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first draft of solution to selaltloc bug #154

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first draft of solution to selaltloc bug #154

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3c82825
first draft of solution to selaltloc bug
mgiulini Feb 8, 2023
e172b64
added test to selaltloc
mgiulini Feb 8, 2023
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19 changes: 17 additions & 2 deletions pdbtools/pdb_selaltloc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -307,15 +307,30 @@ def flush_resloc_occ(altloc_lines, **kw):

# detects which altloc identifier has the highest occupancy
for key, lines2flush in altloc_lines.items():
if key == ' ':
continue
# we check only the first line because all atoms in one identifier
# should have the same occupancy value
occ = float(lines2flush[0][54:60])

if occ > highest:
altloc = key
highest = occ

for line2flush in altloc_lines[altloc]:
yield line2flush[:16] + ' ' + line2flush[17:]
if ' ' in altloc_lines.keys():
# here we concatenate atoms with no altloc with the
# atoms with the highest altloc
output_lines = {' ': altloc_lines[' '] + altloc_lines[altloc]}
sorted_atoms = _get_sort_atoms(output_lines)
for atom, linet in sorted_atoms:
lines = linet[1]
for line in lines:
yield line[:16] + ' ' + line[17:]
else:
# only alternate locations. Just yield all those lines
output_lines = altloc_lines[altloc]
for line2flush in altloc_lines[altloc]:
yield line2flush[:16] + ' ' + line2flush[17:]


