Skip to content

Commit

Permalink
test fetch pdb
Browse files Browse the repository at this point in the history
  • Loading branch information
@rasbt
rasbt committed Nov 22, 2015
1 parent 28b6ca9 commit f123248
Show file tree
Hide file tree
Showing 7 changed files with 4,330 additions and 4,462 deletions.
9 changes: 6 additions & 3 deletions biopandas/pandas_pdb.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -207,8 +207,11 @@ def to_pdb(self, path, records=None, gz=False, append_newline=True):
df = pd.concat(dfs)
df.sort(columns='line_idx', inplace=True)
with openf(path, w_mode) as f:
s = '\n'.join(df['OUT'].tolist())
s = s.rstrip()
f.write(s)

s = df['OUT'].tolist()
for idx in range(len(s)):
if len(s[idx]) < 80:
s[idx] = '%s%s' % (s[idx], ' ' * (80 - len(s[idx])))
f.write('\n'.join(s))
if append_newline:
f.write('\n')
4,294 changes: 2,147 additions & 2,147 deletions biopandas/tests/test_pandas_pdb/data/3eiy.pdb
View file

Large diffs are not rendered by default.

Binary file modified biopandas/tests/test_pandas_pdb/data/3eiy.pdb.gz
View file
Binary file not shown.
2,173 changes: 18 additions & 2,155 deletions biopandas/tests/test_pandas_pdb/test_read_pdb.py
View file

Large diffs are not rendered by default.

5 changes: 5 additions & 0 deletions biopandas/tests/test_pandas_pdb/test_rmsd.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,11 @@ def test_equal():
r = PandasPDB.rmsd(p1t48.df['ATOM'], p1t48.df['ATOM'], s=None)
assert r == 0.000, r

@raises(AttributeError)
def test_wrong_arg():
r = PandasPDB.rmsd(p1t48.df['ATOM'].loc[1:, :], p1t48.df['ATOM'], s='bla')


@raises(AttributeError)
def test_incompatible():
r = PandasPDB.rmsd(p1t48.df['ATOM'].loc[1:, :], p1t48.df['ATOM'], s=None)
Expand Down
164 changes: 7 additions & 157 deletions biopandas/tests/test_pandas_pdb/test_write_pdb.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,20 +18,24 @@
OUTFILE = os.path.join(os.path.dirname(__file__), 'data', 'tmp.pdb')
OUTFILE_GZ = os.path.join(os.path.dirname(__file__), 'data', 'tmp.pdb.gz')

hetatm = ''
with open(TESTDATA_FILENAME, 'r') as f:
for line in f:
if line.startswith('HETATM'):
hetatm += line

def test_defaults():
pass
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
ppdb.to_pdb(path=OUTFILE)
ppdb.to_pdb(path=OUTFILE, records=None)
with open(TESTDATA_FILENAME, 'r') as f:
f1 = f.read()
with open(OUTFILE, 'r') as f:
f2 = f.read()
print(ppdb.df['OTHERS'])
assert f1 == f2
os.remove(OUTFILE)


def test_defaults():
"""Test private _read_pdb"""
ppdb = PandasPDB()
Expand All @@ -41,157 +45,3 @@ def test_defaults():
f1 = f.read()
os.remove(OUTFILE)
assert f1 == hetatm


