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HIN: Apply suggestions from code review
Signed-off-by: Thomas Kemmer <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| # File formats | ||
| ```@meta | ||
| CurrentModule = BiochemicalAlgorithms | ||
| ``` | ||
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| ```@index | ||
| Pages = ["fileformats.md"] | ||
| ``` | ||
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| ```@docs | ||
| load_hinfile | ||
| write_hinfile | ||
| ``` |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,52 +1,56 @@ | ||
| @testitem "reading HIN files" begin | ||
| sys = load_hinfile(ball_data_path("../test/data/hinfile_test.hin")) | ||
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| @test natoms(sys) == 648 | ||
| @test nmolecules(sys) == 216 | ||
| @test nfragments(sys) == 0 | ||
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| a = first(atoms(sys)) | ||
| @test a.name == "O" | ||
| @test a.element == Elements.O | ||
| @test a.charge ≈ -0.834 | ||
| @test a.r ≈ Vector3(0.59038, -0.410275, -0.860515) | ||
| @test nbonds(a) == 2 | ||
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| @test get_property(sys, :temperature) ≈ 297.5626 | ||
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| @test get_property(sys, :periodic_box_width) ≈ 18.70136 | ||
| @test get_property(sys, :periodic_box_height) ≈ 18.70136 | ||
| @test get_property(sys, :periodic_box_depth) ≈ 18.70136 | ||
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| sys = load_hinfile(ball_data_path("../test/data/AlaGlySer.hin")) | ||
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| @test natoms(sys) == 31 | ||
| @test nmolecules(sys) == 1 | ||
| @test nfragments(sys) == 3 | ||
| @test nresidues(sys) == 3 | ||
| @test nchains(sys) == 1 | ||
| @test nbonds(sys) == 30 | ||
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| @test_throws SystemError load_hinfile(ball_data_path("../test/data/ASDFASDFASEFADSFASDFAEW.hin")) | ||
| @test_throws MethodError load_hinfile(ball_data_path("../test/data/hinfile_test_invalid.hin")) | ||
| for T in [Float32, Float64] | ||
| sys = load_hinfile(ball_data_path("../test/data/hinfile_test.hin"), T) | ||
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| @test natoms(sys) == 648 | ||
| @test nmolecules(sys) == 216 | ||
| @test nfragments(sys) == 0 | ||
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| a = first(atoms(sys)) | ||
| @test a.name == "O" | ||
| @test a.element == Elements.O | ||
| @test a.charge ≈ -0.834 | ||
| @test a.r ≈ Vector3{T}(0.5903809, -0.4102751, -0.8605154) | ||
| @test nbonds(a) == 2 | ||
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| @test get_property(sys, :temperature) ≈ 297.5626 | ||
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| @test get_property(sys, :periodic_box_width) ≈ 18.70136 | ||
| @test get_property(sys, :periodic_box_height) ≈ 18.70136 | ||
| @test get_property(sys, :periodic_box_depth) ≈ 18.70136 | ||
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| sys = load_hinfile(ball_data_path("../test/data/AlaGlySer.hin"), T) | ||
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| @test natoms(sys) == 31 | ||
| @test nmolecules(sys) == 1 | ||
| @test nfragments(sys) == 3 | ||
| @test nresidues(sys) == 3 | ||
| @test nchains(sys) == 1 | ||
| @test nbonds(sys) == 30 | ||
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| @test_throws SystemError load_hinfile(ball_data_path("../test/data/ASDFASDFASEFADSFASDFAEW.hin"), T) | ||
| @test_throws MethodError load_hinfile(ball_data_path("../test/data/hinfile_test_invalid.hin"), T) | ||
| end | ||
| end | ||
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| @testitem "writing HIN files" begin | ||
| sys = load_hinfile(ball_data_path("../test/data/hinfile_test.hin")) | ||
| for T in [Float32, Float64] | ||
| sys = load_hinfile(ball_data_path("../test/data/hinfile_test.hin"), T) | ||
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| outfname = tempname() | ||
| write_hinfile(outfname, sys) | ||
| outfname = tempname() | ||
| write_hinfile(outfname, sys) | ||
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| sys2 = load_hinfile(outfname) | ||
| sys2 = load_hinfile(outfname, T) | ||
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| @test sys == sys2 | ||
| @test sys == sys2 | ||
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| # test name truncation | ||
| first(atoms(sys)).name = "TEST NAME" | ||
| # test name truncation | ||
| first(atoms(sys)).name = "TEST NAME" | ||
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| write_hinfile(outfname, sys) | ||
| write_hinfile(outfname, sys) | ||
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| sys2 = load_hinfile(outfname) | ||
| sys2 = load_hinfile(outfname, T) | ||
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| @test first(atoms(sys2)).name == "TEST" | ||
| end | ||
| @test first(atoms(sys2)).name == "TEST" | ||
| end | ||
| end |