Basic Examples

Find the SMILES string from a chemical name:
[◼]
ChemicalNameToSMILES
["2-amino-14,16-dimethyloctadecan-3-ol"]
NC(C)C(CCCCCCCCCCC(CC(CC)C)C)O
Out[]=
Use a chemical name with defined stereochemistry:
[◼]
ChemicalNameToSMILES
["(2R,3S,4S,5R)-3-(dimethylamino)-2,4,5-trihydroxyhexanal"]
CN([C@H]([C@H](C=O)O)[C@@H]([C@@H](C)O)O)C
Out[]=

Scope

When given an invalid chemical name,
ChemicalNameToSMILES
will return a
Failure
identifying the uninterpretable portion of the name:
[◼]
ChemicalNameToSMILES
["3,6-Dideoxy-3-(dimethylamina)-D-glucose"]
Failure

Input: 3,6-Dideoxy-3-(dimethylamina)-D-glucose
Uninterpretable: a)-D-glucose
Tag: OpsinParseFailure

Out[]=
Fixing the typographical error allows the name to be parsed:
[◼]
ChemicalNameToSMILES
["3,6-Dideoxy-3-(dimethylamino)-D-glucose"]
CN([C@H]([C@H](C=O)O)[C@H](O)[C@H](O)C)C
Out[]=

Options

By default,
ChemicalNameToSMILES
will parse fragment names such as “oxo” and “keto” as radicals with unpaired electrons. Use the option "AllowRadicals" to disable this behavior:
[◼]
ChemicalNameToSMILES
["carboxyl","AllowRadicals"#]&/@{True,False}
[C](=O)O,Failure

Input: carboxyl
Message: carboxyl could be parsed but OPSIN was unsure of the meaning of the words. This error will occur, by default, if a name is just a substituent
Tag: OpsinParseFailure

Out[]=
When parsing a chemical substituent, it is possible to add dummy atoms at the relevant attachment points:
[◼]
ChemicalNameToSMILES
["carboxyl","AddDummyAtoms"#]&/@{True,False}
{C(=O)(O)*,[C](=O)O}
Out[]=