hetatm = """HETATM 1332 K K A 176 24.990 43.276 0.005 0.50 24.45 K
HETATM 1333 NA NA A 177 1.633 34.181 11.897 1.00 26.73 NA
HETATM 1334 NA NA A 178 6.489 35.143 8.444 1.00 30.89 NA
HETATM 1335 P1 POP A 179 1.233 37.542 11.212 1.00 32.68 P
HETATM 1336 O1 POP A 179 1.910 38.831 11.612 1.00 32.62 O
HETATM 1337 O2 POP A 179 1.288 37.475 9.712 1.00 33.46 O
HETATM 1338 O3 POP A 179 1.948 36.362 11.841 1.00 30.47 O
HETATM 1339 O POP A 179 -0.339 37.641 11.573 1.00 33.48 O
HETATM 1340 P2 POP A 179 -1.193 36.552 12.370 1.00 36.05 P
HETATM 1341 O4 POP A 179 -2.611 36.792 11.954 1.00 33.39 O
HETATM 1342 O5 POP A 179 -1.079 36.873 13.870 1.00 33.69 O
HETATM 1343 O6 POP A 179 -0.735 35.128 12.124 1.00 33.11 O
HETATM 1344 O1 PG4 A 180 25.225 36.156 6.596 1.00 42.63 O
HETATM 1345 C1 PG4 A 180 25.070 35.591 5.302 1.00 44.20 C
HETATM 1346 C2 PG4 A 180 25.728 36.597 4.386 1.00 46.03 C
HETATM 1347 O2 PG4 A 180 24.774 36.857 3.380 1.00 48.37 O
HETATM 1348 C3 PG4 A 180 25.201 37.981 2.614 1.00 47.94 C
HETATM 1349 C4 PG4 A 180 25.268 39.174 3.548 1.00 46.48 C
HETATM 1350 O3 PG4 A 180 26.617 39.507 3.811 1.00 45.59 O
HETATM 1351 C5 PG4 A 180 26.819 40.888 3.597 1.00 45.33 C
HETATM 1352 C6 PG4 A 180 28.266 41.161 3.954 1.00 47.26 C
HETATM 1353 O4 PG4 A 180 28.982 41.378 2.738 1.00 48.16 O
HETATM 1354 C7 PG4 A 180 30.163 40.616 2.604 1.00 47.41 C
HETATM 1355 C8 PG4 A 180 31.331 41.437 3.117 1.00 51.14 C
HETATM 1356 O5 PG4 A 180 32.081 40.607 4.011 1.00 53.41 O
HETATM 1357 C1 PEG A 181 13.856 28.176 23.722 1.00 59.47 C
HETATM 1358 O1 PEG A 181 14.416 29.487 23.735 1.00 59.79 O
HETATM 1359 C2 PEG A 181 13.605 27.741 22.291 1.00 59.20 C
HETATM 1360 O2 PEG A 181 12.908 26.499 22.379 1.00 59.79 O
HETATM 1361 C3 PEG A 181 11.848 26.393 21.440 1.00 59.65 C
HETATM 1362 C4 PEG A 181 10.883 25.309 21.906 1.00 59.90 C
HETATM 1363 O4 PEG A 181 10.045 25.835 22.942 1.00 58.85 O
HETATM 1364 C1 PEG A 182 19.721 56.811 7.363 1.00 56.17 C
HETATM 1365 O1 PEG A 182 18.409 56.724 7.966 1.00 55.97 O
HETATM 1366 C2 PEG A 182 20.835 56.288 8.271 1.00 54.49 C
HETATM 1367 O2 PEG A 182 21.824 57.291 8.516 1.00 56.31 O
HETATM 1368 C3 PEG A 182 23.176 56.838 8.332 1.00 57.82 C
HETATM 1369 C4 PEG A 182 23.815 57.479 7.094 1.00 58.58 C
HETATM 1370 O4 PEG A 182 24.621 56.536 6.357 1.00 59.04 O
HETATM 1371 O HOH A 183 -6.268 35.297 21.123 1.00 22.39 O
HETATM 1372 O HOH A 184 18.291 50.223 3.964 1.00 24.68 O
HETATM 1373 O HOH A 185 22.029 42.728 8.623 1.00 20.47 O
HETATM 1374 O HOH A 186 15.767 55.114 9.164 1.00 20.81 O
HETATM 1375 O HOH A 187 0.754 45.724 20.847 1.00 21.83 O
HETATM 1376 O HOH A 188 11.338 47.709 21.125 1.00 19.21 O
HETATM 1377 O HOH A 189 19.695 33.152 21.711 1.00 38.29 O
HETATM 1378 O HOH A 190 10.491 50.293 22.101 1.00 18.65 O
HETATM 1379 O HOH A 191 4.344 42.176 9.606 1.00 23.68 O
HETATM 1380 O HOH A 192 22.154 49.578 16.234 1.00 24.18 O
HETATM 1381 O HOH A 193 19.540 33.045 0.367 0.50 15.02 O
