Work at SourceForge, help us to make it a better place! We have an immediate need for a Support Technician in our San Francisco or Denver office.

Close

#864 XYZ to SMILES conversion is wrong with cations

2.3.x
open
nobody
None
1
2013-02-20
2013-02-20
Charnley
No

Hi,

if I try to convert the attached molecule (ethenylazanium) from XYZ to SMILES

obabel -ixyz coordinates.xyz -osmiles

I receive

C=C[NH3]

which is wrong. The correct SMILES string should be

C=C[NH3+]

cheers
Jimmy

Discussion

  • Charnley
    Charnley
    2013-02-20

    coordinates

     
    Attachments