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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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Add option for passing new, SMARTS-specified atomtypes #56

Closed althea-hansel closed 11 months ago

diogomart commented 11 months ago

Works great for a single new type, but not for multiple, for example:

mk_prepare_ligand.py -i has-selenium.sdf -aa '[{"smarts": "[Se]", "atype": "SA"}, {"smarts": "[Ch3][C]", "IDX": [1], "atype": "OX"}]' -
mk_prepare_ligand.py -i has-selenium.sdf -aa '{"smarts": "[Se]", "atype": "SA"}' -aa '{"smarts": "[Ch3][C]", "IDX": [1], "atype": "OX"}'

Maybe this was not the intended syntax?

althea-hansel commented 11 months ago

Correct syntax is 

mk_prepare_ligand.py -i has-selenium.sdf -aa '{"smarts": "[Se]", "atype": "SA"} {"smarts": "[Ch3][C]", "IDX": [1], "atype": "OX"}'