def flush_resloc_id_same_residue(selloc, altloc_lines):
Expand Down
120 changes: 120 additions & 0 deletions tests/data/pdb4xoj-small.pdb
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Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,120 @@
ATOM 511 N SER A 81 -2.125 6.104 21.775 1.00 8.48 N
ANISOU 511 N SER A 81 1227 964 1028 -36 224 13 N
ATOM 512 CA SER A 81 -1.772 4.741 22.205 1.00 8.74 C
ANISOU 512 CA SER A 81 1233 1007 1077 11 199 56 C
ATOM 513 C SER A 81 -2.262 3.698 21.215 1.00 8.42 C
ANISOU 513 C SER A 81 1167 989 1041 -75 90 138 C
ATOM 514 O SER A 81 -3.353 3.829 20.638 1.00 9.44 O
ANISOU 514 O SER A 81 1153 1058 1375 -48 41 62 O
ATOM 515 CB SER A 81 -2.424 4.479 23.564 1.00 10.45 C
ANISOU 515 CB SER A 81 1683 1191 1094 -49 249 19 C
ATOM 516 OG SER A 81 -1.889 5.387 24.506 1.00 13.63 O
ANISOU 516 OG SER A 81 2449 1531 1199 -52 258 -6 O
ATOM 517 N AALA A 82 -1.494 2.619 21.079 0.50 8.56 N
ANISOU 517 N AALA A 82 1205 991 1055 55 81 1 N
ATOM 518 N BALA A 82 -1.502 2.619 21.093 0.50 8.57 N
ANISOU 518 N BALA A 82 1221 989 1047 51 73 3 N
ATOM 519 CA AALA A 82 -2.054 1.440 20.442 0.50 8.66 C
ANISOU 519 CA AALA A 82 1292 950 1046 -2 73 22 C
ATOM 520 CA BALA A 82 -2.004 1.455 20.381 0.50 9.05 C
ANISOU 520 CA BALA A 82 1452 961 1024 -102 -44 33 C
ATOM 521 C AALA A 82 -3.189 0.918 21.328 0.50 8.99 C
ANISOU 521 C AALA A 82 1375 993 1045 73 344 138 C
ATOM 522 C BALA A 82 -3.028 0.721 21.197 0.50 9.88 C
ANISOU 522 C BALA A 82 1773 960 1018 -222 -222 -32 C
ATOM 523 O AALA A 82 -3.041 0.736 22.520 0.80 10.64 O
ANISOU 523 O AALA A 82 1631 1389 1020 -117 191 98 O
ATOM 524 O BALA A 82 -2.558 0.035 22.148 0.20 9.90 O
ANISOU 524 O BALA A 82 1963 1076 722 -39 43 189 O
ATOM 525 CB AALA A 82 -0.983 0.385 20.289 0.50 8.83 C
ANISOU 525 CB AALA A 82 1351 1028 974 41 216 30 C
ATOM 526 CB BALA A 82 -0.809 0.503 20.120 0.50 11.15 C
ANISOU 526 CB BALA A 82 1719 1117 1399 107 -281 -110 C
ATOM 527 N SER A 83 -4.261 0.519 20.678 1.00 9.47 N
ANISOU 527 N SER A 83 1432 1102 1061 -125 244 55 N
ATOM 528 CA ASER A 83 -5.308 -0.275 21.345 0.70 10.42 C
ANISOU 528 CA ASER A 83 1524 1180 1256 61 497 220 C
ATOM 529 CA BSER A 83 -5.296 -0.225 21.292 0.30 9.99 C
ANISOU 529 CA BSER A 83 1473 1149 1171 -81 344 -232 C
ATOM 530 C SER A 83 -5.324 -1.728 20.924 1.00 10.39 C
ANISOU 530 C SER A 83 1457 1076 1412 -6 466 118 C
ATOM 531 O SER A 83 -5.811 -2.551 21.683 1.00 12.89 O
ANISOU 531 O SER A 83 2075 1194 1628 -49 830 133 O
ATOM 532 CB ASER A 83 -6.691 0.285 21.121 0.70 11.38 C
ANISOU 532 CB ASER A 83 1538 1167 1615 116 448 25 C
ATOM 533 CB BSER A 83 -6.610 0.424 20.946 0.30 12.23 C
ANISOU 533 CB BSER A 83 1463 1397 1784 -157 274 -151 C
ATOM 534 OG ASER A 83 -6.965 0.397 19.729 0.70 11.09 O
ANISOU 534 OG ASER A 83 1338 1455 1418 106 285 72 O
ATOM 535 OG BSER A 83 -7.621 -0.353 21.495 0.30 20.97 O
ANISOU 535 OG BSER A 83 2290 2191 3486 -53 1535 585 O
ATOM 536 N LYS A 84 -4.827 -2.055 19.735 1.00 9.68 N
ANISOU 536 N LYS A 84 1326 1010 1339 101 429 46 N
ATOM 537 CA ALYS A 84 -4.644 -3.431 19.279 0.70 10.05 C
ANISOU 537 CA ALYS A 84 1522 1007 1287 42 336 144 C
ATOM 538 CA BLYS A 84 -4.643 -3.451 19.329 0.30 10.14 C
ANISOU 538 CA BLYS A 84 1491 993 1368 139 550 68 C
ATOM 539 C LYS A 84 -3.278 -3.508 18.640 1.00 9.20 C
ANISOU 539 C LYS A 84 1375 1055 1064 95 218 67 C
ATOM 540 O LYS A 84 -2.951 -2.592 17.884 1.00 9.59 O
ANISOU 540 O LYS A 84 1298 1105 1241 165 244 147 O
ATOM 541 CB ALYS A 84 -5.744 -3.907 18.283 0.70 10.32 C
