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SMILES (.smi)

Background & Context

    • MIME type: chemical/x-daylight-smiles
    • SMILES chemical format.
    • Commonly used to describe the structure of chemical molecules.
    • SMILES is an acronym for Simplified Molecular Input Line Entry Specification.
    • Used in cheminformatics applications and in chemistry databases to represent chemical formulas.
    • ASCII format.
    • Uses a linear notation to represent the connectivity graph of a molecule.
    • Can store data for multiple molecules.
    • Additional properties can be stored on the same line as the SMILES string.
    • Developed in the 1980s by Arthur Weininger and David Weininger.

Import & Export

  • Import["file.smi"] imports a list of molecules from a SMILES file.
  • Import["file.smi"] converts SMILES data to a Molecule.
  • Import["file.smi",elem] imports the specified element from SMILES.
  • Import["file.smi",{{elem1,elem2,…}}] imports multiple elements.
  • The import format can be specified with Import["file","SMILES"] or Import["file",{"SMILES",elem,…}].
  • Export["file.smi",mol] creates a SMILES file by treating mol as a Molecule.
  • Export["file.smi",expr,elem] creates a SMILES file by treating expr as specifying element elem.
  • Export["file.smi",{expr1,expr2,…},{{elem1,elem2,…}}] treats each expri as specifying the corresponding elemi.
  • Export["file.smi",expr,opt1->val1,…] exports expr with the specified option elements taken to have the specified values.
  • Export["file.smi",{elem1->expr1,elem2->expr2,…},"Rules"] uses rules to specify the elements to be exported.
  • See the following reference pages for full general information:
  • Import, Exportimport from or export to a file
    CloudImport, CloudExportimport from or export to a cloud object
    ImportString, ExportStringimport from or export to a string
    ImportByteArray, ExportByteArrayimport from or export to a byte array

Import Elements

  • General Import elements:
  • "Elements" list of elements and options available in this file
    "Summary"summary of the file
    "Rules"list of rules for all available elements
  • Data elements:
  • "Molecule"a symbolic representation of the molecule model
    "Molecule", na symbolic representation of the n^(th) molecule
    "Metadata"an Association containing the metadata from the file
    "Metadata", nthe metadata for the n^(th) molecule
  • Import by default uses the "Molecule" element when converting from SMILES.
  • SMILES strings are interpreted by Molecule.
  • Data representation elements:
  • "EdgeRules"connectivity data, given as a list of rules
    "EdgeTypes"bond types, given as a list of strings
    "FormalCharges"charges of the atoms given by "VertexTypes"
    "VertexTypes"all atoms or groups constituting the molecule, typically given as a list of chemical element abbreviations

Examples

Basic Examples  (6)

Import the SMILES string for caffeine:

Wolfram Language code: ImportString["CN1C=NC2=C1C(=O)N(C(=O)N2C)C", "SMILES"]

Find the corresponding chemical entity:

Wolfram Language code: ToEntity[First[%]]

Import a list of molecules from a SMILES file string:

Wolfram Language code: ImportString["CC(C(=O)c1c([nH][n+]2c1cccc2)C(C)C)C O=N(=O)[C@@H]1[C@@H](N)[C@H](N(=O)=O)[C@@H]2[C@H]([C@@H]1N)[N+]2 N[C@H](C(=O)Nc1ccc(cc1)N(=O)=O)CC(C)C", "SMILES"]
Wolfram Language code: ExportString[%, "SMILES"]

Import a list of molecules along with meta information:

Wolfram Language code: mols = ImportString["SMILES Name melting_point CC=O acetaldehyde -123 CC1=CC=C(C=C1)C(=O)O 4-methylbenzoic_acid 178 CC(=O)OC1CC2CCC1(C2(C)C)C L-bornyl_acetate 27", "SMILES"]

The metadata is stored in the molecule expressions:

Wolfram Language code: MoleculeValue[mols, "MetaInformation"]
Wolfram Language code: ExportString[mols, "SMILES"]

Export a list of molecules as SMILES strings:

Wolfram Language code: mols = {Molecule["1,4-dimethoxyanthracene"], Molecule["benzene"], Molecule["5,5-diprop-2-enyl-1,3-diazinane-2,4,6-trione"]}
Wolfram Language code: ExportString[mols, "SMILES"]

Include a data column in the output:

Wolfram Language code: ExportString[{mols, {1, 2, 3}}, {"SMILES", {"Molecule", "Metadata"}}]

Use associations for the metadata to generate a header line:

Wolfram Language code: ExportString[{mols, {<|"a" -> 1, "b" -> 2|>, <|"a" -> 11, "b" -> 12|>, <|"a" -> 21, "b" -> 22|>}}, {"SMILES", {"Molecule", "Metadata"}}]
Wolfram Language code: ImportString[%, {"SMILES", "Metadata"}]

Import from a SMILES string, keeping hydrogen atoms implicit:

Wolfram Language code: ImportString["CCCC", "SMILES"]
Wolfram Language code: AtomList[First[%], IncludeHydrogens -> "ExplicitOnly"]

Control whether aromatic bonds are found:

Wolfram Language code: ImportString["C1=CC=CC=C1", "SMILES", IncludeAromaticBonds -> False]
Wolfram Language code: BondList[First[%], Bond[{"C", "C"}]]