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nlesc-nano
Failed to employ polyatomic core anchors
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?
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).
