mmagnus /
rna-tools
| @@ 38-61 (lines=24) @@ | ||
| 35 | from rna_tools.tools.mq.lib.timex import timex |
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| 36 | ||
| 37 | ||
| 38 | def get_parser(): |
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| 39 | parser = argparse.ArgumentParser( |
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| 40 | description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) |
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| 41 | parser.add_argument('-s', "--steps", type=int, help="", default=100) |
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| 42 | parser.add_argument('-n', "--nsim", type=int, help="", default=500000) |
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| 43 | # 500000 to get 1 ns |
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| 44 | # 50000 |
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| 45 | parser.add_argument('-r', "--run", help="", default='_') |
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| 46 | parser.add_argument('-p', "--prefix", help="", default='') |
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| 47 | parser.add_argument("-v", "--verbose", |
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| 48 | action="store_true", help="be verbose") |
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| 49 | parser.add_argument("--dcd", |
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| 50 | action="store_true", help="save also as dcd") |
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| 51 | parser.add_argument("file", help="", default="") # nargs='+') |
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| 52 | ||
| 53 | parser.add_argument("--min", |
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| 54 | action="store_true", help="be verbose") |
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| 55 | parser.add_argument("--pymol", |
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| 56 | action="store_true", help="be verbose") |
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| 57 | parser.add_argument("--box-size", help="", default=1, type=float) # nargs='+') |
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| 58 | parser.add_argument("--solv-padding", |
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| 59 | action="store_true", help="be verbose") |
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| 60 | ||
| 61 | return parser |
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| 62 | ||
| 63 | ||
| 64 | if __name__ == '__main__': |
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| @@ 275-296 (lines=22) @@ | ||
| 272 | return l |
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| 273 | ||
| 274 | ||
| 275 | def get_parser(): |
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| 276 | parser = argparse.ArgumentParser( |
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| 277 | description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) |
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| 278 | ||
| 279 | parser.add_argument('-t',"--target", |
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| 280 | help="target file") |
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| 281 | parser.add_argument('--result', #default='out.rmsd', |
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| 282 | help="result file") |
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| 283 | parser.add_argument('--ignore-files', default='aligned', help="use to ignore files, .e.g. with 'aligned'") |
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| 284 | parser.add_argument('--suffix', default='aligned', help="used with --saved, by default: aligned") |
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| 285 | parser.add_argument('--way', help="e.g., backbone+sugar, c1, c1+Nx") |
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| 286 | parser.add_argument('--triple-mode', help="same crazy strategy to align triples", default=True, action="store_true") |
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| 287 | parser.add_argument('--column-name', help="name column for rmsd, by default 'rmsd', but can also be a name of the target file", default="rmsd") |
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| 288 | parser.add_argument("-s", "--save", action="store_true", help="set suffix with --suffix, by default: aligned") |
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| 289 | parser.add_argument("--folder-prefix", default = '', help="folder name, t2-3-UAU_NAME_aligned") |
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| 290 | ||
| 291 | parser.add_argument("--debug", action="store_true") |
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| 292 | parser.add_argument("--show", action="store_true", help="show the results in the terminal") |
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| 293 | parser.add_argument("--sort", action="store_true", help='sort results based on rmsd (ascending), --result must be set up') |
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| 294 | parser.add_argument("--tseq", help='target sequence, e.g. acu, find only triples of this sequence [use the order for the seq taken from the input PDB file, literally order of residues in a pdb file]') |
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| 295 | parser.add_argument('--files', help='files', nargs='+', default=RT + '/rna_tools/tools/triplexibility/db/triples-all-v2-rpr/*.pdb') |
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| 296 | return parser |
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| 297 | ||
| 298 | # main |
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| 299 | if __name__ == '__main__': |
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| @@ 334-354 (lines=21) @@ | ||
| 331 | return l |
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| 332 | ||
| 333 | ||
| 334 | def get_parser(): |
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| 335 | parser = argparse.ArgumentParser( |
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| 336 | description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) |
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| 337 | ||
| 338 | parser.add_argument('-t',"--target", |
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| 339 | help="target file") |
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| 340 | parser.add_argument('--result', #default='out.rmsd', |
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| 341 | help="result file") |
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| 342 | parser.add_argument('--ignore-files', default='aligned', help="use to ignore files, .e.g. with 'aligned'") |
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| 343 | parser.add_argument('--suffix', default='aligned', help="used with --saved, by default: aligned") |
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| 344 | parser.add_argument('--way', help="e.g., backbone+sugar, c1, c1+Nx") |
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| 345 | parser.add_argument('--triple-mode', help="same crazy strategy to align triples", default=True, action="store_true") |
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| 346 | parser.add_argument('--column-name', help="name column for rmsd, by default 'rmsd', but can also be a name of the target file", default="rmsd") |
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| 347 | parser.add_argument("-s", "--save", action="store_true", help="set suffix with --suffix, by default: aligned") |
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| 348 | parser.add_argument("--folder-prefix", default = '', help="folder name, t2-3-UAU_NAME_aligned") |
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| 349 | ||
| 350 | parser.add_argument("--debug", action="store_true") |
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| 351 | parser.add_argument("--sort", action="store_true", help='sort results based on rmsd (ascending), --result must be set up') |
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| 352 | parser.add_argument("--tseq", help='target sequence, e.g. acu, find only triples of this sequence [use the order for the seq taken from the input PDB file, literally order of residues in a pdb file]') |
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| 353 | parser.add_argument('--files', help='files', nargs='+', default=RT + '/rna_tools/tools/triplexibility/db/triples-all-v2-rpr/*.pdb') |
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| 354 | return parser |
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| 355 | ||
| 356 | # main |
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| 357 | if __name__ == '__main__': |
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