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nlesc-nano / CAT

A collection of tools designed for the automatic construction, and subsequent analysis, of chemical compounds.
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optional.ligand.anchor.mean #251

Closed juliette1996 closed 2 years ago

juliette1996 commented 2 years ago

Hi there,

sorry to disturb but we are facing some troubles with the optional.ligand.anchor.mean option.

In particular we are trying to attach the two oxygens of a carboxylic acid to an In atom using the following the incl3.xyz core file:

4

In     0.000000     0.000000     0.000000
Cl     0.000000     0.000000     2.410000
Cl     2.272173     0.000000    -0.803325
Cl    -1.514773     0.000000    -1.874450

and input file:

input_cores:
    - incl3.xyz:
        guess_bonds: False

input_ligands:
    - CCCC(=O)O

optional:
    core:
        dirname: core
        anchor: Cl

    ligand:
        dirname: ligand
        anchor:
             group: "[H]OC(=O)"  # Remove H and attach at the mean position of both oxygens
             group_idx: [1, 3]
             remove: 0
             kind: mean
        optimize: False
        split: False

The program seems to recognize that two oxygens are to be attached (the qd file name is in fact Cl3In1__3_CCCC[=O][O-]@O5O6.xyz) but only one oxygen is actually anchored instead of the "mean" position...

can you please have a look at this?

thanks in advance! :)