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Pass match_water parameter to specialised solvation functions #190

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merged 3 commits into from
Oct 24, 2023
Merged

Pass match_water parameter to specialised solvation functions #190

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3d3ed62
Pass match_water through to specialised water model functions.
lohedges Oct 18, 2023
d55d93f
Test generic solvate function as well as specialised tip3p function.
lohedges Oct 18, 2023
222f2c8
Use sandpit conftest.
lohedges Oct 23, 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
10 changes: 8 additions & 2 deletions tests/Sandpit/Exscientia/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.Sandpit.Exscientia 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:
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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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