ANISOU 541 CB ALYS A 84 1408 1097 1416 -68 49 -77 C
ATOM 542 CB BLYS A 84 -5.751 -3.940 18.359 0.30 11.80 C
ANISOU 542 CB BLYS A 84 1533 1237 1712 95 111 84 C
ATOM 543 CG ALYS A 84 -7.150 -3.728 18.755 0.70 12.75 C
ANISOU 543 CG ALYS A 84 1483 1417 1942 -138 412 254 C
ATOM 544 CG BLYS A 84 -7.189 -3.845 18.791 0.30 12.58 C
ANISOU 544 CG BLYS A 84 1623 1474 1683 204 124 -240 C
ATOM 545 CD ALYS A 84 -8.204 -4.287 17.849 0.70 14.48 C
ANISOU 545 CD ALYS A 84 1679 1886 1936 -324 273 150 C
ATOM 546 CD BLYS A 84 -8.139 -4.069 17.666 0.30 12.72 C
ANISOU 546 CD BLYS A 84 1610 888 2335 -136 -285 -181 C
ATOM 547 CE ALYS A 84 -9.569 -4.039 18.445 0.70 21.19 C
ANISOU 547 CE ALYS A 84 1246 3570 3235 -471 223 759 C
ATOM 548 CE BLYS A 84 -9.604 -4.051 18.097 0.30 16.57 C
ANISOU 548 CE BLYS A 84 2201 1973 2122 -543 402 -985 C
ATOM 549 NZ ALYS A 84 -10.614 -4.841 17.764 0.70 22.64 N
ANISOU 549 NZ ALYS A 84 2289 3604 2707 -1098 686 -21 N
ATOM 550 NZ BLYS A 84 -9.825 -4.761 19.395 0.30 16.91 N
ANISOU 550 NZ BLYS A 84 1927 1989 2508 -957 607 -278 N
ATOM 551 N ASER A 85 -2.563 -4.588 18.881 0.50 9.32 N
ANISOU 551 N ASER A 85 1536 976 1028 171 216 66 N
ATOM 552 N BSER A 85 -2.513 -4.566 18.859 0.50 9.48 N
ANISOU 552 N BSER A 85 1610 922 1068 188 342 63 N
ATOM 553 CA ASER A 85 -1.332 -4.882 18.202 0.50 8.74 C
ANISOU 553 CA ASER A 85 1455 1080 786 116 49 -76 C
ATOM 554 CA BSER A 85 -1.229 -4.752 18.163 0.50 9.42 C
ANISOU 554 CA BSER A 85 1467 1050 1060 398 267 26 C
ATOM 555 C ASER A 85 -1.483 -6.317 17.695 0.50 9.92 C
ANISOU 555 C ASER A 85 1752 836 1179 282 208 -106 C
ATOM 556 C BSER A 85 -1.244 -6.199 17.691 0.50 8.70 C
ANISOU 556 C BSER A 85 1254 1236 813 315 160 171 C
ATOM 557 O ASER A 85 -1.652 -7.279 18.484 0.50 11.61 O
ANISOU 557 O ASER A 85 2551 941 916 222 215 86 O
ATOM 558 O BSER A 85 -1.048 -7.069 18.528 0.50 10.44 O
ANISOU 558 O BSER A 85 1973 1010 981 389 -113 130 O
ATOM 559 CB ASER A 85 -0.160 -4.700 19.129 0.50 12.48 C
ANISOU 559 CB ASER A 85 1350 1725 1666 185 -278 -2 C
ATOM 560 CB BSER A 85 -0.049 -4.451 19.125 0.50 12.99 C
ANISOU 560 CB BSER A 85 2150 1600 1183 804 -217 -517 C
ATOM 561 OG ASER A 85 -0.049 -3.356 19.526 0.50 16.00 O
ANISOU 561 OG ASER A 85 1752 2069 2256 354 -901 -970 O
ATOM 562 OG BSER A 85 -0.099 -3.127 19.634 0.50 16.22 O
ANISOU 562 OG BSER A 85 2356 1937 1869 867 -163 -876 O
ATOM 563 N ILE A 86 -1.504 -6.433 16.390 1.00 7.88 N
ANISOU 563 N ILE A 86 1184 936 872 61 178 65 N
ATOM 564 CA ILE A 86 -1.872 -7.694 15.783 1.00 7.95 C
ANISOU 564 CA ILE A 86 1192 863 963 -21 192 154 C
ATOM 565 C ILE A 86 -0.722 -8.196 14.932 1.00 7.58 C
ANISOU 565 C ILE A 86 1181 748 949 -103 205 87 C
ATOM 566 O ILE A 86 -0.535 -7.767 13.777 1.00 8.17 O
ANISOU 566 O ILE A 86 1249 887 967 -55 242 135 O
ATOM 567 CB ILE A 86 -3.164 -7.571 14.969 1.00 8.30 C
ANISOU 567 CB ILE A 86 1190 920 1043 -32 175 224 C
ATOM 568 CG1 ILE A 86 -4.302 -7.000 15.799 1.00 9.14 C
ANISOU 568 CG1 ILE A 86 1182 1078 1211 15 159 194 C
ATOM 569 CG2 ILE A 86 -3.524 -8.934 14.351 1.00 8.71 C
ANISOU 569 CG2 ILE A 86 1228 984 1097 -91 80 176 C
ATOM 570 CD1 ILE A 86 -5.630 -6.861 15.071 1.00 10.85 C
ANISOU 570 CD1 ILE A 86 1307 1331 1482 31 162 271 C
99 changes: 99 additions & 0 deletions tests/test_pdb_selaltloc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -869,6 +869,105 @@ def test_captures_previous_residue_maxocc_B(self):
"ATOM 201 CB GLY A 22 -7.405 -25.428 33.847 0.60 0.00 C ",
]
)

