Code name: smiles, smarts=smiles:s

Marvin imports and exports SMILES strings with the following additional features:

Import options

Import data fields from a multi-column file. The first column contains the SMILES strings, the second contains the data field called FIELD1, the third contains FIELD2, etc.
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.

Export options

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

a or +a     Aromatize. Example: "smiles:a"
-a Dearomatize. Example: "smiles:-a"
-H Remove explicit Hydrogen atoms. Example: "smiles:-H"
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.
Note: Use this option if you want unique smiles export.
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 uniqe smiles (considering chirality info also [4]).
h Convert explicit H atoms to query hydrogen count.


[3] 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
[4] 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