From ef3c93cdbc7cdcc818283e23b40715962a035655 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 24 Jul 2024 12:43:04 +0100
Subject: [PATCH] Add missing extra_args kwarg. [closes #318]

---
 python/BioSimSpace/Process/_somd.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/python/BioSimSpace/Process/_somd.py b/python/BioSimSpace/Process/_somd.py
index 2d1c5e508..f51d56774 100644
--- a/python/BioSimSpace/Process/_somd.py
+++ b/python/BioSimSpace/Process/_somd.py
@@ -78,6 +78,7 @@ def __init__(
         seed=None,
         extra_options={},
         extra_lines=[],
+        extra_args={},
         property_map={},
         **kwargs,
     ):
@@ -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
@@ -136,6 +140,7 @@ def __init__(
             seed=seed,
             extra_options=extra_options,
             extra_lines=extra_lines,
+            extra_args=extra_args,
             property_map=property_map,
         )
 
@@ -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.