fix #216: angle parameters are not being read from topology file #264
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| import gromacs as gmx | ||
| from unittest.mock import patch, mock_open | ||
| import random | ||
| import pytest | ||
| from gromacs.fileformats import blocks | ||
|
|
||
|
|
||
| def generate_topology_line(func_type: blocks.AngleFunctionType) -> str: | ||
| # Generates random parameters for the different function types | ||
| def random_params(num) -> list[float]: | ||
| return [random.uniform(0.0, 100.0) for _ in range(num)] | ||
|
|
||
| # 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}", | ||
| } | ||
|
|
||
| atoms = [1, 2, 3] | ||
| params = random_params(func_type.num_params) | ||
| line = patterns[func_type].format(*atoms, *params) | ||
| return line | ||
|
|
||
|
|
||
| def create_topology_data(func_type: blocks.AngleFunctionType) -> str: | ||
| """ | ||
| https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#tab-topfile2 | ||
| """ | ||
| line = generate_topology_line(func_type) | ||
| return f""" | ||
| [ 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 | ||
| """ | ||
|
|
||
|
|
||
| @pytest.mark.parametrize("func_type", blocks.AngleFunctionType) | ||
| def test_angles(func_type: blocks.AngleFunctionType): | ||
| with patch( | ||
| "builtins.open", mock_open(read_data=create_topology_data(func_type)) | ||
| ) as mock: | ||
| topol = gmx.fileformats.top.TOP("topol.top") | ||
| [molecule] = topol.molecules | ||
| [angle] = molecule.angles | ||
| assert len(angle.gromacs["param"].keys()) == func_type.num_params | ||
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Can you use pytest's mocking support https://docs.pytest.org/en/7.1.x/how-to/monkeypatch.html so that it stays within pytest? Alternatively, we could install pytest-mock.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
ah, what's the motivation here – is it just consistency? I really, really don't enjoy how monkeypatch solves the problem. unittest is mock is basically a built-in and I see it used more frequently.
Happy to add more tests – that's always a good idea – but i will need some direction as to what to cover? My tests already covered all the possible fu values.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
consistency to stay within one testing framework
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
test coverage itself looks decent enough