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-type-8-bonds-to-covalent
-
convert all type 8 bonds to single covalent bonds
- --no-adjust-charges
-
do not adjust atom charges when converting type 8 bonds
- --no-estimate-attached-hydrogens
-
do not estimate the number of attached hydrogens
- --ignore-flat-tetrahedra
-
when considering tetrahedral chiral centers, ignore flat tetrahedra (based on volume threshold) [default]
- --require-tetrahedral-angles
-
when considering tetrahedral chiral centers, ignore tetrahedra with average bond angle far from 109.5 degrees
- --planarity-threshold NUM
-
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
-
normalise vectors used for chiral volume calculation
- --mark-square-planar-centers
-
mark chirality in square planar centers
- --no-generate-racemates
-
do not attempt to fully represent racemates in non-Sohncke space groups
- --remove-excess-stereochemistry
-
remove excess stereochemistry settings (experimental)
- --help
-
print usage message and exit