examples/testdata/7WKP-rna1.xml

   1 <?xml version="1.0"?>
   2 <!DOCTYPE rnaml SYSTEM "rnaml.dtd">
   3
   4 <rnaml version="1.0">
   5
   6    <molecule id="1">
   7       <sequence>
   8          <numbering-system id="1" used-in-file="false">
   9             <numbering-range>
  10                <start>1</start>
  11                <end>20</end>
  12             </numbering-range>
  13          </numbering-system>
  14          <numbering-table length="20" comment="sequence number in pdb file">
  15             1    2    3    4    5    6    7    8    9   10
  16            11   12   13   14   15   16   17   18   19   20
  17
  18          </numbering-table>
  19          <seq-data>
  20             GUUAGCAGCC GCAUAGGCUG
  21          </seq-data>
  22          <seq-annotation comment="?">
  23             <segment>
  24                <seg-name>LOOP1</seg-name>
  25                <base-id-5p><base-id><position>12</position></base-id></base-id-5p>
  26                <base-id-3p><base-id><position>14</position></base-id></base-id-3p>
  27             </segment>
  28          </seq-annotation>
  29       </sequence>
  30       <structure>
  31          <model id="?">
  32             <model-info>
  33                <method>Crystallography ?</method>
  34                <resolution>? Angstroms</resolution>
  35             </model-info>
  36             <base>
  37                <position>1</position>
  38                <base-type>G</base-type>
  39                <atom serial="1">
  40                   <atom-type> P  </atom-type>
  41                      <coordinates>7.232 28.529 -12.305</coordinates>
  42                </atom>
  43                <atom serial="9">
  44                   <atom-type> O3'</atom-type>
  45                      <coordinates>4.752 23.963 -11.820</coordinates>
  46                </atom>
  47             </base>
  48             <base>
  49                <position>2</position>
  50                <base-type>U</base-type>
  51                <atom serial="24">
  52                   <atom-type> P  </atom-type>
  53                      <coordinates>3.868 23.252 -12.962</coordinates>
  54                </atom>
  55                <atom serial="32">
  56                   <atom-type> O3'</atom-type>
  57                      <coordinates>0.983 18.432 -13.409</coordinates>
  58                </atom>
  59             </base>
  60             <base>
  61                <position>3</position>
  62                <base-type>U</base-type>
  63                <atom serial="44">
  64                   <atom-type> P  </atom-type>
  65                      <coordinates>1.438 17.540 -14.670</coordinates>
  66                </atom>
  67                <atom serial="52">
  68                   <atom-type> O3'</atom-type>
  69                      <coordinates>-1.417 16.962 -19.633</coordinates>
  70                </atom>
  71             </base>
  72             <base>
  73                <position>4</position>
  74                <base-type>A</base-type>
  75                <atom serial="64">
  76                   <atom-type> P  </atom-type>
  77                      <coordinates>-2.710 16.020 -19.430</coordinates>
  78                </atom>
  79                <atom serial="72">
  80                   <atom-type> O3'</atom-type>
  81                      <coordinates>-7.138 19.555 -19.112</coordinates>
  82                </atom>
  83             </base>
  84             <base>
  85                <position>5</position>
  86                <base-type>G</base-type>
  87                <atom serial="86">
  88                   <atom-type> P  </atom-type>
  89                      <coordinates>-7.829 20.393 -20.298</coordinates>
  90                </atom>
  91                <atom serial="94">
  92                   <atom-type> O3'</atom-type>
  93                      <coordinates>-11.316 24.166 -18.659</coordinates>
  94                </atom>
  95             </base>
  96             <base>
  97                <position>6</position>
  98                <base-type>C</base-type>
  99                <atom serial="109">
 100                   <atom-type> P  </atom-type>
 101                      <coordinates>-12.021 24.790 -19.958</coordinates>
 102                </atom>
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 104                   <atom-type> O3'</atom-type>
 105                      <coordinates>-14.686 21.023 -22.223</coordinates>
 106                </atom>
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 110                <base-type>A</base-type>
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 112                   <atom-type> P  </atom-type>
 113                      <coordinates>-16.102 21.690 -22.577</coordinates>
 114                </atom>
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 116                   <atom-type> O3'</atom-type>
