Failed to employ polyatomic core anchors

[juliette1996]

Hello there, I'm trying to use the new option core.optional.allignment = "anchor" but it's apparently failing with this error message:

Traceback (most recent call last):
  File "C:\Users\jzito\Miniconda3\envs\escience\Scripts\init_cat-script.py", line 33, in <module>
    sys.exit(load_entry_point('nlesc-CAT', 'console_scripts', 'init_cat')())
  File "c:\users\jzito\escience\cat\CAT\data_handling\entry_points.py", line 62, in main
    base.prep(extract_args(args), return_mol=False)
  File "c:\users\jzito\escience\cat\CAT\base.py", line 121, in prep
    core_df = prep_core(core_df)
  File "c:\users\jzito\escience\cat\CAT\base.py", line 220, in prep_core
    idx_tuples = [set_core_anchors(i, anchor_tup, allignment_tup, subset) for i in core_df[MOL]]
  File "c:\users\jzito\escience\cat\CAT\base.py", line 220, in <listcomp>
    idx_tuples = [set_core_anchors(i, anchor_tup, allignment_tup, subset) for i in core_df[MOL]]
  File "c:\users\jzito\escience\cat\CAT\attachment\core_anchoring.py", line 51, in set_core_anchors
    anchor_idx = anchor_idx_group[:, anchor_tup.group_idx[0]].copy()
IndexError: too many indices for array

Here are the core and input files.

path: .

input_cores:
        - geo_opt.xyz

input_ligands:
        - CCC(=O)O

optional:
    database:
            mol_format: ['xyz']

    core:
        dirname: core
        allignment: "anchor"  # Define the core vectors based on the dummy acetate's vectors
        anchor:
            group: "[O-]C(C([H])([H])[H])=O"  # Acetate anion (with explicit hydrogens!)
            group_idx: [0, 6]  # Represent the anchor by the mean position of both oxyanions
            kind: "mean"
            remove: [0, 1, 2, 3, 4, 5, 6]  # Remove the entirety of the dummy acetate

    ligand:
        dirname: ligand
        split: True

    qd:
        dirname: qd
        construct_qd: True
        optimize: False

Can you help me with this?

[juliette1996]

@RobertaPascazio do you have a .pdb file of this structure?

[BvB93]

The problem here was the lack of bonds in the passed core, which caused CAT to fail in identifying the anchoring sites within the passed molecules. The error message here is problematic though and should be way more explicit (fixed as of https://github.com/nlesc-nano/CAT/commit/b8349e6ad04a12774faa0e321b8d802e07ff273b).

[RobertaPascazio]

There you have it!

geo_opt.zip

[juliette1996]

Same error as before when using the pdb file