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PDB structures without H atoms #909

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icamps opened this issue Nov 22, 2023 · 1 comment · Fixed by #910
Closed

PDB structures without H atoms #909

icamps opened this issue Nov 22, 2023 · 1 comment · Fixed by #910
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bug Something isn't working

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@icamps
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icamps commented Nov 22, 2023

Is your feature request related to a problem? Please describe.
When using PDB files without H, we got an error message, and the calculation stopped:

########################################################################
[ERROR] Program stopped due to fatal error
-2- reading geometry input 'CO2.pdb' failed
-1- io_reader_readMolecule: PDB structure without hydrogen atoms found, aborting due to incomplete input geometry
########################################################################

Describe the solution you'd like
PDB without H atoms be allowed to continue all the calculation types supported by xTB.

Describe alternatives you've considered
Using other file formats, but we lose the idea of having "residues" in further analysis.

If possible state how you can assist in providing data or code to to implement the feature
Any PDB without H atoms will give this error. I think that stopping checking for H atoms in PDB will "fix" the error.

Additional context

@MtoLStoN MtoLStoN added the bug Something isn't working label Nov 22, 2023
@MtoLStoN
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Thank you for reporting this Issue. I have opened a PR (#910) to raise a warning instead of an error, to allow the usage of pdb files without hydrogen atoms. This should fix your Issue.

All the best
Marcel

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