Removing component types for custom CIF files

[ljmartin]

Hi all,
Thanks for making the package open source. TLDR: can I avoid using the chem_comp labels added in 3dc288c?

I'd like to use this on structures that originated from outside the PDB - custom crystal structures, for instance, or docked poses. Converting with gemmi is reasonably straightforward (example file was from the RCSB in this case):

gemmi convert 1x7a.pdb 1x7a_converted.cif

but these .cif files don't work with pdbe-arpeggio:

pdbe-arpeggio -s RESNAME:187 -o ./out/ -m 1x7a_converted.cif

Traceback (most recent call last):
  File "/Users/ljmartin/miniconda3/envs/compchem/bin/pdbe-arpeggio", line 8, in <module>
    sys.exit(main())
  File "/Users/ljmartin/miniconda3/envs/compchem/lib/python3.9/site-packages/arpeggio/scripts/process_protein_cli.py", line 150, in main
    run_arpeggio(args)
  File "/Users/ljmartin/miniconda3/envs/compchem/lib/python3.9/site-packages/arpeggio/scripts/process_protein_cli.py", line 159, in run_arpeggio
    i_complex = InteractionComplex(
  File "/Users/ljmartin/miniconda3/envs/compchem/lib/python3.9/site-packages/arpeggio/core/interactions.py", line 70, in __init__
    self.component_types = protein_reader.get_component_types(filename)
  File "/Users/ljmartin/miniconda3/envs/compchem/lib/python3.9/site-packages/arpeggio/core/protein_reader.py", line 425, in get_component_types
    cmp_type  = config.ComponentType.from_chem_comp_type(chem_comp['type'][i])
  File "/Users/ljmartin/miniconda3/envs/compchem/lib/python3.9/site-packages/arpeggio/core/config.py", line 1199, in from_chem_comp_type
    return ComponentType(component_types[type.upper()]).name
AttributeError: 'bool' object has no attribute 'upper'

The source of the problem is maybe obvious - 1x7a_converted.cif doesn't have a chem_comp label, it looks like this:

loop_
_chem_comp.id
_chem_comp.type
187 .
ALA .
ARG .
ASN .
...

When loaded by gemmi, these fields are present, but are a bool (False). ComponentType in core/config.py requires a string, instead.
It looks like the chem_comp labelling was added fairly recently - in 3dc288c - is there a way to avoid using this label at all?

Thanks
PS this conversion does work with pdbe-arpeggio when using maxit, where the chem_comp records look like this:

loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
187 non-polymer         . "1-{3-[AMINO(IMINO)METHYL]PHENYL}-N-[4-(1H-BENZIMIDAZOL-1-YL)-2-FLUOROPHENYL]-3-(TRIFLUOROMETHYL)-1H-PYRAZOLE-5-CARBOXAMIDE" ? "C25 H17 F4 N7 O" 507.442
ALA "L-peptide linking" y ALANINE                                                                                                                      ? "C3 H7 N O2"      89.093
ARG "L-peptide linking" y ARGININE                                                                                                                     ? "C6 H15 N4 O2 1"  175.209
ASN "L-peptide linking" y ASPARAGINE                                                                                                                   ? "C4 H8 N2 O3"     132.118