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1dd5d7eab6
* update LomapAtomMapper default settings to established best practices * fixup tests for relative_alchemical_network_planner following lomap default change make these tests use the legacy default settings for Lomap, they're just smoke testing and the actual mappings don't matter * fixup regression tests for command line plan-rbfe these are different now that the lomap defaults have been changed for 1.0 --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
121 lines
4.2 KiB
Python
121 lines
4.2 KiB
Python
"""
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Tests the easy start guide
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- runs plan_rbfe_network with tyk2 inputs and checks the network created
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- mocks the calculations and performs gathers on the mocked outputs
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"""
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import pytest
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from importlib import resources
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from click.testing import CliRunner
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from os import path
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from unittest import mock
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from openff.units import unit
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from openfecli.commands.plan_rbfe_network import plan_rbfe_network
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from openfecli.commands.quickrun import quickrun
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from openfecli.commands.gather import gather
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@pytest.fixture
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def tyk2_ligands():
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with resources.files('openfecli.tests.data.rbfe_tutorial') as d:
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yield str(d / 'tyk2_ligands.sdf')
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@pytest.fixture
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def tyk2_protein():
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with resources.files('openfecli.tests.data.rbfe_tutorial') as d:
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yield str(d / 'tyk2_protein.pdb')
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@pytest.fixture
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def expected_transformations():
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return ['easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json',
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'easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json',
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'easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json',
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'easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json',
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'easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json',
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'easy_rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json',
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'easy_rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json',
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'easy_rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json',
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'easy_rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json',
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'easy_rbfe_lig_ejm_42_complex_lig_ejm_50_complex.json',
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'easy_rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json',
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'easy_rbfe_lig_ejm_42_solvent_lig_ejm_50_solvent.json',
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'easy_rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json',
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'easy_rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json',
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'easy_rbfe_lig_jmc_23_complex_lig_jmc_27_complex.json',
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'easy_rbfe_lig_jmc_23_solvent_lig_jmc_27_solvent.json',
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'easy_rbfe_lig_jmc_27_complex_lig_jmc_28_complex.json',
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'easy_rbfe_lig_jmc_27_solvent_lig_jmc_28_solvent.json']
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def test_plan_tyk2(tyk2_ligands, tyk2_protein, expected_transformations):
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runner = CliRunner()
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with runner.isolated_filesystem():
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result = runner.invoke(plan_rbfe_network, ['-M', tyk2_ligands,
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'-p', tyk2_protein])
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assert result.exit_code == 0
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assert path.exists('alchemicalNetwork/transformations')
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for f in expected_transformations:
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assert path.exists(
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path.join('alchemicalNetwork/transformations', f))
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@pytest.fixture
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def mock_execute(expected_transformations):
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def fake_execute(*args, **kwargs):
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return {
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'repeat_id': kwargs['repeat_id'],
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'generation': kwargs['generation'],
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'nc': 'file.nc',
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'last_checkpoint': 'checkpoint.nc',
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'unit_estimate': 4.2 * unit.kilocalories_per_mole
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}
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with mock.patch('openfe.protocols.openmm_rfe.equil_rfe_methods.'
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'RelativeHybridTopologyProtocolUnit._execute') as m:
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m.side_effect = fake_execute
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yield m
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@pytest.fixture
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def ref_gather():
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return """\
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ligand_i\tligand_j\tDDG(i->j) (kcal/mol)\tuncertainty (kcal/mol)
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lig_ejm_31\tlig_ejm_46\t0.0\t0.0
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lig_ejm_31\tlig_ejm_47\t0.0\t0.0
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lig_ejm_31\tlig_ejm_48\t0.0\t0.0
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lig_ejm_31\tlig_ejm_50\t0.0\t0.0
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lig_ejm_42\tlig_ejm_43\t0.0\t0.0
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lig_ejm_42\tlig_ejm_50\t0.0\t0.0
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lig_ejm_46\tlig_jmc_27\t0.0\t0.0
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lig_jmc_23\tlig_jmc_27\t0.0\t0.0
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lig_jmc_27\tlig_jmc_28\t0.0\t0.0
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"""
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def test_run_tyk2(tyk2_ligands, tyk2_protein, expected_transformations,
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mock_execute, ref_gather):
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runner = CliRunner()
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with runner.isolated_filesystem():
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result = runner.invoke(plan_rbfe_network, ['-M', tyk2_ligands,
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'-p', tyk2_protein])
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assert result.exit_code == 0
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for f in expected_transformations:
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fn = path.join('alchemicalNetwork/transformations', f)
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result2 = runner.invoke(quickrun, [fn])
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assert result2.exit_code == 0
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gather_result = runner.invoke(gather, ["--report", "ddg", '.'])
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assert gather_result.exit_code == 0
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assert gather_result.stdout == ref_gather
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