine_sites=False. | 4 |
| tst_4 | Not yet written | |
| tst_5 | Exercise max_atoms. | 4 |
| tst_6 | Exercise altlocs. (NO ASSERT) | 6 |
| tst_7 | Exercise interaction graph construction. | 6 |
| tst_8 | Exercise interaction graph clustering. | 5 |
| tst_9 | Exercise buffer region of cluster. | 0 |
| tst_10 | Exercise combined energy and gradients from cluster qm. | 10 |
| tst_11 | Exercise structure completion by finalise.py | Skipped |
| tst_12 | Exercise structure preparation including charge, capping, completion | 29 |
| tst_13 | Compare gradients from entire qm and clustered qm. | Skipped |
| tst_14 | Exercise supercell. | 0 |
| tst_15 | Exercise gradients match: small vs large box clustering vs not clustering. | 410 |
| tst_16 | Exercise gradients match: Non-P1 case (P212121) | 24 |
| tst_17 | Exercise altlocs | 1 |
| tst_18 | Exercise gradients match: pdbs with altlocs | 174 |
| tst_19 | Exercise altlocs using subtract vs using average | 273 |
| tst_20 | Make sure expand works for this particular file. | 18 |
| tst_21 | Exercise charges are calculated correctly | ? |
| tst_22 | Exercise charges are calculated correctly on pdb | 5 |
| tst_23 | Exercise charges are calculated correctly | 5 |
| tst_24 | Exercise finalise and charges both work | 8 |
| tst_25 | Exercise finalise and charges both work | 7 |
| tst_26 | Exercise charges are calculated correctly | 3 |
| tst_27 | Exercise finalise and charges both work | 11 |
| tst_28 | Exercise finalise and charges both work | 8 |
| tst_29 | Exercise charges are calculated correctly | 3 |
| tst_30 | Exercise standard (cctbx-based restraints) optimization (no data required) | 38 |
| tst_31 | Exercise TorchANI calculator works as expected | 0 |
| tst_32 | Exercise TorchANI calculator raising an error with non supported atoms | 0 |
| tst_33 | Exercise PySCF can compute an Energy and Gradient for a given system | 0 |