Merge branch 'master' of github.com:brianjimenez/lightdock

Author: brianjimenez

bin/post/lgd_rank_swarm.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+
+"""Calculates the ranking file by scoring intra-swarm"""
+
+from __future__ import print_function
+import sys
+import os
+import argparse
+from lightdock.util.logger import LoggingManager
+from lightdock.constants import DEFAULT_SWARM_FOLDER, GSO_OUTPUT_FILE
+from lightdock.util.analysis import read_ranking_file
+from lightdock.util.analysis import read_lightdock_output
+from lightdock.util.analysis import write_ranking_to_file
+
+
+log = LoggingManager.get_logger('lgd_rank_swarm')
+
+
+def parse_command_line():
+    parser = argparse.ArgumentParser(prog='lgd_rank_swarm')
+    parser.add_argument("num_swarms", help="number of swarms to consider", type=int, metavar="num_swarms")
+    parser.add_argument("steps", help="steps to consider", type=int, metavar="steps")
+    return parser.parse_args()
+
+
+if __name__ == '__main__':
+
+    try:
+        CURRENT_FOLDER = os.getcwd()
+        args = parse_command_line()
+
+        for swarm_id in range(args.num_swarms):
+            os.chdir(os.path.join(DEFAULT_SWARM_FOLDER + str(swarm_id)))
+            result_file_name = os.path.join(GSO_OUTPUT_FILE % args.steps)
+            lightdock_output = read_lightdock_output(result_file_name)
+            for g in lightdock_output:
+                g.id_cluster = swarm_id
+                g.pdb_file = "lightdock_" + str(g.id_glowworm) + ".pdb"
+            write_ranking_to_file(lightdock_output, order_by="scoring")
+            os.chdir(CURRENT_FOLDER)
+    except IOError:
+        log.warning("Either num_clusters or steps not found. Exiting...")
+        raise SystemExit()