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Most output formats destroy non-standard bond information #138

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avirshup opened this issue Feb 28, 2017 · 1 comment
Open

Most output formats destroy non-standard bond information #138

avirshup opened this issue Feb 28, 2017 · 1 comment
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mol = mdt.from_smiles('CCCC')
print mol.write('pdb')

Gives

HETATM    1  C0  UNL     1       0.928  -0.017  -0.007  0.00  0.00           C  
[...]
HETATM   14  H9  UNL     1       0.809   2.183   1.709  0.00  0.00           H  
END

But we expect a CONECT section ... at least for the HETATMs
@avirshup avirshup self-assigned this Feb 28, 2017
@avirshup avirshup added the bug label Feb 28, 2017
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Implemented moldesign._tests.test_topology_preserved_in_serialization, which for now only has SDF bonds working correctly ...

@avirshup avirshup changed the title Output PDBs missing CONECT records Most output formats destroy bond information Feb 28, 2017
@avirshup avirshup changed the title Most output formats destroy bond information Most output formats destroy non-standard bond information Feb 28, 2017
avirshup added a commit that referenced this issue Mar 1, 2017
@avirshup
Get CONECTs to work with arbitrary serial numbers (part of #138)
9206984
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