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Pass match_water parameter to specialised solvation functions #186

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Pass match_water parameter to specialised solvation functions #186

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aceb0e4
Pass match_water through to specialised water model functions.
lohedges Oct 18, 2023
0ab849a
Test generic solvate function as well as specialised tip3p function.
lohedges Oct 18, 2023
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1 change: 1 addition & 0 deletions python/BioSimSpace/Sandpit/Exscientia/Solvent/_solvent.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,7 @@ def solvate(
ion_conc,
is_neutral,
is_aligned,
match_water,
work_dir,
property_map,
)
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1 change: 1 addition & 0 deletions python/BioSimSpace/Solvent/_solvent.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,7 @@ def solvate(
ion_conc,
is_neutral,
is_aligned,
match_water,
work_dir,
property_map,
)
Expand Down
12 changes: 9 additions & 3 deletions tests/Sandpit/Exscientia/Solvent/test_solvent.py
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Original file line number Diff line number Diff line change
@@ -1,11 +1,13 @@
import pytest
import tempfile

from functools import partial

from sire.legacy.IO import GroTop

import BioSimSpace.Sandpit.Exscientia as BSS

from tests.Sandpit.Exscientia.conftest import has_gromacs
from tests.conftest import has_gromacs


@pytest.fixture(scope="module")
Expand All @@ -18,8 +20,12 @@ def system():


@pytest.mark.parametrize("match_water", [True, False])
@pytest.mark.parametrize(
"function",
[partial(BSS.Solvent.solvate, "tip3p"), BSS.Solvent.tip3p],
)
@pytest.mark.skipif(not has_gromacs, reason="Requires GROMACS to be installed")
def test_crystal_water(system, match_water):
def test_crystal_water(system, match_water, function):
"""
Test that user defined crystal waters can be preserved during
solvation and on write to GroTop format.
Expand All @@ -35,7 +41,7 @@ def test_crystal_water(system, match_water):
box, angles = BSS.Box.cubic(5.5 * BSS.Units.Length.nanometer)

# Create the solvated system.
solvated = BSS.Solvent.tip3p(system, box, angles, match_water=match_water)
solvated = function(system, box, angles, match_water=match_water)

# Search for the crystal waters in the solvated system.
try:
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10 changes: 8 additions & 2 deletions tests/Solvent/test_solvent.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
import pytest
import tempfile

from functools import partial

from sire.legacy.IO import GroTop

import BioSimSpace as BSS
Expand All @@ -18,8 +20,12 @@ def system():


@pytest.mark.parametrize("match_water", [True, False])
@pytest.mark.parametrize(
"function",
[partial(BSS.Solvent.solvate, "tip3p"), BSS.Solvent.tip3p],
)
@pytest.mark.skipif(not has_gromacs, reason="Requires GROMACS to be installed")
def test_crystal_water(system, match_water):
def test_crystal_water(system, match_water, function):
"""
Test that user defined crystal waters can be preserved during
solvation and on write to GroTop format.
Expand All @@ -35,7 +41,7 @@ def test_crystal_water(system, match_water):
box, angles = BSS.Box.cubic(5.5 * BSS.Units.Length.nanometer)

# Create the solvated system.
solvated = BSS.Solvent.tip3p(system, box, angles, match_water=match_water)
solvated = function(system, box, angles, match_water=match_water)

# Search for the crystal waters in the solvated system.
try:
Expand Down
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