def test_handle_multiple_residues(self):
"""
pdb_selaltloc data/pdb4xoj-small.pdb.

The test checks that the SER85 residue is not removed by pdb_selaltloc
as it happened until version 2.5.0.
"""
sys.argv = ['', os.path.join(data_dir, 'pdb4xoj-small.pdb')]
print("executing")
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 80)
self.assertEqual(len(self.stderr), 0)
self.assertEqual(
self.stdout,
[
"ATOM 511 N SER A 81 -2.125 6.104 21.775 1.00 8.48 N ",
"ANISOU 511 N SER A 81 1227 964 1028 -36 224 13 N ",
"ATOM 512 CA SER A 81 -1.772 4.741 22.205 1.00 8.74 C ",
"ANISOU 512 CA SER A 81 1233 1007 1077 11 199 56 C ",
"ATOM 513 C SER A 81 -2.262 3.698 21.215 1.00 8.42 C ",
"ANISOU 513 C SER A 81 1167 989 1041 -75 90 138 C ",
"ATOM 514 O SER A 81 -3.353 3.829 20.638 1.00 9.44 O ",
"ANISOU 514 O SER A 81 1153 1058 1375 -48 41 62 O ",
"ATOM 515 CB SER A 81 -2.424 4.479 23.564 1.00 10.45 C ",
"ANISOU 515 CB SER A 81 1683 1191 1094 -49 249 19 C ",
"ATOM 516 OG SER A 81 -1.889 5.387 24.506 1.00 13.63 O ",
"ANISOU 516 OG SER A 81 2449 1531 1199 -52 258 -6 O ",
"ATOM 517 N ALA A 82 -1.494 2.619 21.079 0.50 8.56 N ",
"ANISOU 517 N ALA A 82 1205 991 1055 55 81 1 N ",
"ATOM 519 CA ALA A 82 -2.054 1.440 20.442 0.50 8.66 C ",
"ANISOU 519 CA ALA A 82 1292 950 1046 -2 73 22 C ",
"ATOM 521 C ALA A 82 -3.189 0.918 21.328 0.50 8.99 C ",
"ANISOU 521 C ALA A 82 1375 993 1045 73 344 138 C ",
"ATOM 523 O ALA A 82 -3.041 0.736 22.520 0.80 10.64 O ",
"ANISOU 523 O ALA A 82 1631 1389 1020 -117 191 98 O ",
"ATOM 525 CB ALA A 82 -0.983 0.385 20.289 0.50 8.83 C ",
"ANISOU 525 CB ALA A 82 1351 1028 974 41 216 30 C ",
"ATOM 527 N SER A 83 -4.261 0.519 20.678 1.00 9.47 N ",
"ANISOU 527 N SER A 83 1432 1102 1061 -125 244 55 N ",
"ATOM 528 CA SER A 83 -5.308 -0.275 21.345 0.70 10.42 C ",
"ANISOU 528 CA SER A 83 1524 1180 1256 61 497 220 C ",
"ATOM 530 C SER A 83 -5.324 -1.728 20.924 1.00 10.39 C ",
"ANISOU 530 C SER A 83 1457 1076 1412 -6 466 118 C ",
"ATOM 531 O SER A 83 -5.811 -2.551 21.683 1.00 12.89 O ",
"ANISOU 531 O SER A 83 2075 1194 1628 -49 830 133 O ",
"ATOM 532 CB SER A 83 -6.691 0.285 21.121 0.70 11.38 C ",
"ANISOU 532 CB SER A 83 1538 1167 1615 116 448 25 C ",
"ATOM 534 OG SER A 83 -6.965 0.397 19.729 0.70 11.09 O ",
"ANISOU 534 OG SER A 83 1338 1455 1418 106 285 72 O ",
"ATOM 536 N LYS A 84 -4.827 -2.055 19.735 1.00 9.68 N ",
"ANISOU 536 N LYS A 84 1326 1010 1339 101 429 46 N ",
"ATOM 537 CA LYS A 84 -4.644 -3.431 19.279 0.70 10.05 C ",
