Add option for passing new, SMARTS-specified atomtypes

[althea-hansel]

No description provided.

[diogomart]

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]

Correct syntax is

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