#668 wrong mol2 -> SMILES conversion

[filips]

there is a problem with indicating Z/E isomers in SMILES generated from mol2 files.

Eg. for 1,2-dichloroethane. For structures saved in mol files, smiles (smi or can) are generated correctly:

babel Z.mol -o can
Cl/C=C\Cl Z
1 molecule converted
32 audit log messages

babel E.mol -o can
Cl/C=C/Cl E
1 molecule converted
32 audit log messages

while for files saved in mol2 format, we dont get the E/Z isomerism:

babel Z.mol2 -o can
ClC=CCl Z
1 molecule converted
32 audit log messages

babel E.mol2 -o can
ClC=CCl E
1 molecule converted
32 audit log messages

Converting mol2 back to mol fixes the problem.

greetings,
F

[Noel O'Boyle]

Can you provide a test file?

[filips]

E isomer

[filips]

Z isomer

[filips]

Here they are. Files generated in ChemSketch 12 v. 12.01 and exported as mol2000.

[Noel O'Boyle]

This bug refers to MOL2 files, but the examples you provided are MOL files. Which is the problem?