On 11/07/2012 18:51, James Jack wrote:
>
> When I convert this to a 3D molfile with "add explicit H" checked in the
> OpenBabel GUI or I try the same in code the OH seems to become O- (O
> with a negative charge).
>
In the GUI you need to check "Add hydrogens (make explicit)" but have
the editbox labelled "Add hydrogens appropriate for this pH" on the next
line empty.
In code something like
pMol->AddHydrogens(false, false);
But this may not be necessary.
If you use "Generate 3D coordinates" in the GUI or something like
OBOp* pOp = OBOp::FindType("gen3D");
if(pOp)
pOp->Do(pMol);
in code, explicit hydrogens are added automatically.
Chris
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