Skip to content
Snippets Groups Projects
Select Git revision
  • 53c3a52243fc255456ff0f455d657059c90350f3
  • master default protected
  • pipeline
  • dev
  • quality
  • docs
  • issue-65
  • issue-30
  • issue-19
  • issue-28
  • 0.1.1
  • 0.1.0
12 results

admin.py

Blame
  • pycgtool.py 2.25 KiB
    #!/usr/bin/env python3
    
    import argparse
    import sys
    
    from pycgtool.pycgtool import main, map_only
    from pycgtool.interface import Options
    
    if __name__ == "__main__":
        parser = argparse.ArgumentParser(description="Perform coarse-grain mapping of atomistic trajectory")
        input_files = parser.add_argument_group("Input files")
        input_files.add_argument('-g', '--gro', type=str, required=True, help="GROMACS GRO file")
        input_files.add_argument('-m', '--map', type=str, help="Mapping file")
        input_files.add_argument('-x', '--xtc', type=str, help="GROMACS XTC file")
        input_files.add_argument('-b', '--bnd', type=str, help="Bonds file")
        input_files.add_argument('-i', '--itp', type=str, help="GROMACS ITP file")
    
        parser.add_argument('--interactive', default=False, action='store_true')
        parser.add_argument('--outputxtc', default=False, action='store_true')
        parser.add_argument('--quiet', default=False, action='store_true')
        input_files.add_argument('--begin', type=int, default=0, help="Frame number to begin")
        input_files.add_argument('--end', type=int, default=-1, help="Frame number to end")
    
        args = parser.parse_args()
        config = Options([("output_name", "out"),
                          ("output", "gro"),
                          ("output_xtc", args.outputxtc),
                          ("map_only", not bool(args.bnd)),
                          ("map_center", "geom"),
                          ("constr_threshold", 100000),
                          ("dump_measurements", bool(args.bnd) and not bool(args.map)),
                          ("dump_n_values", 100000),
                          ("output_forcefield", False),
                          ("temperature", 310),
                          ("angle_default_fc", True),
                          ("generate_angles", True),
                          ("generate_dihedrals", False)],
                         args)
    
        if not args.map and not args.bnd:
            parser.error("One or both of -m and -b is required.")
    
        if args.interactive:
            try:
                config.interactive()
            except KeyboardInterrupt:
                sys.exit(0)
        else:
            print("Using GRO: {0}".format(args.gro))
            print("Using XTC: {0}".format(args.xtc))
    
        if config.map_only:
            map_only(args, config)
        else:
            main(args, config)