Add Protparam

[e-osipov]

Created protparam script to calculate common properties for a model.

Depends on Biopython. Since it might be missing from standard PyMOL installation, the script installs it if import fails.

[e-osipov]

Hi @speleo3 , I have updated the code according to the proposed changes. I also removed a test because it was failing😁

[speleo3]

I also removed a test because it was failing

How about a test that works?

def test_protparam(capsys):
    cmd.reinitialize()
    cmd.fab("A// ACD B// EFG", "m1")
    cmd.fab("HIKL", "m2")
    cmd.alter("resn CYS", "resn='UNK'")
    protparam()
    captured = capsys.readouterr()
    assert "Protein name: m1" in captured.out
    assert "Protein name: m2" in captured.out
    assert "Sequence: ADEFG\n" in captured.out
    assert "Sequence: HIKL\n" in captured.out
    assert "Protein length: 2 aa" not in captured.out
    assert "Protein length: 3 aa" not in captured.out
    assert "Protein length: 4 aa" in captured.out
    assert "Protein length: 5 aa" in captured.out
    assert "Count of aminoacids: {'A': 1," in captured.out
    protparam(bychain=1)
    captured = capsys.readouterr()
    assert "Protein name: m1" in captured.out
    assert "Protein name: m2" in captured.out
    assert "Sequence: AD\n" in captured.out
    assert "Sequence: EFG\n" in captured.out
    assert "Protein length: 2 aa" in captured.out
    assert "Protein length: 3 aa" in captured.out
    assert "Protein length: 4 aa" in captured.out
    assert "Protein length: 5 aa" not in captured.out
    assert "Molecular Weight: 204.2 Da" in captured.out
    protparam("resn LYS")
    captured = capsys.readouterr()
    assert "Protein name: m1" not in captured.out
    assert "Protein name: m2" in captured.out
    assert "Protein length: 1 aa" in captured.out
    assert "Isoelectric point: 8.75" in captured.out

[e-osipov]

Thanks! I've updated the code with this test. I added extra test for "empty" output. I am not very familiar with pytests so it might fail. In that case, I will try to fix and push it again.

Update: since ci.yml doesn't install biopython, tests fail with an error:

NameError: name 'SeqIO' is not defined

I could "fix" it by adding biopython to ci.yml but perhaps there is better way to handle this error?

[speleo3]

I could "fix" it by adding biopython to ci.yml but perhaps there is better way to handle this error?

That's the correct solution, please add biopython to ci.yml, thanks.

[speleo3]

Looks good now, thank you