Initial commit

functions.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python3
+import os
+import re
+import argparse
+
+
+def natural_key(string_):
+    return [int(s) if s.isdigit() else s for s in re.split(r'(\d+)', string_)]
+
+
+def abs_path(path):
+    abs_path = os.path.abspath(path)
+    return abs_path
+
+def parser():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--steps', type=int,
+                    help='Number of steps to run the simulation')
+    parser.add_argument('--jobs_path', type=str, nargs='+', action='append',
+                    help='Jobs 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