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",
    "spelling_failures": [],
    "producer": "inner:tier_a_ring"
}

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, producer (the code that built the name) among them.

When there is no name#

Orthonym says so. The plain call prints an empty name and, on the error stream, the reason (a limit code and a label); --provenance gives the reason as a row:

$ orthonym "O=[U](=O)=O"

O=[U](=O)=O	UNSUPPORTED_ELEMENT: inorganic compound (not supported)