Correspondance lipid name / residue name

[patrickfuchs]

By creating a notebook example, I realized we don't check the correspondance between the lipid name given with -l option and the residue name in the PDB. For example:

Constructing the system...
System has 28526 atoms
Traceback (most recent call last):
  File "/home/fuchs/software/miniconda3/envs/buildh/bin/buildH", line 33, in <module>
    sys.exit(load_entry_point('buildh', 'console_scripts', 'buildH')())
  File "/home/fuchs/papers/buildH_Amelie/buildH/buildh/cli.py", line 232, in main
    core.fast_build_all_Hs_calc_OP(universe_woH, begin, end, dic_OP, dic_lipid, dic_Cname2Hnames)
  File "/home/fuchs/papers/buildH_Amelie/buildH/buildh/core.py", line 466, in fast_build_all_Hs_calc_OP
    dic_lipids_with_indexes = make_dic_lipids_with_indexes(universe_woH,
  File "/home/fuchs/papers/buildH_Amelie/buildH/buildh/core.py", line 365, in make_dic_lipids_with_indexes
    first_lipid_residue = universe_woH.select_atoms(selection).residues[0]
  File "/home/fuchs/software/miniconda3/envs/buildh/lib/python3.8/site-packages/MDAnalysis/core/groups.py", line 540, in __getitem__
    return self.level.singular(self.ix[item], self.universe)
IndexError: index 0 is out of bounds for axis 0 with size 0

Rather unclear, isn't it 😆 ???

The error above comes from the use of Berger_POPC instead of Berger_PLA with the -l option.

Additionnally, I'm thinking maybe we should also make a check between the argument passed to -l option and that passed to -d option. Imagine, for example, -l CHARMM-UA -d order_parameter_definitions_MODEL_Berger_POPC.def (could be solved in another issue)

[HubLot]

One solution is to check that residue name is present before going in the rebuild + compute OP phase.

Same for the link between -l and -d options.

[patrickfuchs]

👍 Yes definitely!