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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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Ligand order in CAT #262

Closed RobertaPascazio closed 1 year ago

RobertaPascazio commented 1 year ago

Hi Bas,

In the ligand_order.zip directory, I have attached the files I have been working with. I wanted to attach a DDA ligand (dda.xyz) to a NC core (nc.xyz) I have, and I want the order of the ligand atoms to be the same as the .xyz file. I have tried bypassing the smiles string and directly providing the .xyz file to CAT, but the atom order isn't preserved (as shown by nc_cat.xyz and dda_cat.xyz). Am I missing something in the .yaml script, or could you maybe add an additional keyword to do it? Thanks in advance!

BvB93 commented 1 year ago

Hi Roberta,

I can confirm that there's currently no way of disabling the ligand canonicalization in CAT. This shouldn't be too difficult to add though, considering canonicalization is already explicitly disabled for the core.