Initial commit

run.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+
+import glob
+import os
+
+from job import get_next_job, get_jobs_from_path, create_job_instances
+from simulate import Simulate
+from functions import abs_path, parser
+
+
+def main(jobs_path, ffs_path, steps, namdbin, params):
+
+    jobs_path = abs_path(jobs_path)
+    job_dirs_l = get_jobs_from_path(jobs_path)
+    jobs = create_job_instances(job_dirs_l)
+    job = get_next_job(jobs)
+    job.prepare_sim(ffs_path, steps)
+    job.info()
+    Simulate(job, namdbin, params)
+
+
+if __name__ == '__main__':
+
+    args = parser()
+
+    if args.jobs_path is not None and os.path.isdir(args.jobs_path):
+        jobs_path = args.jobs_path
+    else:
+        jobs_path = '/home/bryan/MD/CFTR/4-jobs'
+
+    if args.namd_params is not None:
+        params = args.namd_params
+    else:
+        params = '+p7'
+
+    main(jobs_path=jobs_path,
+         ffs_path='/home/bryan/MD/CFTR/0-forcefields',
+         steps=1000000,
+         namdbin='/home/bryan/bin/namd2',
+         params=params)