Arpeggio fails when chem_comp.name == "."

[Matt Crown]

Arpeggio processes chem_comp names using Gemmi. When Gemmi encounters a value of "." it evaluates this as False, and "?" as None.

In for example 2c16
the chem_comp name for all chemical components is "." - and when False is evaluate with .upper() in the get_component_types function, an error is raised (see bottom).

A potential solution to this problem would be to evaluate the presence of water using :
if chem_comp['id'][i].upper() == 'HOH' instead of chem_comp['name'][i].upper() == 'WATER'

as the id column is more likely to be stable than the name column

If you think this is a suitable workaround, let me know and I can make a PR.

  INFO//00:16:26.032//Program begin.                                                                                                                                                               [5/94114]
  INFO//00:16:26.047//Selection perceived: ['/A/1336/', '/A_2/1336/', '/A_3/1336/', '/A_4/1336/', '/A/1337/', '/A_2/1337/', '/A_3/1337/', '/A_4/1337/', '/A/1338/', '/A_2/1338/', '/A_3/1338/', '/A[4/94114]
, '/A/1339/', '/A_2/1339/', '/A_3/1339/', '/A_4/1339/', '/B/1336/', '/B_2/1336/', '/B_3/1336/', '/B_4/1336/', '/B/1337/', '/B_2/1337/', '/B_3/1337/', '/B_4/1337/', '/B/1338/', '/B_2/1338/', '/B_3[3/94114]
'/B_4/1338/', '/B/1339/', '/B_2/1339/', '/B_3/1339/', '/B_4/1339/']                                                                                                                                [2/94114]
  DEBUG//00:16:26.879//Loaded PDB structure (BioPython)                                                                                                                                            [1/94114]
  ==============================
  *** Open Babel Warning  in PerceiveBondOrders
    Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
  
  DEBUG//00:16:39.395//Loaded MMCIF structure (OpenBabel)
  Traceback (most recent call last):
    File "/home/crk_w20032671/ProCogGraph/nextflow/work/conda/arpeggio-env-dbdf2f54a83bf8f7e2494af81181aee8/bin/pdbe-arpeggio", line 8, in <module>
      sys.exit(main())
    File "/home/crk_w20032671/ProCogGraph/nextflow/work/conda/arpeggio-env-dbdf2f54a83bf8f7e2494af81181aee8/lib/python3.9/site-packages/arpeggio/scripts/process_protein_cli.py", line 150, in main
      run_arpeggio(args)
    File "/home/crk_w20032671/ProCogGraph/nextflow/work/conda/arpeggio-env-dbdf2f54a83bf8f7e2494af81181aee8/lib/python3.9/site-packages/arpeggio/scripts/process_protein_cli.py", line 159, in run_arpeggio
      i_complex = InteractionComplex(
    File "/home/crk_w20032671/ProCogGraph/nextflow/work/conda/arpeggio-env-dbdf2f54a83bf8f7e2494af81181aee8/lib/python3.9/site-packages/arpeggio/core/interactions.py", line 70, in __init__
      self.component_types = protein_reader.get_component_types(filename)
    File "/home/crk_w20032671/ProCogGraph/nextflow/work/conda/arpeggio-env-dbdf2f54a83bf8f7e2494af81181aee8/lib/python3.9/site-packages/arpeggio/core/protein_reader.py", line 431, in get_component_types
      if chem_comp['name'][i].upper() == 'WATER':
  AttributeError: 'bool' object has no attribute 'upper'```

[Xavier Robin]

We got hit by this issue as well (in our case chem_comp.name was missing altogether in the file).

The chem_comp.name data item is not mandatory free text. It seems unsafe to rely on it.

In addition the commit also recognizes DOD as water (which wouldn't have been the case previously).