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Fix issue #339 #342

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merged 1 commit into from
Sep 25, 2024
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Merged

Fix issue #339 #342

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29 changes: 22 additions & 7 deletions python/BioSimSpace/Process/_gromacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2131,16 +2131,31 @@ def _add_position_restraints(self):
)

with open(restraint_file, "w") as file:
# Write the header.
file.write("[ position_restraints ]\n")
file.write("; i funct fcx fcy fcz\n")

# Write restraints for each atom.
for atom_idx in restrained_atoms:
if isinstance(self._protocol, _FreeEnergyMixin):
# Write the header.
file.write("[ position_restraints ]\n")
file.write(
f"{atom_idx+1:4} 1 {force_constant} {force_constant} {force_constant}\n"
"; i funct fcx_A fcy_A fcz_A fcx_B fcy_B fcz_B\n"
)
# Write restraints for each atom.
for atom_idx in restrained_atoms:
file.write(
f"{atom_idx+1:4} 1 {force_constant} {force_constant} {force_constant} {force_constant} {force_constant} {force_constant}\n"
)

else:
# Write the header.
file.write("[ position_restraints ]\n")
file.write(
"; i funct fcx fcy fcz\n"
)

# Write restraints for each atom.
for atom_idx in restrained_atoms:
file.write(
f"{atom_idx+1:4} 1 {force_constant} {force_constant} {force_constant}\n"
)

# Work out the offset.
offset = num_restraint - 1

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11 changes: 11 additions & 0 deletions tests/Process/test_gromacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,17 @@ def test_restraints(perturbable_system, restraint):
process = BSS.Process.Gromacs(perturbable_system, protocol)


@pytest.mark.skipif(has_gromacs is False, reason="Requires GROMACS to be installed.")
def test_perturbable_restraint(perturbable_system):
"""Test a free energy perturbation protocol."""

# Create a short minimisation protocol with a restraint.
protocol = BSS.Protocol.Minimisation(steps=100, restraint="heavy")

# Run the process, check that it finished without error, and returns a system.
run_process(perturbable_system, protocol)


def run_process(system, protocol, **kwargs):
"""Helper function to run various simulation protocols."""

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