Add modules

auto_namd/functions.py

@@ -0,0 +1,46 @@
+import os
+import re
+import argparse
+
+# Natural sort
+def natural_key(string_):
+    return [int(s) if s.isdigit() else s for s in re.split(r'(\d+)', string_)]
+
+
+# Return absolute path from relative or absolute path
+def abs_path(path):
+    abs_path = os.path.abspath(path)
+    return abs_path
+
+
+# Sanitize user input paths
+def san_path(path):
+    san_path = os.path.normpath(path)
+    return san_path
+
+
+# Argument parser for run_simulations.py
+def sim_parser(defaults):
+    # Use default settings from run_simulation.py to generate argument parser
+    parser = argparse.ArgumentParser()
+    for _arg, _val in defaults.items():
+            parser.add_argument(f'--{_arg}', type=type(_val[0]), default=_val[0], help=_val[1])
+    args_dict = vars(parser.parse_args())
+    return args_dict
+
+
+# Argument parser for run_analysis.py
+def analysis_parser():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--steps', type=int,
+                    help='Number of timesteps to run the simulation')
+    parser.add_argument('--jobs_path', type=str, nargs='+', action='append',
+                    help='Directory path containing the jobs to be run')
+    parser.add_argument('--namd_params', type=str,
+                    help='Optional parameters to send to namd')
+    parser.add_argument('--ffs_path', type=str,
+                    help='Location of the forcefield files')
+    parser.add_argument('--namd2_bin', type=str,
+                    help='Location of the namd2 executable')
+    args = parser.parse_args()
+    return args