pdb line is longer than 80

[LilySnow]

Describe the bug When using pdb2sql to calculate iRMSD of Zdock models, pdb2sql reports an error: pdb line is longer than 80.

It is not clear to me why we need this function _format_pdb_linelength and why we have 80 as a cutoff. It seems that we can simply increase 80 to 150, for example.

Error message:

File "/Applications/anaconda3/lib/python3.7/site-packages/pdb2sql/pdb2sqlcore.py", line 136, in _create_table line = pdb2sql._format_pdb_linelength(line) File "/Applications/anaconda3/lib/python3.7/site-packages/pdb2sql/pdb2sqlcore.py", line 255, in _format_pdb_linelength f'pdb line is longer than 80:\n{pdb_line}') ValueError: pdb line is longer than 80: ATOM 1 N GLN A 1 1.795 -7.034 21.703 19 1 1.63 -.15

To Reproduce

model = 'complex_6.pdb'
ref = 'cleaned_1oga_b_differently_numbered.pdb'
sim = StructureSimilarity(model,ref)
irmsd = sim.compute_irmsd_pdb2sql(method='svd')

complex_6.pdb.txt cleaned_1oga_b_differently_numbered.pdb.txt

[CunliangGeng]

It's required by the PDB format standard. We must follow the standard to make sure the community has the same format of PDB files.

[github-actions[bot]]

This issue is stale because it has been open for 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

[github-actions[bot]]

This issue was closed because it has been inactive for 7 days since being marked as stale.

[CunliangGeng]

The issue is reopened, is there any more questions about it?

[NicoRenaud]

We rarely do anything with then data after the contained in the columns that are after the coordinates in the PDB. So we could limit the parsing to the cols up to the xyz coordinate. Then we could read the ZDOCK files ... It would be kinda nice to be able to read these files as well

[github-actions[bot]]

This issue is stale because it has been open for 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

[github-actions[bot]]

This issue was closed because it has been inactive for 7 days since being marked as stale.