HETATM 1382 O HOH A 194 -0.281 31.958 19.977 1.00 27.04 O
HETATM 1383 O HOH A 195 0.714 43.186 11.724 1.00 31.86 O
HETATM 1384 O HOH A 196 3.567 51.947 22.586 1.00 23.51 O
HETATM 1385 O HOH A 197 -1.180 48.644 17.742 1.00 15.53 O
HETATM 1386 O HOH A 198 1.948 54.836 16.377 1.00 21.93 O
HETATM 1387 O HOH A 199 2.509 44.733 28.229 1.00 21.51 O
HETATM 1388 O HOH A 200 2.391 38.378 14.597 1.00 23.11 O
HETATM 1389 O HOH A 201 1.535 33.854 14.371 1.00 27.83 O
HETATM 1390 O HOH A 202 -6.330 29.284 19.591 1.00 32.67 O
HETATM 1391 O HOH A 203 -2.980 54.585 7.752 1.00 25.04 O
HETATM 1392 O HOH A 204 -1.529 52.313 21.859 1.00 28.95 O
HETATM 1393 O HOH A 205 -4.219 37.228 18.172 1.00 29.05 O
HETATM 1394 O HOH A 206 -9.725 38.390 17.936 1.00 25.82 O
HETATM 1395 O HOH A 207 -0.251 50.231 15.527 1.00 41.88 O
HETATM 1396 O HOH A 208 -7.548 43.260 22.219 1.00 19.57 O
HETATM 1397 O HOH A 209 24.427 35.212 14.096 1.00 31.41 O
HETATM 1398 O HOH A 210 17.913 38.657 31.156 1.00 36.76 O
HETATM 1399 O HOH A 211 23.606 42.865 12.451 1.00 25.35 O
HETATM 1400 O HOH A 212 -10.993 36.660 20.173 1.00 34.07 O
HETATM 1401 O HOH A 213 12.726 35.081 31.604 1.00 41.53 O
HETATM 1402 O HOH A 214 11.555 34.813 2.535 1.00 32.40 O
HETATM 1403 O HOH A 215 26.985 45.074 13.907 1.00 33.93 O
HETATM 1404 O HOH A 216 22.305 31.774 11.176 1.00 27.99 O
HETATM 1405 O HOH A 217 -5.311 51.156 18.105 1.00 23.06 O
HETATM 1406 O HOH A 218 4.813 38.197 26.560 1.00 30.39 O
HETATM 1407 O HOH A 219 16.429 31.381 6.556 1.00 31.04 O
HETATM 1408 O HOH A 220 2.094 31.244 8.621 1.00 39.67 O
HETATM 1409 O HOH A 221 3.282 37.464 7.811 1.00 36.79 O
HETATM 1410 O HOH A 222 12.081 42.928 -4.465 1.00 35.63 O
HETATM 1411 O HOH A 223 10.457 52.853 26.328 1.00 29.83 O
HETATM 1412 O HOH A 224 -10.834 37.817 15.537 1.00 32.13 O
HETATM 1413 O HOH A 225 11.844 46.500 23.826 1.00 35.48 O
HETATM 1414 O HOH A 226 4.136 40.856 6.472 1.00 40.41 O
HETATM 1415 O HOH A 227 27.046 47.404 15.617 1.00 32.79 O
HETATM 1416 O HOH A 228 27.357 54.793 8.601 1.00 45.22 O
HETATM 1417 O HOH A 229 23.653 47.745 22.742 1.00 50.33 O
HETATM 1418 O HOH A 230 13.464 46.940 -3.502 1.00 32.04 O
HETATM 1419 O HOH A 231 3.976 32.286 14.525 1.00 31.56 O
HETATM 1420 O HOH A 232 20.596 34.827 26.319 1.00 49.91 O
HETATM 1421 O HOH A 233 0.268 53.053 17.314 1.00 42.31 O
HETATM 1422 O HOH A 234 8.635 54.732 26.919 1.00 33.52 O
HETATM 1423 O HOH A 235 8.723 45.643 25.830 1.00 31.33 O
HETATM 1424 O HOH A 236 9.525 50.219 24.646 1.00 32.19 O
HETATM 1425 O HOH A 237 29.165 40.813 21.487 1.00 56.55 O
HETATM 1426 O HOH A 238 2.494 40.055 8.917 1.00 36.15 O
HETATM 1427 O HOH A 239 -0.777 34.809 9.090 1.00 37.11 O
HETATM 1428 O HOH A 240 23.455 48.536 9.084 1.00 28.44 O
HETATM 1429 O HOH A 241 24.600 49.610 11.229 1.00 23.81 O
HETATM 1430 O HOH A 242 21.015 49.121 7.957 1.00 22.66 O
HETATM 1431 O HOH A 243 24.242 43.201 9.915 1.00 27.87 O
HETATM 1432 O HOH A 244 26.271 42.655 13.711 1.00 28.13 O
