Generate canonical smiles

A program that generates the canonical SMILES of the molecules in the input file. It has a number of options such as -from3d, which perceives stereo from the 3D coordinates, -isomeric, which produces the canonical isomeric SMILES, and -kekule, which produces the Kekulé SMILES form.

Example

prompt> cansmi.py dbase.oeb.gz output.smi
prompt> cansmi.py  -from3d true -i dbase.sdf -o output.smi

Code

Download code

cansmi.py

See also

• OEFindRingAtomsAndBonds function

• OEAssignAromaticFlags function

• OEKekulize function

• OECanonicalOrderAtoms function

• OECanonicalOrderBonds function