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 125                      <coordinates>-21.555 19.844 -22.854</coordinates>
 126                </atom>
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 141                      <coordinates>-30.900 21.877 -16.104</coordinates>
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 149                      <coordinates>-31.737 23.147 -16.621</coordinates>
 150                </atom>
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 155             </base>
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 158                <base-type>G</base-type>
 159                <atom serial="214">
 160                   <atom-type> P  </atom-type>
 161                      <coordinates>-34.360 27.602 -14.877</coordinates>
 162                </atom>
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 164                   <atom-type> O3'</atom-type>
 165                      <coordinates>-34.025 32.801 -15.050</coordinates>
 166                </atom>
 167             </base>
 168             <base>
 169                <position>12</position>
 170                <base-type>C</base-type>
 171                <atom serial="237">
 172                   <atom-type> P  </atom-type>
 173                      <coordinates>-35.037 32.875 -16.296</coordinates>
 174                </atom>
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 176                   <atom-type> O3'</atom-type>
 177                      <coordinates>-31.850 33.486 -20.341</coordinates>
 178                </atom>
 179             </base>
 180             <base>
 181                <position>13</position>
 182                <base-type>A</base-type>
 183                <atom serial="257">
 184                   <atom-type> P  </atom-type>
 185                      <coordinates>-30.767 32.411 -19.837</coordinates>
 186                </atom>
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 188                   <atom-type> O3'</atom-type>
 189                      <coordinates>-25.756 33.919 -20.714</coordinates>
 190                </atom>
 191             </base>
 192             <base>
 193                <position>14</position>
 194                <base-type>U</base-type>
 195                <atom serial="279">
 196                   <atom-type> P  </atom-type>
 197                      <coordinates>-24.465 33.135 -20.171</coordinates>
 198                </atom>
 199                <atom serial="287">
 200                   <atom-type> O3'</atom-type>
 201                      <coordinates>-21.219 37.107 -19.013</coordinates>
 202                </atom>
 203             </base>
 204             <base>
 205                <position>15</position>
 206                <base-type>A</base-type>
 207                <atom serial="299">
 208                   <atom-type> P  </atom-type>
 209                      <coordinates>-22.129 38.268 -18.376</coordinates>
 210                </atom>
 211                <atom serial="307">
 212                   <atom-type> O3'</atom-type>
 213                      <coordinates>-20.542 37.656 -12.798</coordinates>
 214                </atom>
 215             </base>
 216             <base>
 217                <position>16</position>
 218                <base-type>G</base-type>
 219                <atom serial="321">
 220                   <atom-type> P  </atom-type>
 221                      <coordinates>-19.666 36.373 -12.391</coordinates>
 222                </atom>
 223                <atom serial="329">
 224                   <atom-type> O3'</atom-type>
 225                      <coordinates>-21.101 34.091 -7.803</coordinates>
 226                </atom>
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 228             <base>
 229                <position>17</position>
 230                <base-type>G</base-type>
 231                <atom serial="344">
 232                   <atom-type> P  </atom-type>
 233                      <coordinates>-20.251 32.728 -7.687</coordinates>
 234                </atom>
 235                <atom serial="352">
 236                   <atom-type> O3'</atom-type>
 237                      <coordinates>-22.951 28.722 -5.266</coordinates>
 238                </atom>
 239             </base>
 240             <base>
 241                <position>18</position>
 242                <base-type>C</base-type>
 243                <atom serial="367">
 244                   <atom-type> P  </atom-type>
 245                      <coordinates>-21.797 27.634 -5.014</coordinates>
 246                </atom>
 247                <atom serial="375">
 248                   <atom-type> O3'</atom-type>
 249                      <coordinates>-23.692 22.611 -5.084</coordinates>
 250                </atom>
 251             </base>
 252             <base>
