test_standardise_2

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Last edited time	@January 17, 2023 10:32 AM

Hi Maria,

I've just gone through and fixed this test locally, it relies on gemmi code and it looks like the atom ordering has changed (see c at pos 3 where it was previous pos 7). This shouldn't impact how the program works so I'd just ignore it for now and it will get into a future SIMBAD update.

Best wishes,

Adam

Wrote to Adam 22/12/2022

Dear Adam,

Simbad test (test_pdb_util.py::Test::test_standardise_2) fails on all OS. Is it just test need to be updated?

reference_data = [

"CRYST1 64.200 77.800 38.280 90.00 90.00 90.00 P 21 21 21 \n",

"ATOM 1 N ASP A 1 44.446 13.220 8.556 1.00 13.50 N \n",

"ATOM 2 CA ASP A 1 44.430 12.980 7.111 1.00 14.06 C \n",

"ATOM 3 CB ASP A 1 43.907 14.215 6.393 1.00 19.18 C \n",

"ATOM 4 CG ASP A 1 42.510 14.608 6.756 1.00 23.17 C \n",

"ATOM 5 OD1 ASP A 1 41.884 14.041 7.647 1.00 25.19 O \n",

"ATOM 6 OD2 ASP A 1 41.979 15.572 6.153 1.00 34.30 O \n",

"ATOM 7 C ASP A 1 45.890 12.779 6.690 1.00 13.21 C \n",

"ATOM 8 O ASP A 1 46.785 13.367 7.265 1.00 15.90 O \n",

"ATOM 9 N VAL A 2 46.068 11.965 5.678 1.00 14.01 N \n",

]

Actual data =

CRYST1 64.200 77.800 38.280 90.00 90.00 90.00 P 21 21 21 0

ATOM 1 N ASP A 1 44.433 13.208 8.560 1.00 13.64 N

ATOM 2 CA ASP A 1 44.447 13.009 7.129 1.00 14.33 C

ATOM 3 C ASP A 1 45.887 12.787 6.694 1.00 13.28 C

ATOM 4 O ASP A 1 46.792 13.384 7.254 1.00 15.83 O

ATOM 5 CB ASP A 1 43.901 14.240 6.407 1.00 18.69 C

ATOM 6 CG ASP A 1 42.483 14.625 6.750 1.00 22.80 C

ATOM 7 OD1 ASP A 1 41.912 14.023 7.666 1.00 25.27 O

ATOM 8 OD2 ASP A 1 41.945 15.532 6.100 1.00 31.97 O

ATOM 9 N VAL A 2 46.061 11.960 5.672 1.00 14.23 N

message from Adam:

Hi Maria,

I'll have a look into it, given only 1 test is failing, I probably need to update something.

Best wishes,

Adam