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UCL-CCS / TIES

Topology Superimposition based on joint graph traversal
MIT License
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Mached atom exception #295

Closed adw62 closed 2 years ago

adw62 commented 2 years ago

This input I have attached seems to trip an exception here: https://github.com/UCL-CCS/TIES20/blob/6c5dafdb6e138eff93bf25031882ace177377b09/ties/generator.py#L236

Not sure what causes this? Recording here for future investigations. input.zip

bieniekmateusz commented 2 years ago

The lig/build/hybrid.mol2 has the right atom name (HOAB1), but this information is lost in lig/build/complex_nofep.pdb because the PDB format only allows for 4 characters "HOAB" for the atom name. Therefore creating a mismatch later during the check.

One way out: while renaming the atom names to our format, we can ensure that it has 2 characters and 2 digits. So here HOAB would be HO1

adw62 commented 2 years ago

I see makes sense thanks. The fix you suggest sounds good, let's add it if we have time. Otherwise I'll just rename my mol2 for now.

bieniekmateusz commented 2 years ago

Thanks, that's now addressed in 610c2ad31aad1ad31fdd6e813683706bdb39401d and 2daa2189b9b3f28133f640cc46e929d61ce73836