 253                <position>19</position>
 254                <base-type>U</base-type>
 255                <atom serial="387">
 256                   <atom-type> P  </atom-type>
 257                      <coordinates>-22.583 21.449 -4.989</coordinates>
 258                </atom>
 259                <atom serial="395">
 260                   <atom-type> O3'</atom-type>
 261                      <coordinates>-22.919 16.822 -7.040</coordinates>
 262                </atom>
 263             </base>
 264             <base>
 265                <position>20</position>
 266                <base-type>G</base-type>
 267                <atom serial="407">
 268                   <atom-type> P  </atom-type>
 269                      <coordinates>-21.585 16.199 -6.397</coordinates>
 270                </atom>
 271                <atom serial="415">
 272                   <atom-type> O3'</atom-type>
 273                      <coordinates>-18.522 13.024 -10.277</coordinates>
 274                </atom>
 275             </base>
 276             <str-annotation>
 277                <base-pair comment="?">
 278                   <base-id-5p>
 279                      <base-id><position>1</position></base-id>
 280                   </base-id-5p>
 281                   <base-id-3p>
 282                      <base-id><position>2</position></base-id>
 283                   </base-id-3p>
 284                   <edge-5p>S</edge-5p>
 285                   <edge-3p>H</edge-3p>
 286                   <bond-orientation>c</bond-orientation>
 287                </base-pair>
 288                <base-pair comment="?">
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 290                      <base-id><position>6</position></base-id>
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 293                      <base-id><position>20</position></base-id>
 294                   </base-id-3p>
 295                   <edge-5p>+</edge-5p>
 296                   <edge-3p>+</edge-3p>
 297                   <bond-orientation>c</bond-orientation>
 298                </base-pair>
 299                <base-pair comment="?">
 300                   <base-id-5p>
 301                      <base-id><position>7</position></base-id>
 302                   </base-id-5p>
 303                   <base-id-3p>
 304                      <base-id><position>19</position></base-id>
 305                   </base-id-3p>
 306                   <edge-5p>-</edge-5p>
 307                   <edge-3p>-</edge-3p>
 308                   <bond-orientation>c</bond-orientation>
 309                </base-pair>
 310                <base-pair comment="?">
 311                   <base-id-5p>
 312                      <base-id><position>8</position></base-id>
 313                   </base-id-5p>
 314                   <base-id-3p>
 315                      <base-id><position>18</position></base-id>
 316                   </base-id-3p>
 317                   <edge-5p>+</edge-5p>
 318                   <edge-3p>+</edge-3p>
 319                   <bond-orientation>c</bond-orientation>
 320                </base-pair>
 321                <base-pair comment="?">
 322                   <base-id-5p>
 323                      <base-id><position>9</position></base-id>
 324                   </base-id-5p>
 325                   <base-id-3p>
 326                      <base-id><position>17</position></base-id>
 327                   </base-id-3p>
 328                   <edge-5p>+</edge-5p>
 329                   <edge-3p>+</edge-3p>
 330                   <bond-orientation>c</bond-orientation>
 331                </base-pair>
 332                <base-pair comment="?">
 333                   <base-id-5p>
 334                      <base-id><position>10</position></base-id>
 335                   </base-id-5p>
 336                   <base-id-3p>
 337                      <base-id><position>16</position></base-id>
 338                   </base-id-3p>
 339                   <edge-5p>+</edge-5p>
 340                   <edge-3p>+</edge-3p>
 341                   <bond-orientation>c</bond-orientation>
 342                </base-pair>
 343                <base-pair comment="?">
 344                   <base-id-5p>
 345                      <base-id><position>11</position></base-id>
 346                   </base-id-5p>
 347                   <base-id-3p>
 348                      <base-id><position>15</position></base-id>
 349                   </base-id-3p>
 350                   <edge-5p>S</edge-5p>
 351                   <edge-3p>H</edge-3p>
 352                   <bond-orientation>t</bond-orientation>
 353                </base-pair>
 354                <base-pair comment="?">
 355                   <base-id-5p>
 356                      <base-id><position>3</position></base-id>
 357                   </base-id-5p>
 358                   <base-id-3p>
