SMILES™, SMARTS™

Codenames: smiles, smarts=smiles:s

Contents:


SMILES

Marvin imports and exports SMILES strings with the following specification rules:


SMARTS

Marvin imports and exports SMARTS strings with the following features:

In case of SMARTS:

Implicit bond types: The default bond types for import and export strongly depend on the atoms connected by the bond.


Import options

f
{fFIELD1,fFIELD2,...}  
Import data fields from a multi-column file. The fields should be separated by tab character. The first column contains the SMILES/SMARTS strings, the second contains the data field called FIELD1, the third contains FIELD2, etc.
Example:
molconvert sdf "foo.smi{fname,fID}" 
reads the smiles string, the name and the ID from the foo.smi file and converts it to sdf format.
d
Import with Daylight compatiblity for query H.
In daylight smarts, H is only considered as H atom when the atom expression has the syntax [<mass>H<charge><map>] (mass, charge and map are optional). Otherwise it is considered as query H count.
Examples: [!H!#6] without d option is imported as an atom which is not H and not C. However with d option it is imported as an atom which has not one H attached, and which is not C.
Use "H1" or "#1" or "#1A" instead of "H" to avoid ambiguous meaning of H. "H1" always means query H count. "#1" always means H atom, "#1A" means aliphatic H atom.
c
Ignore fixing of double bond stereo information in small rings.
Double bonds in small rings (ring size < 8) is imported automatically with CIS stereo information. If c options is set, the double bond stereo information is not changed to CIS during the import.

Export options

Export options can be specified in the format string. The format descriptor and the options are separated by a colon.

... Basic options for aromatization and H atom adding/removal.
0 Do not include parity and double bond stereo (cis/trans) information.
Examples: "smiles:0" (not stereo), "smiles:a0" (aromatic, not stereo)
q Check atom equivalences using graph invariants at double bonds.
The graph invariant is used for symmetry description at each atom in the molecule. If one end of the double bond is symmetric (the ligands' graph invariants equal), then the / and \ signs are not used in the description of the double bond, if this option is set.
Example: molconvert smiles:q -s "C/C=C(/C)C" results CC=C(C)C
s Write query smarts. (See query Smarts for details.)
u Write unique smiles (considering chirality info also [2]). Note: Use this option if you want unique smiles export.
h Convert explicit H atoms to query hydrogen count.
Tf1:f2:... Export f1, f2 ... SDF fields. The fields are separated by tab character.
n Export molecule name (the first line of an MDL molfile).

See also

References

[1] SMILES 2. Algorithm for Generation of Unique SMILES Notation; D. Weininger, A. Weininger, J. L. Weininger; J. Chem. Inf. Comput. Sci. 1989, 29, 97-101
[2] A New Effective Algorithm for the Unambiguous Identification of the Stereochemical Characteristics of Compounds During Their Registration in Databases; T. Cieplak and J.L. Wisniewski; Molecules 2001, 6, 915-926

™: SMILES, SMARTS, and SMIRKS are trademarks of Daylight Chemical Information Systems.