example started for getting a walker lineage DCD

Author: salotz

examples/seh_tppu_unbinding/analysis/walker_lineage.py

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+import sys
+import os.path as osp
+
+from wepy.hdf5 import WepyHDF5
+from wepy.analysis.tree import ancestors
+from wepy.resampling.wexplore1 import WExplore1Resampler
+
+if sys.argv[1] == '-h' or sys.argv[1] == '--help':
+    print("walker_lineage.py run_index walker_index output_DCD_path")
+else:
+    run_idx = sys.argv[1]
+    walker_idx = sys.argv[2]
+    dcd_path = sys.argv[3]
+
+    outputs_dir = osp.realpath('../outputs')
+
+    hdf5_filename = 'results.wepy.h5'
+
+    hdf5_path = osp.join(outputs_dir, hdf5_filename)
+
+    wepy_h5 = WepyHDF5(hdf5_path, mode='r')
+
+    wepy_h5.open()
+
+    cycle_idx = wepy_h5.traj(run_idx, walker_idx)['positions'].shape[0]
+
+    resampling_panel = wepy_h5.run_resampling_panel(run_idx)
+
+    parent_panel = WExplore1.DECISION.parent_panel(resampling_panel)
+    parent_table = WExplore1.DECISION.net_parent_panel(parent_panel)
+
+    lineage = ancestors(parent_table, cycle_idx, walker_idx)
+
+    mdj_traj = wepy_h5.trace_to_mdtraj(lineage)
+
+    mdj_traj.save_dcd(dcd_path)