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SDF-TO-SMI(1) User Commands SDF-TO-SMI(1)

NAME

sdf-to-smi - convert SDF to SMILES

DESCRIPTION

USAGE

sdf-to-smi [<args>] [<files>]

DESCRIPTION

sdf-to-smi converts SDF files into SMILES.

OPTIONS

convert all type 8 bonds to single covalent bonds
do not adjust atom charges when converting type 8 bonds
do not estimate the number of attached hydrogens
when considering tetrahedral chiral centers, ignore flat tetrahedra (based on volume threshold) [default]
when considering tetrahedral chiral centers, ignore tetrahedra with average bond angle far from 109.5 degrees
planarity volume threshold in cubic angstroms; tetrahedra with chiral volume less or equal to the given one will be understood as flat [default: 1e-06]
normalise vectors used for chiral volume calculation
Method used to mark aromatic atoms and bonds. Supported methods: 'Huckel': marks flat rings as aromatic after ensuring they follow H??ckel's rule as implemented in Chemistry::Ring. 'electron-cycles': marks flat rings as aromatic following Richard L. Apodaca's electron cycle-based approach (slow for large conjugated systems). 'external-list': uses aromaticity defined using --aromatic-atoms or --aromatic-bonds options.
comma-separated list of 1-based aromatic atom numbers to be consulted during aromaticity detection. Implies --aromatisation-method 'external-list'.
comma-separated list of bonds, expressed as dash-separated pairs of 1-based aromatic atom numbers. The list is consulted during aromaticity detection. Implies --aromatisation-method 'external-list'.
mark chirality in square planar centers
do not attempt to fully represent racemates in non-Sohncke space groups
remove excess stereochemistry settings (experimental)
print usage message and exit
February 2026 sdf-to-smi 0.4.0+dfsg