 359                      <base-id><position>4</position></base-id>
 360                   </base-id-3p>
 361                   <edge-5p>!</edge-5p>
 362                   <edge-3p>!</edge-3p>
 363                   <bond-orientation>!</bond-orientation>
 364                </base-pair>
 365                <base-pair comment="?">
 366                   <base-id-5p>
 367                      <base-id><position>14</position></base-id>
 368                   </base-id-5p>
 369                   <base-id-3p>
 370                      <base-id><position>15</position></base-id>
 371                   </base-id-3p>
 372                   <edge-5p>!</edge-5p>
 373                   <edge-3p>!</edge-3p>
 374                   <bond-orientation>!</bond-orientation>
 375                </base-pair>
 376                <helix id="H1">
 377                   <base-id-5p>
 378                      <base-id><position>6</position></base-id>
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 380                   <base-id-3p>
 381                      <base-id><position>20</position></base-id>
 382                   </base-id-3p>
 383                   <length>6</length>
 384                </helix>
 385                <single-strand>
 386                   <segment>
 387                      <seg-name>SG1</seg-name>
 388                      <base-id-5p><base-id><position>1</position></base-id></base-id-5p>
 389                      <base-id-3p><base-id><position>5</position></base-id></base-id-3p>
 390                   </segment>
 391                </single-strand>
 392                <single-strand>
 393                   <segment>
 394                      <seg-name>SG2</seg-name>
 395                      <base-id-5p><base-id><position>12</position></base-id></base-id-5p>
 396                      <base-id-3p><base-id><position>14</position></base-id></base-id-3p>
 397                   </segment>
 398                </single-strand>
 399             </str-annotation>
 400             <secondary-structure-display comment="x,y coodinates">
 401                <ss-base-coord>
 402                   <base-id><position>1</position></base-id>
 403                   <coordinates>133.930 0.000</coordinates>
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 406                   <base-id><position>2</position></base-id>
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 410                   <base-id><position>3</position></base-id>
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 435                   <coordinates>133.930 334.825</coordinates>
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 437                <ss-base-coord>
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 439                   <coordinates>133.930 390.629</coordinates>
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 442                   <base-id><position>11</position></base-id>
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 445                <ss-base-coord>
 446                   <base-id><position>12</position></base-id>
 447                   <coordinates>128.630 516.439</coordinates>
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 450                   <base-id><position>13</position></base-id>
 451                   <coordinates>66.965 550.000</coordinates>
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 453                <ss-base-coord>
 454                   <base-id><position>14</position></base-id>
 455                   <coordinates>5.300 516.439</coordinates>
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 457                <ss-base-coord>
 458                   <base-id><position>15</position></base-id>
 459                   <coordinates>0.000 446.433</coordinates>
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 462                   <base-id><position>16</position></base-id>
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 467                   <coordinates>0.000 334.825</coordinates>
 468                </ss-base-coord>
 469                <ss-base-coord>
 470                   <base-id><position>18</position></base-id>
 471                   <coordinates>0.000 279.021</coordinates>
 472                </ss-base-coord>
 473                <ss-base-coord>
 474                   <base-id><position>19</position></base-id>
 475                   <coordinates>0.000 223.216</coordinates>
 476                </ss-base-coord>
 477                <ss-base-coord>
 478                   <base-id><position>20</position></base-id>
 479                   <coordinates>0.000 167.412</coordinates>
 480                </ss-base-coord>
 481             </secondary-structure-display>
 482          </model>
 483       </structure>
 484    </molecule>
 485
 486
 487    <interactions>
 488             <str-annotation>
 489             </str-annotation>
 490    </interactions>
 491 </rnaml>