SMILES (.smi)

Import and Export fully support the SMILES file format.

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 expr_i as specifying the corresponding elem_i.
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, Export	import from or export to a file
	CloudImport, CloudExport	import from or export to a cloud object
	ImportString, ExportString	import from or export to a string
	ImportByteArray, ExportByteArray	import 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", n	a symbolic representation of the n molecule
	"Metadata"	an Association containing the metadata from the file
	"Metadata", n	the metadata for the n 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)Summary of the most common use cases

Import the SMILES string for caffeine:

In[1]:=1

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-f9jtyn

Out[1]=1

Find the corresponding chemical entity:

In[2]:=2

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-i55fxv

Out[2]=2

Import a list of molecules from a SMILES file string:

In[1]:=1

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-j0kecq

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-0qtguy

Out[2]=2

Import a list of molecules along with meta information:

In[1]:=1

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-ml8lhj

Out[1]=1

The metadata is stored in the molecule expressions:

In[2]:=2

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-q8sbpe

Out[2]=2

In[3]:=3

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-qzg0ez

Out[3]=3

Export a list of molecules as SMILES strings:

In[1]:=1

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-jg50f8

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-qg1khs

Out[2]=2

Include a data column in the output:

In[3]:=3

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-rmqcrv

Out[3]=3

Use associations for the metadata to generate a header line:

In[4]:=4

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-hn25qd

Out[4]=4

In[5]:=5

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-s9g1pl

Out[5]=5

Import from a SMILES string, keeping hydrogen atoms implicit:

In[1]:=1

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-1jlcm4

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-fbikq0

Out[2]=2

Control whether aromatic bonds are found:

In[1]:=1

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-3zv725

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0ca09tk1nqsshmy-u8mkdx

Out[2]=2

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