Command line

orthonym names one SMILES, or a file of them. python -m orthonym is the same program. Every option is listed below in plain words, grouped by what it is for; the option reference prints the program’s own help text.

$ orthonym "c1ccccc1"
benzene

Naming

orthonym "SMILES"

Print the name of one structure.

--style {pin,general,cas}

pin (the default) aims at the Preferred IUPAC Name. general allows a few general IUPAC forms where the recommendations offer one. cas is accepted and at present gives the same names as pin.

--enable-triviality-controller

Where the IUPAC 2013 recommendations prefer a retained parent name (benzene, phenol, aniline, benzoic acid and others) to the systematic one, use it (P-15.1.8). Every change is checked by an OPSIN round trip. ORTHONYM_ENABLE_TRIVIALITY_CONTROLLER=1 turns it on too.

--trivial

When no preferred name can be built, also allow a retained trivial name that is not a preferred name. A preferred name that can be built is never replaced: glycerol stays propane-1,2,3-triol. Without this option a small table of retained trivial names is still used as a last resort at the wider tiers (the default tier declines those names); the provenance row labels them systematic_verified with source trivial_retained.

Tiers

--emit-tier {pin,valid,complete,best-effort,full-coverage}

Which names to return. The default, pin, returns a name only when the pipeline can build the preferred IUPAC name (PIN), that is when the strict PIN path built the name and verified it (pin_verified). The only exceptions are names from the natural-product and metal-complex lists, the name formats absent from OPSIN’s grammar (for example inositols, phanes and thioperoxols), and PINs whose stereodescriptors OPSIN cannot read, for which the default tier compares the constitution. Otherwise it declines, with the reason code NO_VERIFIED_PIN when it built a name that is not a verified PIN. valid adds names from the general engine, complete adds general names for aromatic and heterocyclic ring systems, best-effort adds the last-resort producers, von Baeyer and spiro names for ring systems of up to 100 skeletal atoms and 11 rings (the other tiers build these names for ring systems of up to 40 skeletal atoms and 8 rings), and adducts with a one-atom ion such as chloride, and full-coverage adds the coordination-name builder for metal tetrapyrrole and corrin complexes. The wider tiers also return the names the default tier declines, each labelled with its tier. See Output tiers.

Output

--provenance

Print a JSON row instead of the bare name: the name, its tier, and how it was checked. One SMILES at a time. See The provenance row.

--confidence

Print the name with a coverage score, the part of the engine that built it, and the parts of the score. When no measurement was taken it says so: Confidence: unverified (no coverage measurement was taken).

--verbose, -v

Also print the SMILES and the style. With --batch and --output, also say how many lines were named and how many failed.

--dump-tree, --format {text,json}

Print the parts of the name as a tree instead of the name.

$ orthonym --dump-tree "OC1CCCCC1"
NameTree: cyclohexanol  (class_id=general_acyclic, cite=P-14+P-23+P-44)
+- parent_stem: 'cyclohex'
   |- suffix: 'ol'

Batch

--batch FILE, -b FILE

Name every SMILES in the file, one per line. See Batch files.

--output FILE, -o FILE

With --batch, write the lines to this file instead of the screen.

Diagnostics

These are for looking inside the engine. None of them changes a name, except --binding-proof enforce, which can decline one.

--fetch-jars

Download the OPSIN and centres jars if they are missing, check them, print where they are, and stop. See Install.

--validation-stats

After the name, print on the error stream how often the OPSIN grammar pre-check passed or repaired a candidate name.

--dispatch-stats

After the name, print on the error stream which compound-class routes the engine took.

--engine-only

Skip the strict path and print, as JSON, the general engine’s own name, checked for atom coverage but not by OPSIN. Never a preferred name; do not use it as a name.

--binding-proof {off,audit,enforce}

An extra check that every part of a general-engine name still maps onto its atoms in the final name. audit records the result and never changes the name; enforce also declines when the check fails.

--version, -V

Print the installed version, in the form orthonym 1.0.2.

Exit status

0 when the name (or the label for a decline) was printed; 1 for a SMILES that RDKit cannot read, or a batch with at least one such line; 2 when a jar can be neither found nor downloaded.