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Fix issue #318 #319

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Jul 29, 2024
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9 changes: 9 additions & 0 deletions python/BioSimSpace/Process/_somd.py
Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,7 @@ def __init__(
seed=None,
extra_options={},
extra_lines=[],
extra_args={},
property_map={},
**kwargs,
):
Expand Down Expand Up @@ -118,6 +119,9 @@ def __init__(
extra_lines : [str]
A list of extra lines to put at the end of the configuration file.

extra_args : dict
A dictionary of extra command-line arguments to pass to the AMBER executable.

property_map : dict
A dictionary that maps system "properties" to their user defined
values. This allows the user to refer to properties with their
Expand All @@ -136,6 +140,7 @@ def __init__(
seed=seed,
extra_options=extra_options,
extra_lines=extra_lines,
extra_args=extra_args,
property_map=property_map,
)

Expand Down Expand Up @@ -478,6 +483,10 @@ def _generate_args(self):
self.setArg("-C", "%s.cfg" % self._name) # Config file.
self.setArg("-p", self._platform) # Simulation platform.

# Add the extra arguments.
for key, value in self._extra_args.items():
self.setArg(key, value)

def start(self):
"""
Start the SOMD process.
Expand Down