diff --git a/pycgtool.py b/pycgtool.py index b653f04014150b46fcb870953c8d56da43493d8a..0bc112391d17040023a19afd2f55c29921629530 100755 --- a/pycgtool.py +++ b/pycgtool.py @@ -26,7 +26,7 @@ def main(args, config): if args.map: mapping = Mapping(args.map, config, itp=args.itp) cgframe = mapping.apply(frame, exclude={"SOL"}) - cgframe.output("out.gro", format=config.output) + cgframe.output(config.output_name + ".gro", format=config.output) # Main loop - perform mapping and measurement on every frame in XTC numframes = frame.numframes - args.begin if args.end == -1 else args.end - args.begin @@ -45,16 +45,16 @@ def main(args, config): if args.map: bonds.boltzmann_invert() if config.output_forcefield: - ff = ForceField("fftest.ff") - ff.write_rtp("test.rtp", mapping, bonds) + ff = ForceField("ff" + config.output_name + ".ff") + ff.write_rtp(config.output_name + ".rtp", mapping, bonds) else: - bonds.write_itp("out.itp", mapping=mapping) + bonds.write_itp(config.output_name + ".itp", mapping=mapping) if config.dump_measurements: bonds.dump_values(config.dump_n_values) if args.map and (config.output_xtc or args.outputxtc): - cgframe.flush_xtc_buffer("out.xtc") + cgframe.flush_xtc_buffer(config.output_name + ".xtc") def map_only(args, config): @@ -67,14 +67,14 @@ def map_only(args, config): frame = Frame(gro=args.gro, xtc=args.xtc) mapping = Mapping(args.map, config) cgframe = mapping.apply(frame, exclude={"SOL"}) - cgframe.output("out.gro", format=config.output) + cgframe.output(config.output_name + ".gro", format=config.output) if args.xtc and (config.output_xtc or args.outputxtc): numframes = frame.numframes - args.begin if args.end == -1 else args.end - args.begin for _ in Progress(numframes, postwhile=frame.next_frame): cgframe = mapping.apply(frame, cgframe=cgframe, exclude={"SOL"}) cgframe.write_to_xtc_buffer() - cgframe.flush_xtc_buffer("out.xtc") + cgframe.flush_xtc_buffer(config.output_name + ".xtc") if __name__ == "__main__": @@ -93,7 +93,8 @@ if __name__ == "__main__": input_files.add_argument('--end', type=int, default=-1, help="Frame number to end") args = parser.parse_args() - config = Options([("output", "gro"), + config = Options([("output_name", "out"), + ("output", "gro"), ("map_only", False), ("map_center", "geom"), ("constr_threshold", 100000),