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 reference pages for full general information on Import.
  • ImportString and ExportString support the SMILES format.

Import Elements

  • General Import elements:
  • "Elements"list of elements and options available in this file
    "Rules"full list of rules for each element and option
  • 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


Basic Examples  (6)

Import the SMILES string for caffeine:

Find the corresponding chemical entity:

Import a list of molecules from a SMILES file string:

Import a list of molecules along with meta information:

The metadata is stored in the molecule expressions:

Export a list of molecules as SMILES strings:

Include a data column in the output:

Use associations for the metadata to generate a header line:

Import from a SMILES string, keeping hydrogen atoms implicit:

Control whether aromatic bonds are found: