cpptraj add "Z" column to pdb output?

[hainm]

hi,
pytraj has been failing for awhile due to the change in pdb format.
In below line, the 'Z' column is new. Is it expected?
ATOM 1 N SER Z 1 -1.889 9.159 7.569 1.00 0.00 N
Here is the the assertion in pytraj:
https://github.com/Amber-MD/pytraj/blob/7ee64bd01060606b55b6ec464f3ab2f0e418df2b/tests/test_io/test_io.py#L336

Here is the input commands:

parm tz2.parm7
trajin tz2.nc 1 1
trajout test.pdb

cheers

[drroe]

Is it expected?

Yes. This change was made at the suggestion of @dacase in order to better conform to the PDB standard. See #747

Seems I need to improve my CI testing with pytraj. I may just have to add a full pytraj build and test somewhere.

[hainm]

thanks @drroe. I will update pytraj tests.

Seems I need to improve my CI testing with pytraj. I may just have to add a full pytraj build and test somewhere.

I think it's ok to let it as is for now. pytraj has nightly testing and it detects the failure but I was too lazy to fix (since it's not critical, just a matter of clarifying with you and updating the test).

By the way, the full pytest test does not take that long, only about 1 minute.

[swails]

cpptraj should test pytraj via the Jenkins pipeline. It's worth seeing why this failed to catch the pytraj issue.

[drroe]

cpptraj should test pytraj via the Jenkins pipeline. It's worth seeing why this failed to catch the pytraj issue.

OK, so it's weird. If I look at a PR from after the introduction of the PDB chain ID change (#753), the associated pytraj build + test on Jenkins passed. @hainm is this because the tests were run with --simple?

[hainm]

Yeah, the —simple only make sure cpptraj wont break pytraj compilation.

[drroe]

@hainm so would you recommend that run_tests.py be run without the --simple option?

[hainm]

Yeah I think so, given that full pytraj test only takes 1-2 minutes.

[drroe]

@swails this may be a silly question, but where is run_tests.py called from on Jenkins? I can't seem to find it in any of the files in the repo. Is it part of the docker image?

[swails]

It's called from here: https://github.com/Amber-MD/pytraj/blob/master/Jenkinsfile#L30

The pytraj job is triggered from inside the cpptraj job from here: https://github.com/Amber-MD/cpptraj/blob/master/Jenkinsfile#L150-L152

[hainm]

It's called from here: https://github.com/Amber-MD/pytraj/blob/master/Jenkinsfile#L30

I don't see it. J/K, updated.