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* fix #216: angle parameters are not being read from topology file * refactored heavily to support all angle types * add tests (with pytest.MonkeyPatch) * update CHANGES
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| import gromacs as gmx | ||
| import io | ||
| import random | ||
| import pytest | ||
| from gromacs.fileformats import blocks | ||
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| # This class simulates a file object | ||
| class MockFile(io.StringIO): | ||
| def __init__(self, text): | ||
| super(MockFile, self).__init__(text) | ||
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| def __enter__(self): | ||
| return self | ||
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| def __exit__(self, exc_type, exc_val, exc_tb): | ||
| self.close() | ||
| return False | ||
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| def generate_topology_line(func_type): | ||
| # Generates random parameters for the different function types | ||
| def random_params(num): | ||
| return [random.uniform(0.0, 100.0) for _ in range(num)] | ||
|
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| # Define the pattern for each function type | ||
| patterns = { | ||
| blocks.AngleFunctionType.HARMONIC: "{:5d}{:5d}{:5d} 1{:10.4f}{:10.4f}", | ||
| blocks.AngleFunctionType.G96_ANGLE: "{:5d}{:5d}{:5d} 2{:10.4f}{:10.4f}", | ||
| blocks.AngleFunctionType.CROSS_BOND_BOND: "{:5d}{:5d}{:5d} 3{:10.4f}{:10.4f}{:10.4f}", | ||
| blocks.AngleFunctionType.CROSS_BOND_ANGLE: "{:5d}{:5d}{:5d} 4{:10.4f}{:10.4f}{:10.4f}{:10.4f}", | ||
| blocks.AngleFunctionType.UREY_BRADLEY: "{:5d}{:5d}{:5d} 5{:10.4f}{:10.4f}{:10.4f}{:10.4f}", | ||
| blocks.AngleFunctionType.QUARTIC_ANGLE: "{:5d}{:5d}{:5d} 6{:10.4f}{:10.4f}{:10.4f}{:10.4f}{:10.4f}{:10.4f}", | ||
| blocks.AngleFunctionType.TABULATED_ANGLE: "{:5d}{:5d}{:5d} 8{:10.4f}{:10.4f}", | ||
| blocks.AngleFunctionType.LINEAR_ANGLE: "{:5d}{:5d}{:5d} 9{:10.4f}{:10.4f}", | ||
| blocks.AngleFunctionType.RESTRICTED_BENDING: "{:5d}{:5d}{:5d} 10{:10.4f}{:10.4f}", | ||
| } | ||
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| atoms = [1, 2, 3] | ||
| params = random_params(func_type.num_params) | ||
| line = patterns[func_type].format(*(atoms + params)) | ||
| return line | ||
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| def create_topology_data(func_type): | ||
| """ | ||
| https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#tab-topfile2 | ||
| """ | ||
| line = generate_topology_line(func_type) | ||
| return """ | ||
| [ moleculetype ] | ||
| ; Name nrexcl | ||
| Example 3 | ||
| [ atoms ] | ||
| ; nr type resnr residue atom cgnr charge mass typeB cha | ||
| ; residue 1 ASN rtp ASN q +1.0 | ||
| 1 NH3 1 ASN N 1 -0.3 14.007 ; qtot -0.3 | ||
| 2 HC 1 ASN H1 2 0.33 1.008 ; qtot 0.03 | ||
| 3 HC 1 ASN H2 3 0.33 1.008 ; qtot 0.36 | ||
| [ angles ] | ||
| ; ai aj ak funct c0 c1 c2 c3 | ||
| {line} | ||
| [ molecules ] | ||
| ; Compound #mols | ||
| Example 1 | ||
| """.format( | ||
| line=line | ||
| ) | ||
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| @pytest.mark.parametrize("func_type", blocks.AngleFunctionType) | ||
| def test_angles(func_type, monkeypatch): | ||
| # Create a custom function that will replace 'open' | ||
| def mock_open(*args, **kwargs): | ||
| if args[0] == "topol.top": | ||
| return MockFile(create_topology_data(func_type)) | ||
| else: | ||
| return open(*args, **kwargs) | ||
|
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| # Use monkeypatch to replace 'open' with 'mock_open' | ||
| monkeypatch.setattr("builtins.open", mock_open) | ||
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| topol = gmx.fileformats.top.TOP("topol.top") | ||
| [molecule] = topol.molecules | ||
| [angle] = molecule.angles | ||
| assert len(angle.gromacs["param"].keys()) == func_type.num_params |