"ANISOU 537 CA LYS A 84 1522 1007 1287 42 336 144 C ",
"ATOM 539 C LYS A 84 -3.278 -3.508 18.640 1.00 9.20 C ",
"ANISOU 539 C LYS A 84 1375 1055 1064 95 218 67 C ",
"ATOM 540 O LYS A 84 -2.951 -2.592 17.884 1.00 9.59 O ",
"ANISOU 540 O LYS A 84 1298 1105 1241 165 244 147 O ",
"ATOM 541 CB LYS A 84 -5.744 -3.907 18.283 0.70 10.32 C ",
"ANISOU 541 CB LYS A 84 1408 1097 1416 -68 49 -77 C ",
"ATOM 543 CG LYS A 84 -7.150 -3.728 18.755 0.70 12.75 C ",
"ANISOU 543 CG LYS A 84 1483 1417 1942 -138 412 254 C ",
"ATOM 545 CD LYS A 84 -8.204 -4.287 17.849 0.70 14.48 C ",
"ANISOU 545 CD LYS A 84 1679 1886 1936 -324 273 150 C ",
"ATOM 547 CE LYS A 84 -9.569 -4.039 18.445 0.70 21.19 C ",
"ANISOU 547 CE LYS A 84 1246 3570 3235 -471 223 759 C ",
"ATOM 549 NZ LYS A 84 -10.614 -4.841 17.764 0.70 22.64 N ",
"ANISOU 549 NZ LYS A 84 2289 3604 2707 -1098 686 -21 N ",
"ATOM 551 N SER A 85 -2.563 -4.588 18.881 0.50 9.32 N ",
"ANISOU 551 N SER A 85 1536 976 1028 171 216 66 N ",
"ATOM 553 CA SER A 85 -1.332 -4.882 18.202 0.50 8.74 C ",
"ANISOU 553 CA SER A 85 1455 1080 786 116 49 -76 C ",
"ATOM 555 C SER A 85 -1.483 -6.317 17.695 0.50 9.92 C ",
"ANISOU 555 C SER A 85 1752 836 1179 282 208 -106 C ",
"ATOM 557 O SER A 85 -1.652 -7.279 18.484 0.50 11.61 O ",
"ANISOU 557 O SER A 85 2551 941 916 222 215 86 O ",
"ATOM 559 CB SER A 85 -0.160 -4.700 19.129 0.50 12.48 C ",
"ANISOU 559 CB SER A 85 1350 1725 1666 185 -278 -2 C ",
"ATOM 561 OG SER A 85 -0.049 -3.356 19.526 0.50 16.00 O ",
"ANISOU 561 OG SER A 85 1752 2069 2256 354 -901 -970 O ",
"ATOM 563 N ILE A 86 -1.504 -6.433 16.390 1.00 7.88 N ",
"ANISOU 563 N ILE A 86 1184 936 872 61 178 65 N ",
"ATOM 564 CA ILE A 86 -1.872 -7.694 15.783 1.00 7.95 C ",
"ANISOU 564 CA ILE A 86 1192 863 963 -21 192 154 C ",
"ATOM 565 C ILE A 86 -0.722 -8.196 14.932 1.00 7.58 C ",
"ANISOU 565 C ILE A 86 1181 748 949 -103 205 87 C ",
"ATOM 566 O ILE A 86 -0.535 -7.767 13.777 1.00 8.17 O ",
"ANISOU 566 O ILE A 86 1249 887 967 -55 242 135 O ",
"ATOM 567 CB ILE A 86 -3.164 -7.571 14.969 1.00 8.30 C ",
"ANISOU 567 CB ILE A 86 1190 920 1043 -32 175 224 C ",
"ATOM 568 CG1 ILE A 86 -4.302 -7.000 15.799 1.00 9.14 C ",
"ANISOU 568 CG1 ILE A 86 1182 1078 1211 15 159 194 C ",
"ATOM 569 CG2 ILE A 86 -3.524 -8.934 14.351 1.00 8.71 C ",
"ANISOU 569 CG2 ILE A 86 1228 984 1097 -91 80 176 C ",
"ATOM 570 CD1 ILE A 86 -5.630 -6.861 15.071 1.00 10.85 C ",
"ANISOU 570 CD1 ILE A 86 1307 1331 1482 31 162 271 C "
]
)


def test_file_not_found(self):
Expand Down