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haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.
https://haddocking.github.io/pdb-tools/
Apache License 2.0
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pdb_tidy discards ENDMDL statements for HETATM ensembles #160

Closed amjjbonvin closed 6 months ago

amjjbonvin commented 6 months ago

Describe the bug

Running pdb_tidy on an ensemble of molecules defined as HETATM discards the ENDMDL statement, generating effectively a wrong PDB file.

To Reproduce Steps to reproduce the behavior. Preferrably, a code snippet.

pdb_tidy test-ensemble.pdb

Expected behavior The output PDB file should contain the ENDMDL statements after each model in the ensemble.

Desktop (please complete the following information): -Mac OS

Example PDB file:

MODEL        1
HETATM    1  C1  G39 B 500     -30.374 -53.143   6.122  1.00 31.18           C  
HETATM    2  O1A G39 B 500     -31.439 -52.533   5.850  1.00 30.30           O  
HETATM    3  O1B G39 B 500     -29.257 -52.625   5.879  1.00 31.23           O  
HETATM    4  C2  G39 B 500     -30.437 -54.486   6.725  1.00 30.48           C  
HETATM    5  C3  G39 B 500     -29.159 -55.188   7.132  1.00 30.04           C  
HETATM    6  C4  G39 B 500     -29.380 -56.162   8.294  1.00 30.37           C  
HETATM    7  N4  G39 B 500     -28.195 -56.994   8.430  1.00 30.09           N1+
HETATM    8  C5  G39 B 500     -30.627 -57.033   8.097  1.00 29.53           C  
HETATM    9  N5  G39 B 500     -30.803 -57.955   9.206  1.00 28.16           N  
HETATM   10  C6  G39 B 500     -31.883 -56.178   7.937  1.00 30.53           C  
HETATM   11  C7  G39 B 500     -31.632 -55.093   6.901  1.00 30.75           C  
HETATM   12  O7  G39 B 500     -33.007 -56.989   7.531  1.00 31.80           O  
HETATM   13  C8  G39 B 500     -34.158 -56.905   8.398  1.00 30.52           C  
HETATM   14  C9  G39 B 500     -34.879 -55.553   8.283  1.00 31.36           C  
HETATM   15  C10 G39 B 500     -30.683 -59.283   9.087  1.00 27.13           C  
HETATM   16  O10 G39 B 500     -30.629 -59.863   8.010  1.00 26.14           O  
HETATM   17  C11 G39 B 500     -30.611 -60.040  10.380  1.00 26.05           C  
HETATM   18  C81 G39 B 500     -35.153 -58.020   8.079  1.00 29.88           C  
HETATM   19  C82 G39 B 500     -34.654 -59.395   8.467  1.00 28.23           C  
HETATM   20  C91 G39 B 500     -35.425 -55.279   6.891  1.00 32.33           C  
ENDMDL
MODEL        2
HETATM    1  C1  G39 B 500     -30.374 -53.143   6.122  1.00 31.18           C  
HETATM    2  O1A G39 B 500     -31.439 -52.533   5.850  1.00 30.30           O  
HETATM    3  O1B G39 B 500     -29.257 -52.625   5.879  1.00 31.23           O  
HETATM    4  C2  G39 B 500     -30.437 -54.486   6.725  1.00 30.48           C  
HETATM    5  C3  G39 B 500     -29.159 -55.188   7.132  1.00 30.04           C  
HETATM    6  C4  G39 B 500     -29.380 -56.162   8.294  1.00 30.37           C  
HETATM    7  N4  G39 B 500     -28.195 -56.994   8.430  1.00 30.09           N1+
HETATM    8  C5  G39 B 500     -30.627 -57.033   8.097  1.00 29.53           C  
HETATM    9  N5  G39 B 500     -30.803 -57.955   9.206  1.00 28.16           N  
HETATM   10  C6  G39 B 500     -31.883 -56.178   7.937  1.00 30.53           C  
HETATM   11  C7  G39 B 500     -31.632 -55.093   6.901  1.00 30.75           C  
HETATM   12  O7  G39 B 500     -33.007 -56.989   7.531  1.00 31.80           O  
HETATM   13  C8  G39 B 500     -34.158 -56.905   8.398  1.00 30.52           C  
HETATM   14  C9  G39 B 500     -34.879 -55.553   8.283  1.00 31.36           C  
HETATM   15  C10 G39 B 500     -30.683 -59.283   9.087  1.00 27.13           C  
HETATM   16  O10 G39 B 500     -30.629 -59.863   8.010  1.00 26.14           O  
HETATM   17  C11 G39 B 500     -30.611 -60.040  10.380  1.00 26.05           C  
HETATM   18  C81 G39 B 500     -35.153 -58.020   8.079  1.00 29.88           C  
HETATM   19  C82 G39 B 500     -34.654 -59.395   8.467  1.00 28.23           C  
HETATM   20  C91 G39 B 500     -35.425 -55.279   6.891  1.00 32.33           C  
ENDMDL
END