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| parser = argparse.ArgumentParser(description="Track stacking") |
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| help |
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| nargs |
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| type |
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| int |
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| default |
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| action |
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| args = parser.parse_args() |
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str | header = " ".join([f"'{i}'" for i in sys.argv]) |
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| system = loos.createSystem(args.system_file) |
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list | all_trajs = [] |
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| | traj |
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| selection = loos.selectAtoms(system, args.selection_string) |
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| residues = selection.splitByResidue() |
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| scores = np.zeros((len(residues), len(residues))) |
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int | total_frames = 0 |
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| box = loos.GCoord(1000., 1000., 1000.) |
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| p = residues[i].stacking(residues[j], box, 5.0) |
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| stack_values = json.load(jsfile) |
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list | resnames = [] |
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list | key = resnames[i] + "-" + resnames[j] |
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| newval = scores[i, j] / stack_values[key] |
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| outfile_name |
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Track a base stacking through a trajectory. Intended for use with
nucleic acids, to identify base stacking.