HETATM 1433 O HOH A 245 5.960 36.600 6.289 1.00 41.50 O
HETATM 1434 O HOH A 246 18.246 32.111 23.785 1.00 56.31 O
HETATM 1435 O HOH A 247 7.627 32.876 7.134 1.00 33.79 O
HETATM 1436 O HOH A 248 1.165 51.316 -0.972 1.00 46.31 O
HETATM 1437 O HOH A 249 1.154 41.748 26.990 1.00 28.03 O
HETATM 1438 O HOH A 250 5.939 26.535 21.149 1.00 44.12 O
HETATM 1439 O HOH A 251 -5.540 43.055 28.186 1.00 26.47 O
HETATM 1440 O HOH A 252 11.949 30.493 27.231 1.00 52.78 O
HETATM 1441 O HOH A 253 13.331 24.495 13.440 1.00 52.00 O
HETATM 1442 O HOH A 254 -1.435 29.723 20.052 1.00 52.22 O
HETATM 1443 O HOH A 255 2.115 43.165 6.250 1.00 34.91 O
HETATM 1444 O HOH A 256 15.992 53.085 0.933 1.00 34.04 O
HETATM 1445 O HOH A 257 2.292 33.719 9.368 1.00 44.24 O
HETATM 1446 O HOH A 258 3.626 29.350 26.403 1.00 42.97 O
HETATM 1447 O HOH A 259 -3.063 50.429 19.160 1.00 33.64 O
HETATM 1448 O HOH A 260 -4.016 34.810 12.023 1.00 43.84 O
HETATM 1449 O HOH A 261 -7.025 43.005 7.425 1.00 50.38 O
HETATM 1450 O HOH A 262 20.664 37.966 29.449 1.00 39.40 O
HETATM 1451 O HOH A 263 8.219 36.489 7.242 1.00 45.22 O
HETATM 1452 O HOH A 264 7.603 30.314 26.808 1.00 49.95 O
HETATM 1453 O HOH A 265 27.192 38.462 19.035 1.00 38.71 O
HETATM 1454 O HOH A 266 -3.725 41.084 29.707 1.00 44.44 O
HETATM 1455 O HOH A 267 -3.184 38.130 9.900 1.00 31.98 O
HETATM 1456 O HOH A 268 -6.968 37.923 11.495 1.00 40.84 O
HETATM 1457 O HOH A 269 15.958 47.852 -2.923 1.00 44.94 O
HETATM 1458 O HOH A 270 13.106 37.129 -9.048 1.00 35.12 O
HETATM 1459 O HOH A 271 23.944 34.080 16.627 1.00 56.20 O
HETATM 1460 O HOH A 272 17.584 52.420 -1.888 1.00 38.11 O
HETATM 1461 O HOH A 273 5.521 45.450 -0.564 1.00 47.04 O
HETATM 1462 O HOH A 274 25.459 49.006 4.506 1.00 54.02 O
HETATM 1463 O HOH A 275 16.595 27.943 19.928 1.00 49.01 O
HETATM 1464 O HOH A 276 22.019 36.726 26.870 1.00 56.59 O
HETATM 1465 O HOH A 277 10.474 36.654 8.412 1.00 45.47 O
HETATM 1466 O HOH A 278 24.611 33.020 11.703 1.00 47.62 O
HETATM 1467 O HOH A 279 26.899 46.740 4.551 1.00 52.92 O
HETATM 1468 O HOH A 280 6.994 29.354 29.500 1.00 59.06 O
HETATM 1469 O HOH A 281 1.016 41.471 9.152 1.00 46.63 O
HETATM 1470 O HOH A 282 -3.738 28.411 20.723 1.00 58.68 O
HETATM 1471 O HOH A 283 14.325 31.639 5.778 1.00 49.26 O
HETATM 1472 O HOH A 284 27.777 37.727 7.983 1.00 49.01 O
HETATM 1473 O HOH A 285 11.301 44.913 29.125 1.00 47.44 O
HETATM 1474 O HOH A 286 -3.722 51.289 27.893 1.00 28.88 O
HETATM 1475 O HOH A 287 5.173 46.827 -3.289 1.00 59.99 O
HETATM 1476 O HOH A 288 -9.268 38.914 11.481 1.00 39.62 O
HETATM 1477 O HOH A 289 9.346 31.934 27.060 1.00 45.27 O
HETATM 1478 O HOH A 290 24.327 46.350 8.439 1.00 39.23 O
HETATM 1479 O HOH A 291 17.766 26.234 14.240 1.00 58.80 O
HETATM 1480 O HOH A 292 14.667 53.897 27.017 1.00 44.45 O
HETATM 1481 O HOH A 293 13.540 30.919 2.872 1.00 48.68 O
HETATM 1482 O HOH A 294 13.812 54.578 29.178 1.00 37.62 O
"""
Loading

0 comments on commit f123248

Please sign in to comment.