I am using openbabel 2.3.2, on a windows 7 32 bit machine.

I found this discrepancy from the command line, but also using the openbabel GUI

I started with the following SMILES, obtained from the nih cactus server:

[P]2(OC1=C(C(C)(C)C)C=C(C(C)(C)C)C=C1C3=C(O2)C(=CC(=C3)C(C)(C)C)C(C)(C)C)OCCN(CCO[P]5OC4=C(C(C)(C)C)C=C(C(C)(C)C)C=C4C6=C(O5)C(=CC(=C6)C(C)(C)C)C(C)(C)C)CCO[P]8OC7=C(C(C)(C)C)C=C(C(C)(C)C)C=C7C9=C(O8)C(=CC(=C9)C(C)(C)C)C(C)(C)C

if I translate this starting SMILES to SMILES, I get the following result:

p1(oc2c(C(C)(C)C)cc(C(C)(C)C)cc2c2c(o1)c(cc(c2)C(C)(C)C)C(C)(C)C)OCCN(CCOp1oc2c(C(C)(C)C)cc(C(C)(C)C)cc2c2c(o1)c(cc(c2)C(C)(C)C)C(C)(C)C)CCOp1oc2c(C(C)(C)C)cc(C(C)(C)C)cc2c2c(o1)c(cc(c2)C(C)(C)C)C(C)(C)C

and the following formula results from the original smiles, using the -oreport option:

FORMULA: C90H132NO9P3

MASS: 1464.9337

EXACT MASS: 1463.9114947

next, I take the **resulting** smiles, as listed above, copied and pasted, and use it as the input:

p1(oc2c(C(C)(C)C)cc(C(C)(C)C)cc2c2c(o1)c(cc(c2)C(C)(C)C)C(C)(C)C)OCCN(CCOp1oc2c(C(C)(C)C)cc(C(C)(C)C)cc2c2c(o1)c(cc(c2)C(C)(C)C)C(C)(C)C)CCOp1oc2c(C(C)(C)C)cc(C(C)(C)C)cc2c2c(o1)c(cc(c2)C(C)(C)C)C(C)(C)C

When i convert to -report, and view the graphics results, I see that all of the double bonds are converted to sigle bonds:

FORMULA: C90H168NO9P3

MASS: 1501.2195

EXACT MASS: 1500.1931959

I am sure that this is not the intended behavior, to electronically hydrogenate a molecule. Please have a look at this when time allows.

Tim J