mmagnus /
rna-tools
| @@ 219-289 (lines=71) @@ | ||
| 216 | ||
| 217 | return round(kabsch_rmsd(P, Q),2), atomsP |
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| 218 | ||
| 219 | def get_parser(): |
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| 220 | import argparse |
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| 221 | class SmartFormatter(argparse.HelpFormatter): |
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| 222 | def _split_lines(self, text, width): |
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| 223 | if text.startswith('R|'): |
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| 224 | return text[2:].splitlines() |
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| 225 | # this is the RawTextHelpFormatter._split_lines |
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| 226 | return argparse.HelpFormatter._split_lines(self, text, width) |
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| 227 | ||
| 228 | parser = argparse.ArgumentParser(description=__doc__, formatter_class=SmartFormatter)#formatter_class=argparse.RawDescriptionHelpFormatter) |
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| 229 | ||
| 230 | parser.add_argument('-t',"--target-fn", |
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| 231 | default='', required = True, |
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| 232 | help="pdb file") |
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| 233 | ||
| 234 | parser.add_argument('--ignore-files', help='files to be ingored, .e.g, \'solution\'', default='') |
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| 235 | ||
| 236 | parser.add_argument("--target-selection", |
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| 237 | default='', |
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| 238 | help="selection, e.g. A:10-16+20, where #16 residue is included") |
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| 239 | ||
| 240 | parser.add_argument("--target-ignore-selection", |
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| 241 | default='', |
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| 242 | help="A/10/O2\'") |
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| 243 | ||
| 244 | parser.add_argument("--model-selection", |
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| 245 | default='', |
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| 246 | help="selection, e.g. A:10-16+20, where #16 residue is included") |
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| 247 | ||
| 248 | parser.add_argument("--model-ignore-selection", |
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| 249 | default='', |
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| 250 | help="A/10/O2\'") |
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| 251 | ||
| 252 | parser.add_argument('-m', "--method", |
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| 253 | default='all-atom-built-in', |
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| 254 | help="align, fit") |
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| 255 | ||
| 256 | parser.add_argument('-o', "--rmsds-fn", |
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| 257 | default='rmsds.csv', |
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| 258 | help="ouput, matrix") |
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| 259 | ||
| 260 | parser.add_argument("-v", "--verbose", action="store_true", |
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| 261 | help="verbose") |
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| 262 | ||
| 263 | parser.add_argument('-pr', '--print-results', |
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| 264 | action="store_true") |
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| 265 | ||
| 266 | parser.add_argument('-sr', '--sort-results', |
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| 267 | action="store_true") |
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| 268 | ||
| 269 | parser.add_argument('-pp', '--print-progress', |
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| 270 | default=False, |
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| 271 | action="store_true") |
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| 272 | ||
| 273 | parser.add_argument('--way', help="""R|c1p = C1' |
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| 274 | backbone = P OP1 OP2 O5' C5' C4' C3' O3' |
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| 275 | po = P OP1 OP2 |
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| 276 | no-backbone = all - po |
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| 277 | bases, backbone+sugar, sugar |
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| 278 | pooo = P OP1 OP2 O5' |
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| 279 | alpha = P OP1 OP2 O5' C5' |
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| 280 | """, default='all') |
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| 281 | ||
| 282 | parser.add_argument("--name-rmsd-column", help="default: fn,rmsd, with this cols will be fn,<name-rmsd-column>") |
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| 283 | ||
| 284 | parser.add_argument("--target-column-name", action="store_true", |
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| 285 | help="") |
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| 286 | ||
| 287 | parser.add_argument('files', help='files', nargs='+') |
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| 288 | ||
| 289 | return parser |
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| 290 | # main |
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| 291 | if __name__ == '__main__': |
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| 292 | parser = get_parser() |
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| @@ 196-266 (lines=71) @@ | ||
| 193 | ||
| 194 | return round(kabsch_rmsd(P, Q, atoms),2), atomsP |
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| 195 | ||
| 196 | def get_parser(): |
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| 197 | import argparse |
|
| 198 | class SmartFormatter(argparse.HelpFormatter): |
|
| 199 | def _split_lines(self, text, width): |
|
| 200 | if text.startswith('R|'): |
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| 201 | return text[2:].splitlines() |
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| 202 | # this is the RawTextHelpFormatter._split_lines |
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| 203 | return argparse.HelpFormatter._split_lines(self, text, width) |
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| 204 | ||
| 205 | parser = argparse.ArgumentParser(description=__doc__, formatter_class=SmartFormatter)#formatter_class=argparse.RawDescriptionHelpFormatter) |
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| 206 | ||
| 207 | parser.add_argument('-t',"--target-fn", |
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| 208 | default='', required = True, |
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| 209 | help="pdb file") |
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| 210 | ||
| 211 | parser.add_argument('--ignore-files', help='files to be ingored, .e.g, \'solution\'', default='') |
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| 212 | ||
| 213 | parser.add_argument("--target-selection", |
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| 214 | default='', |
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| 215 | help="selection, e.g. A:10-16+20, where #16 residue is included") |
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| 216 | ||
| 217 | parser.add_argument("--target-ignore-selection", |
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| 218 | default='', |
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| 219 | help="A/10/O2\'") |
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| 220 | ||
| 221 | parser.add_argument("--model-selection", |
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| 222 | default='', |
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| 223 | help="selection, e.g. A:10-16+20, where #16 residue is included") |
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| 224 | ||
| 225 | parser.add_argument("--model-ignore-selection", |
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| 226 | default='', |
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| 227 | help="A/10/O2\'") |
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| 228 | ||
| 229 | parser.add_argument('-m', "--method", |
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| 230 | default='all-atom-built-in', |
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| 231 | help="align, fit") |
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| 232 | ||
| 233 | parser.add_argument('-o', "--rmsds-fn", |
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| 234 | default='rmsds.csv', |
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| 235 | help="ouput, matrix") |
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| 236 | ||
| 237 | parser.add_argument("-v", "--verbose", action="store_true", |
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| 238 | help="verbose") |
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| 239 | ||
| 240 | parser.add_argument('-pr', '--print-results', |
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| 241 | action="store_true") |
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| 242 | ||
| 243 | parser.add_argument('-sr', '--sort-results', |
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| 244 | action="store_true") |
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| 245 | ||
| 246 | parser.add_argument('-pp', '--print-progress', |
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| 247 | default=False, |
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| 248 | action="store_true") |
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| 249 | ||
| 250 | parser.add_argument('--way', help="""R|c1p = C1' |
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| 251 | backbone = P OP1 OP2 O5' C5' C4' C3' O3' |
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| 252 | po = P OP1 OP2 |
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| 253 | no-backbone = all - po |
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| 254 | bases, backbone+sugar, sugar |
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| 255 | pooo = P OP1 OP2 O5' |
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| 256 | alpha = P OP1 OP2 O5' C5' |
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| 257 | """, default='all') |
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| 258 | ||
| 259 | parser.add_argument("--name-rmsd-column", help="default: fn,rmsd, with this cols will be fn,<name-rmsd-column>") |
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| 260 | ||
| 261 | parser.add_argument("--target-column-name", action="store_true", |
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| 262 | help="") |
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| 263 | ||
| 264 | parser.add_argument('files', help='files', nargs='+') |
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| 265 | ||
| 266 | return parser |
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| 267 | # main |
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| 268 | if __name__ == '__main__': |
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| 269 | parser = get_parser() |
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