A set of unit tests for qrefine

Contents

Overview

A set of unit tests to exercise specific parts of the qrefine codebase.

Running the program

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.

List of all currently implemented tests

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