Your first name#

Give Orthonym a structure written as SMILES. It prints the name.

From the command line#

$ orthonym "CCO"
ethanol

Put the SMILES in quotes: characters such as (, = and # mean something to the shell. python -m orthonym "CCO" does the same.

Five more, each the engine’s own output:

$ orthonym "CC(=O)Oc1ccccc1C(=O)O"
2-(acetyloxy)benzoic acid
$ orthonym "Cn1cnc2c1c(=O)n(C)c(=O)n2C"
1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione
$ orthonym "C/C=C/C"
(2E)-but-2-ene
$ orthonym "C[C@H](O)CC"
(2S)-butan-2-ol
$ orthonym "CC(C)Cc1ccc(cc1)[C@@H](C)C(=O)O"
(2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid

That is aspirin, caffeine, trans-but-2-ene, (S)-butan-2-ol and (R)-ibuprofen. The stereodescriptors in the SMILES (/, \, @, @@) come back as E, Z, R and S in the name.

From Python#

>>> from orthonym import name_compound
>>> name_compound("CCO")
'ethanol'
>>> name_compound("CC(=O)Oc1ccccc1C(=O)O")
'2-(acetyloxy)benzoic acid'
>>> name_compound("Cn1cnc2c1c(=O)n(C)c(=O)n2C")
'1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione'
>>> name_compound("C/C=C/C")
'(2E)-but-2-ene'
>>> name_compound("C[C@H](O)CC")
'(2S)-butan-2-ol'

How sure is the name? Ask for the provenance#

Add --provenance and Orthonym prints one row of JSON instead of the bare name. It says which tier the name earned and whether OPSIN read it back to your structure:

$ orthonym "CC(=O)Oc1ccccc1C(=O)O" --provenance | python -m json.tool
{
    "name": "2-(acetyloxy)benzoic acid",
    "tier": "pin_verified",
    "is_pin": true,
    "source": "pin_path",
    "opsin": "verified",
    "gates_passed": [
        "self_consistency"
    ],
    "gate_outcome": "self_consistency_verified",
    "formula": null,
    "limit_code": null,
    "stereo_unexpressed": false,
    "suffix_free_prefix_name": false,
    "prefix_order_fallback": false,
    "verified": "opsin"
}

The two lines to read first:

tier is pin_verified: the strict path for the Preferred IUPAC Name built the name and verified it. The other tiers are on Output tiers.
verified is opsin: OPSIN read the name back to the same molecule.

Every other field is explained on The provenance row.

When there is no name#

Orthonym says so. The plain call prints a label in place of a name, and the provenance row gives the reason:

$ orthonym "O=[U](=O)=O"
inorganic compound (not supported)