MDL MOL format (mdl, mol, sd, sdf)

Reads and writes V2000 and V3000 versions

Open Babel supports an extension to the MOL file standard that allows cis/trans and tetrahedral stereochemistry to be stored in 0D MOL files. The tetrahedral stereochemistry is stored as the atom parity, while the cis/trans stereochemistry is stored using Up and Down bonds similar to how it is represented in a SMILES string. Use the S option when reading or writing if you want to avoid storing or interpreting stereochemistry in 0D MOL files.

Read Options


determine chirality from atom parity flags

The default setting for 2D and 3D is to ignore atom parity and work out the chirality based on the bond stereochemistry (2D) or coordinates (3D). For 0D the default is already to determine the chirality from the atom parity.


do not read stereochemistry from 0D MOL files

Open Babel supports reading and writing cis/trans and tetrahedral stereochemistry to 0D MOL files. This is an extension to the standard which you can turn off using this option.

-T read title only

read title and properties only

When filtering an sdf file on title or properties only, avoid lengthy chemical interpretation by using the T or P option together with the copy format.

Write Options

-3 output V3000 not V2000 (used for >999 atoms/bonds)
-a write atomclass if available
-m write no properties
-w use wedge and hash bonds from input (2D only)

always specify the valence in the valence field

The default behavior is to only specify the valence if it is not consistent with the MDL valence model. So, for CH4 we don’t specify it, but we do for CH3. This option may be useful to preserve the correct number of implicit hydrogens if a downstream tool does not correctly implement the MDL valence model (but does honor the valence field).

-S do not store cis/trans stereochemistry in 0D MOL files
-A output in Alias form, e.g. Ph, if present
-E add an ASCII depiction of the molecule as a property
-H use HYD extension (always on if mol contains zero-order bonds)