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Backport fix from PR #361. [ci skip]
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lohedges committed Oct 29, 2024
1 parent 58e8665 commit 7386e9f
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Showing 6 changed files with 74 additions and 0 deletions.
14 changes: 14 additions & 0 deletions python/BioSimSpace/Parameters/_Protocol/_amber.py
Original file line number Diff line number Diff line change
Expand Up @@ -841,6 +841,7 @@ def __init__(
net_charge=None,
ensure_compatible=True,
property_map={},
**kwargs,
):
"""
Constructor.
Expand Down Expand Up @@ -873,6 +874,10 @@ def __init__(
A dictionary that maps system "properties" to their user defined
values. This allows the user to refer to properties with their
own naming scheme, e.g. { "charge" : "my-charge" }
**kwargs: dict
Additional keyword arguments. These can be used to pass custom
parameters to the Antechamber program.
"""

if type(version) is not int:
Expand Down Expand Up @@ -912,6 +917,11 @@ def __init__(
"'net_charge' must be of type 'int', or `BioSimSpace.Types.Charge'"
)

# Check the kwargs to see whether acdoctor is enabled.
self._acdoctor = kwargs.get("acdoctor", True)
if not isinstance(self._acdoctor, bool):
raise TypeError("'acdoctor' must be of type 'bool'")

# Set the version.
self._version = version

Expand Down Expand Up @@ -1086,6 +1096,10 @@ def run(self, molecule, work_dir=None, queue=None):
charge,
)

# Disable acdoctor if requested.
if not self._acdoctor:
command += " -dr no"

with open(_os.path.join(str(work_dir), "README.txt"), "w") as file:
# Write the command to file.
file.write("# Antechamber was run with the following command:\n")
Expand Down
2 changes: 2 additions & 0 deletions python/BioSimSpace/Parameters/_parameters.py
Original file line number Diff line number Diff line change
Expand Up @@ -362,6 +362,7 @@ def gaff(
charge_method=charge_method,
ensure_compatible=ensure_compatible,
property_map=property_map,
**kwargs,
)

# Run the parameterisation protocol in the background and return
Expand Down Expand Up @@ -460,6 +461,7 @@ def gaff2(
charge_method=charge_method,
ensure_compatible=ensure_compatible,
property_map=property_map,
**kwargs,
)

# Run the parameterisation protocol in the background and return
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -841,6 +841,7 @@ def __init__(
net_charge=None,
ensure_compatible=True,
property_map={},
**kwargs,
):
"""
Constructor.
Expand Down Expand Up @@ -873,6 +874,10 @@ def __init__(
A dictionary that maps system "properties" to their user defined
values. This allows the user to refer to properties with their
own naming scheme, e.g. { "charge" : "my-charge" }
**kwargs: dict
Additional keyword arguments. These can be used to pass custom
parameters to the Antechamber program.
"""

if type(version) is not int:
Expand Down Expand Up @@ -912,6 +917,11 @@ def __init__(
"'net_charge' must be of type 'int', or `BioSimSpace.Types.Charge'"
)

# Check the kwargs to see whether acdoctor is enabled.
self._acdoctor = kwargs.get("acdoctor", True)
if not isinstance(self._acdoctor, bool):
raise TypeError("'acdoctor' must be of type 'bool'")

# Set the version.
self._version = version

Expand Down Expand Up @@ -1086,6 +1096,10 @@ def run(self, molecule, work_dir=None, queue=None):
charge,
)

# Disable acdoctor if requested.
if not self._acdoctor:
command += " -dr no"

with open(_os.path.join(str(work_dir), "README.txt"), "w") as file:
# Write the command to file.
file.write("# Antechamber was run with the following command:\n")
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -362,6 +362,7 @@ def gaff(
charge_method=charge_method,
ensure_compatible=ensure_compatible,
property_map=property_map,
**kwargs,
)

# Run the parameterisation protocol in the background and return
Expand Down Expand Up @@ -460,6 +461,7 @@ def gaff2(
charge_method=charge_method,
ensure_compatible=ensure_compatible,
property_map=property_map,
**kwargs,
)

# Run the parameterisation protocol in the background and return
Expand Down
21 changes: 21 additions & 0 deletions tests/Parameters/test_parameters.py
Original file line number Diff line number Diff line change
Expand Up @@ -167,3 +167,24 @@ def test_smiles_stereo():

# Make sure the SMILES strings are the same.
assert rdmol0_smiles == rdmol1_smiles


@pytest.mark.skipif(
has_antechamber is False or has_tleap is False,
reason="Requires AmberTools/antechamber and tLEaP to be installed.",
)
def test_acdoctor():
"""
Test that parameterising negatively charged molecules works when acdoctor
is disabled.
"""

# Load the molecule.
mol = BSS.IO.readMolecules(f"{url}/negative_charge.sdf")[0]

# Make sure parameterisation fails when acdoctor is enabled.
with pytest.raises(BSS._Exceptions.ParameterisationError):
BSS.Parameters.gaff(mol).getMolecule()

# Make sure parameterisation works when acdoctor is disabled.
mol = BSS.Parameters.gaff(mol, acdoctor=False).getMolecule()
21 changes: 21 additions & 0 deletions tests/Sandpit/Exscientia/Parameters/test_parameters.py
Original file line number Diff line number Diff line change
Expand Up @@ -172,3 +172,24 @@ def test_smiles_stereo():

# Make sure the SMILES strings are the same.
assert rdmol0_smiles == rdmol1_smiles


@pytest.mark.skipif(
has_antechamber is False or has_tleap is False,
reason="Requires AmberTools/antechamber and tLEaP to be installed.",
)
def test_acdoctor():
"""
Test that parameterising negatively charged molecules works when acdoctor
is disabled.
"""

# Load the molecule.
mol = BSS.IO.readMolecules(f"{url}/negative_charge.sdf")[0]

# Make sure parameterisation fails when acdoctor is enabled.
with pytest.raises(BSS._Exceptions.ParameterisationError):
BSS.Parameters.gaff(mol).getMolecule()

# Make sure parameterisation works when acdoctor is disabled.
mol = BSS.Parameters.gaff(mol, acdoctor=False).getMolecule()

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