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Improve MolecularContainer.top_up_conformations

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Top up from all conformations, not just first.

Fixes https://github.com/jensengroup/propka/issues/147
This commit is contained in:
Thomas Holder
2023-09-17 15:19:25 +02:00
parent fd7b155171
commit 7d78acac6e
8 changed files with 220 additions and 5 deletions
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23
tests/pdb/conf-alt-AB-mutant.pdb Normal file
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ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N ASER 2 5.576 -1.566 1.473 1.00 0.00 N
ATOM 6 CA ASER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 7 C ASER 2 7.852 -2.130 2.177 1.00 0.00 C
ATOM 8 O ASER 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 9 CB ASER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 10 OG ASER 2 6.285 -4.520 1.474 1.00 0.00 O
ATOM 11 N BVAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 12 CA BVAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 13 C BVAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 14 O BVAL 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 15 CB BVAL 2 5.939 -3.746 2.618 1.00 0.00 C
ATOM 16 CG1BVAL 2 5.960 -4.584 1.310 1.00 0.00 C
ATOM 17 CG2BVAL 2 6.774 -4.559 3.636 1.00 0.00 C
ATOM 18 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 19 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 20 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 21 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
END

19
tests/pdb/conf-alt-AB.pdb Normal file
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ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N SER 2 5.576 -1.566 1.473 1.00 0.00 N
ATOM 6 CA ASER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 7 CA BSER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 8 C SER 2 7.852 -2.130 2.177 1.00 0.00 C
ATOM 9 O SER 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 10 CB ASER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 11 CB BSER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 12 OG ASER 2 6.285 -4.520 1.474 1.00 0.00 O
ATOM 13 OG BSER 2 6.994 -4.577 3.101 1.00 0.00 O
ATOM 14 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 15 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 16 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 17 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
END

19
tests/pdb/conf-alt-BC.pdb Normal file
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ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N SER 2 5.576 -1.566 1.473 1.00 0.00 N
ATOM 6 CA BSER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 7 CA CSER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 8 C SER 2 7.852 -2.130 2.177 1.00 0.00 C
ATOM 9 O SER 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 10 CB BSER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 11 CB CSER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 12 OG BSER 2 6.285 -4.520 1.474 1.00 0.00 O
ATOM 13 OG CSER 2 6.994 -4.577 3.101 1.00 0.00 O
ATOM 14 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 15 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 16 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 17 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
END

45
tests/pdb/conf-model-missing-atoms.pdb Normal file
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MODEL 1
ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N VAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 6 CA VAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 7 C VAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 8 O VAL 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 9 CB VAL 2 5.939 -3.746 2.618 1.00 0.00 C
ATOM 10 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 11 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 12 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 13 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
ENDMDL
MODEL 2
ATOM 14 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 15 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 16 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 17 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 18 N VAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 19 CA VAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 20 C VAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 21 O VAL 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 22 CB VAL 2 5.939 -3.746 2.618 1.00 0.00 C
ATOM 23 CG1 VAL 2 5.960 -4.584 1.310 1.00 0.00 C
ATOM 24 CG2 VAL 2 6.774 -4.559 3.636 1.00 0.00 C
ATOM 25 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 26 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 27 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 28 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
ENDMDL
MODEL 3
ATOM 29 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 30 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 31 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 32 N VAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 33 CA VAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 34 C VAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 35 O VAL 2 8.265 -1.521 1.190 1.00 0.00 O
TER
ENDMDL
END

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tests/pdb/conf-model-mutant.pdb Normal file
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MODEL 1
ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N SER 2 5.576 -1.566 1.473 1.00 0.00 N
ATOM 6 CA SER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 7 C SER 2 7.852 -2.130 2.177 1.00 0.00 C
ATOM 8 O SER 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 9 CB SER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 10 OG SER 2 6.285 -4.520 1.474 1.00 0.00 O
ATOM 11 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 12 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 13 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 14 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
ENDMDL
MODEL 2
ATOM 15 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 16 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 17 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 18 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 19 N VAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 20 CA VAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 21 C VAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 22 O VAL 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 23 CB VAL 2 5.939 -3.746 2.618 1.00 0.00 C
ATOM 24 CG1 VAL 2 5.960 -4.584 1.310 1.00 0.00 C
ATOM 25 CG2 VAL 2 6.774 -4.559 3.636 1.00 0.00 C
ATOM 26 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 27 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 28 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 29 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
ENDMDL
END